Articles de revues : « Charged-residue »

1

Armstrong, K. M., et R. L. Baldwin. « Charged histidine affects alpha-helix stability at all positions in the helix by interacting with the backbone charges ». Proceedings of the National Academy of Sciences 90, n^o 23 (1 décembre 1993) : 11337–40. http://dx.doi.org/10.1073/pnas.90.23.11337.

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To determine whether a charged histidine side chain affects alpha-helix stability only when histidine is close to one end of the helix or also when it is in the central region, we substitute a single histidine residue at many positions in two reference peptides and measure helix stability and histidine pKa. The position of a charged histidine residue has a major effect on helix stability in 0.01 M NaCl: the helix content of a 17-residue peptide is 24% when histidine is at position 3 compared to 76% when it is at position 17. This dependence of helix content on histidine position decreases sharply in 1 M NaCl, as expected for counterion screening of the charge-helix dipole interaction. Results at interior positions indicate that the position of a charged histidine residue affects helix stability at these positions. Unexpectedly high values of the helix content are found when either neutral or charged histidine is at one of the last three C-terminal positions, suggesting that either form can stabilize an isolated helix by hydrogen bonding to a main-chain CO group.

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Zhang, Zhao, Yanfang Xu, Pei Hong Dong, Dipika Sharma et Nipavan Chiamvimonvat. « A negatively charged residue in the outer mouth of rat sodium channel determines the gating kinetics of the channel ». American Journal of Physiology-Cell Physiology 284, n^o 5 (1 mai 2003) : C1247—C1254. http://dx.doi.org/10.1152/ajpcell.00471.2002.

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Previous studies using combined techniques of site-directed mutagenesis and electrophysiology of voltage-gated Na+ channels have demonstrated that there are significant overlaps in the regions that are important for the two fundamental properties of the channels, namely gating and permeation. We have previously shown that a pore-lining residue, W402 in S5-S6 region (P loop) in domain I of the μ1 skeletal muscle Na+channel, was important in the gating of the channel. Here, we determined the role of an adjacent pore-lining negatively charged residue (E403) in channel gating. Charge neutralization or substitution with positively charged side chain at this position resulted in a marked delay in the rate of recovery from slow inactivation. Indeed, the fast inactivation process appeared intact. Restoration of the negatively charged side chain with a sulfhydryl modifier, MTS-ethylsulfonate, resulted in a reactivation profile from a slow-inactivated state, which was indistinguishable from that of the wild-type channels. We propose an additional functional role for the negatively charged residue. Assuming no major changes in the pore structure induced by the mutations, the negatively charged residue E403 may work in concert with other pore regions during recovery from slow inactivation of the channel. Our data represent the first report indicating the role of negative charge in the slow inactivation of the voltage-gated Na+ channel.

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Fernandez de la Mora, J. « Electrospray ionization of large multiply charged species proceeds via Dole’s charged residue mechanism ». Analytica Chimica Acta 406, n^o 1 (février 2000) : 93–104. http://dx.doi.org/10.1016/s0003-2670(99)00601-7.

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Lemire, Isabelle, Patrice Roy et Guy Boileau. « Translocation of neutral endopeptidase 24.11 mutants with deletions of the NH2- terminal cytosolic domain ». Biochemistry and Cell Biology 72, n^o 5-6 (1 mai 1994) : 182–87. http://dx.doi.org/10.1139/o94-027.

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Rabbit neutral endopeptidase 24.11 (NEP) is a type II membrane protein with a positively charged 27 amino acid residue NH2-terminal cytoplasmic domain, a 20 amino acid residue hydrophobic signal peptide/membrane anchor domain, and a large catalytic COOH-terminal domain exposed on the exoplasmic side of the membrane. To study the role of the cytosolic domain in anchoring NEP in the plasma membrane, we constructed two mutants in which this cytosolic domain was deleted. In the first mutant (NEPΔcyto), a Glu residue was present in NH2-terminus, while a Lys residue was substituted at the same position in the second mutant (NEPΔcyto(K)). To better understand the interaction of these mutants with the rough endoplasmic reticulum membrane, the mutated NEP cDNAs were transcribed and translated in vitro in the presence of microsomal membranes. Our studies showed that deletion of the hydrophillic cytosolic domain affects translocation of the NEP polypeptide chain. Substitution of a positively charged Lys residue for the Glu residue at the NH2-terminus of the deletion mutant only partly restored translocation of the polypeptide chain. Furthermore, carbonate extraction and trypsin digestion of the microsomal membranes indicated that the deletion mutants are inserted in the microsomal membranes as type III membrane proteins with their COOH-terminal domain exposed on the exterior of the microsomes. Thus, efficient translocation is dependent on the presence of a charged cytoplasmic domain.Key words: membrane proteins, translocation, cytosolic domain, neutral endopeptidase 24.11.

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Mayol, Eduardo, Mercedes Campillo, Arnau Cordomí et Mireia Olivella. « Inter-residue interactions in alpha-helical transmembrane proteins ». Bioinformatics 35, n^o 15 (19 décembre 2018) : 2578–84. http://dx.doi.org/10.1093/bioinformatics/bty978.

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Abstract Motivation The number of available membrane protein structures has markedly increased in the last years and, in parallel, the reliability of the methods to detect transmembrane (TM) segments. In the present report, we characterized inter-residue interactions in α-helical membrane proteins using a dataset of 3462 TM helices from 430 proteins. This is by far the largest analysis published to date. Results Our analysis of residue–residue interactions in TM segments of membrane proteins shows that almost all interactions involve aliphatic residues and Phe. There is lack of polar–polar, polar–charged and charged–charged interactions except for those between Thr or Ser sidechains and the backbone carbonyl of aliphatic and Phe residues. The results are discussed in the context of the preferences of amino acids to be in the protein core or exposed to the lipid bilayer and to occupy specific positions along the TM segment. Comparison to datasets of β-barrel membrane proteins and of α-helical globular proteins unveils the specific patterns of interactions and residue composition characteristic of α-helical membrane proteins that are the clue to understanding their structure. Availability and implementation Results data and datasets used are available at http://lmc.uab.cat/TMalphaDB/interactions.php. Supplementary information Supplementary data are available at Bioinformatics online.

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Kalchenko, Vitaly, Olga Kalchenko et Sergiy Cherenok. « Complexation of Calix[4]arene bis-Hydroxymethylenediphosphonic Acid with Amino acids. Binding Constants Determination by RP HPLC Method ». French-Ukrainian Journal of Chemistry 3, n^o 2 (2015) : 93–100. http://dx.doi.org/10.17721/fujcv3i2p93-100.

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Host-Guest complexation of calixarene-bis-hydroxymethylenediphosphonic acid with 17 amino acids in water solution had been studied by the RP HPLC and molecular modelling methods. It had been shown the binding constants of the complexes are depended on the nature of the amino acid residue, log P and pKa of the acids. The complexation is mainly determined by the electrostatic interactions between the positively charged nitrogen atom of the amino acid and the negatively charged oxygen atom of phosphonic acid residue of the calixarene, the Host-Guest p-p, СН-p and solvophobic interactions.

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Mahdavi, Atiyeh, Reza H. Sajedi, Saman Hosseinkhani et Majid Taghdir. « Hyperactive Arg39Lys mutated mnemiopsin : implication of positively charged residue in chromophore binding cavity ». Photochemical & ; Photobiological Sciences 14, n^o 4 (2015) : 792–800. http://dx.doi.org/10.1039/c4pp00191e.

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Mnemiopsin, a Ca²⁺-regulated photoprotein isolated fromMnemiopsis leidyi, belongs to the family of ctenophore photoproteins. While there are no charged amino acid residues in the coelenterazine binding cavity of cnidarian photoproteins, ctenophore photoproteins have a positively charged residue (Arg) in this region.

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He, Yuxian, Shuwen Liu, Jingjing Li, Hong Lu, Zhi Qi, Zhonghua Liu, Asim K. Debnath et Shibo Jiang. « Conserved Salt Bridge between the N- and C-Terminal Heptad Repeat Regions of the Human Immunodeficiency Virus Type 1 gp41 Core Structure Is Critical for Virus Entry and Inhibition ». Journal of Virology 82, n^o 22 (3 septembre 2008) : 11129–39. http://dx.doi.org/10.1128/jvi.01060-08.

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ABSTRACT The fusogenic human immunodeficiency virus type 1 (HIV-1) gp41 core structure is a stable six-helix bundle formed by its N- and C-terminal heptad repeat sequences. Notably, the negatively charged residue Asp632 located at the pocket-binding motif in the C-terminal heptad repeat interacts with the positively charged residue Lys574 in the pocket formation region of the N-terminal heptad repeat to form a salt bridge. We previously demonstrated that the residue Lys574 plays an essential role in six-helix bundle formation and virus infectivity and is a key determinant of the target for anti-HIV fusion inhibitors. In this study, the functionality of residue Asp632 has been specifically characterized by mutational analysis and biophysical approaches. We show that Asp632 substitutions with positively charged residues (D632K and D632R) or a hydrophobic residue (D632V) could completely abolish Env-mediated viral entry, while a protein with a conserved substitution (D632E) retained its activity. Similar to the Lys574 mutations, nonconserved substitutions of Asp632 also severely impaired the α-helicity, stability, and conformation of six-helix bundles as shown by N36 and C34 peptides as a model system. Furthermore, nonconserved substitutions of Asp632 significantly reduced the potency of C34 to sequestrate six-helix bundle formation and to inhibit HIV-1-mediated cell-cell fusion and infection, suggesting its importance for designing antiviral fusion inhibitors. Taken together, these data suggest that the salt bridge between the N- and C-terminal heptad repeat regions of the fusion-active HIV-1 gp41 core structure is critical for viral entry and inhibition.

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Miniero, Daniela Valeria, Magnus Monné, Maria Antonietta Di Noia, Luigi Palmieri et Ferdinando Palmieri. « Evidence for Non-Essential Salt Bridges in the M-Gates of Mitochondrial Carrier Proteins ». International Journal of Molecular Sciences 23, n^o 9 (2 mai 2022) : 5060. http://dx.doi.org/10.3390/ijms23095060.

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Mitochondrial carriers, which transport metabolites, nucleotides, and cofactors across the mitochondrial inner membrane, have six transmembrane α-helices enclosing a translocation pore with a central substrate binding site whose access is controlled by a cytoplasmic and a matrix gate (M-gate). The salt bridges formed by the three PX[DE]XX[RK] motifs located on the odd-numbered transmembrane α-helices greatly contribute to closing the M-gate. We have measured the transport rates of cysteine mutants of the charged residue positions in the PX[DE]XX[RK] motifs of the bovine oxoglutarate carrier, the yeast GTP/GDP carrier, and the yeast NAD+ transporter, which all lack one of these charged residues. Most single substitutions, including those of the non-charged and unpaired charged residues, completely inactivated transport. Double mutations of charged pairs showed that all three carriers contain salt bridges non-essential for activity. Two double substitutions of these non-essential charge pairs exhibited higher transport rates than their corresponding single mutants, whereas swapping the charged residues in these positions did not increase activity. The results demonstrate that some of the residues in the charged residue positions of the PX[DE]XX[KR] motifs are important for reasons other than forming salt bridges, probably for playing specific roles related to the substrate interaction-mediated conformational changes leading to the M-gate opening/closing.

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Li, Yuan, Xing Li, Matthew Stremlau, Mark Lee et Joseph Sodroski. « Removal of Arginine 332 Allows Human TRIM5α To Bind Human Immunodeficiency Virus Capsids and To Restrict Infection ». Journal of Virology 80, n^o 14 (15 juillet 2006) : 6738–44. http://dx.doi.org/10.1128/jvi.00270-06.

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ABSTRACT Human TRIM5α (TRIM5αhu) only modestly inhibits human immunodeficiency virus type 1 (HIV-1) and does not inhibit simian immunodeficiency virus (SIVmac). Alteration of arginine 332 in the TRIM5αhu B30.2 domain to proline, the residue found in rhesus monkey TRIM5α, has been shown to create a potent restricting factor for both HIV-1 and SIVmac. Here we demonstrate that the potentiation of HIV-1 inhibition results from the removal of a positively charged residue at position 332 of TRIM5αhu. The increase in restricting activity correlated with an increase in the ability of TRIM5αhu mutants lacking arginine 332 to bind HIV-1 capsid complexes. A change in the cyclophilin A-binding loop of the HIV-1 capsid decreased TRIM5αhu R332P binding and allowed escape from restriction. The ability of TRIM5αhu to restrict SIVmac could be disrupted by the presence of any charged residue at position 332. Thus, charged residues in the v1 region of the TRIM5αhu B30.2 domain can modulate capsid binding and restriction potency. Therapeutic strategies designed to neutralize arginine 332 of TRIM5αhu might potentiate the innate resistance of human cells to HIV-1 infection.

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Schuldiner, Shimon, Dorit Granot, Sonia Steiner Mordoch, Shira Ninio, Dvir Rotem, Michael Soskin, Christopher G. Tate et Hagit Yerushalmi. « Small is Mighty : EmrE, a Multidrug Transporter as an Experimental Paradigm ». Physiology 16, n^o 3 (juin 2001) : 130–34. http://dx.doi.org/10.1152/physiologyonline.2001.16.3.130.

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EmrE is a multidrug transporter from Escherichia coli that functions as a homooligomer and is unique in its small size. In each monomer there are four tightly packed transmembrane segments and one membrane-embedded charged residue. This residue provides the basis for the coupling mechanism as part of a binding site “time shared” by substrates and protons.

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Vostrikov, Vitaly V., Anna E. Daily, Denise V. Greathouse et Roger E. Koeppe. « Charged or Aromatic Anchor Residue Dependence of Transmembrane Peptide Tilt ». Journal of Biological Chemistry 285, n^o 41 (28 juillet 2010) : 31723–30. http://dx.doi.org/10.1074/jbc.m110.152470.

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Hogan, Christopher J., James A. Carroll, Henry W. Rohrs, Pratim Biswas et Michael L. Gross. « Combined Charged Residue-Field Emission Model of Macromolecular Electrospray Ionization ». Analytical Chemistry 81, n^o 1 (janvier 2009) : 369–77. http://dx.doi.org/10.1021/ac8016532.

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Ou, Xinwen, Bin Xue, Yichong Lao, Yanee Wutthinitikornkit, Ranran Tian, Aodong Zou, Lingyun Yang, Wei Wang, Yi Cao et Jingyuan Li. « Structure and sequence features of mussel adhesive protein lead to its salt-tolerant adhesion ability ». Science Advances 6, n^o 39 (septembre 2020) : eabb7620. http://dx.doi.org/10.1126/sciadv.abb7620.

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Mussels can strongly adhere to hydrophilic minerals in sea habitats by secreting adhesive proteins. The adhesion ability of these proteins is often attributed to the presence of Dopa derived from posttranslational modification of Tyr, whereas the contribution of structural feature is overlooked. It remains largely unknown how adhesive proteins overcome the surface-bound water layer to establish underwater adhesion. Here, we use molecular dynamics simulations to probe the conformations of adhesive protein Pvfp-5β and its salt-tolerant underwater adhesion on superhydrophilic mica. Dopa and positively charged basic residues form pairs, in this intrinsically disordered protein, and these residue pairs can lead to firm surface binding. Our simulations further suggest that the unmodified Tyr shows similar functions on surface adhesion by forming pairing structure with a positively charged residue. We confirm the presence of these residue pairs and verify the strong binding ability of unmodified proteins using nuclear magnetic resonance spectroscopy and lap shear tests.

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Verma, Sandhya, Valerie Bednar, Andrew Blount et Brenda G. Hogue. « Identification of Functionally Important Negatively Charged Residues in the Carboxy End of Mouse Hepatitis Coronavirus A59 Nucleocapsid Protein ». Journal of Virology 80, n^o 9 (1 mai 2006) : 4344–55. http://dx.doi.org/10.1128/jvi.80.9.4344-4355.2006.

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ABSTRACT The coronavirus nucleocapsid (N) protein is a multifunctional viral gene product that encapsidates the RNA genome and also plays some as yet not fully defined role in viral RNA replication and/or transcription. A number of conserved negatively charged amino acids are located within domain III in the carboxy end of all coronavirus N proteins. Previous studies suggested that the negatively charged residues are involved in virus assembly by mediating interaction between the membrane (M) protein carboxy tail and nucleocapsids. To determine the importance of these negatively charged residues, a series of alanine and other charged-residue substitutions were introduced in place of those in the N gene within a mouse hepatitis coronavirus A59 infectious clone. Aspartic acid residues 440 and 441 were identified as functionally important. Viruses could not be isolated when both residues were replaced by positively charged amino acids. When either amino acid was replaced by a positively charged residue or both were changed to alanine, viruses were recovered that contained second-site changes within N, but not in the M or envelope protein. The compensatory role of the new changes was confirmed by the construction of new viruses. A few viruses were recovered that retained the D441-to-arginine change and no compensatory changes. These viruses exhibited a small-plaque phenotype and produced significantly less virus. Overall, results from our analysis of a large panel of plaque-purified recovered viruses indicate that the negatively charged residues at positions 440 and 441 are key residues that appear to be involved in virus assembly.

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Shin, Youn-Chul, Sunju Park et Wang-Shick Ryu. « A conserved arginine residue in the terminal protein domain of hepatitis B virus polymerase is critical for RNA pre-genome encapsidation ». Journal of General Virology 92, n^o 8 (1 août 2011) : 1809–16. http://dx.doi.org/10.1099/vir.0.031914-0.

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Hepadnaviruses, including human hepatitis B virus (HBV) and duck hepatitis B virus (DHBV), replicate their DNA genome through reverse transcription. Although hepadnaviral polymerase (Pol) is distantly related to retroviral reverse transcriptases, some of its features are distinct. In particular, in addition to the reverse transcriptase and RNase H domains, which are commonly encoded by retroviral reverse transcriptases, the N-terminally extended terminal protein (TP) domain confers unique features such as protein-priming capability. Importantly, the TP domain is also essential for encapsidation of the viral RNA pre-genome. To gain further insight into the TP domain, this study used clustered charged residue-to-alanine mutagenesis of HBV Pol. Of the 20 charged residues examined, only one arginine (R105) was critical for RNA encapsidation. This result contrasts with previous findings for DHBV Pol regarding the critical residue of the TP domain required for RNA binding. Firstly, R128 of DHBV Pol, which corresponds to R105 of HBV Pol, was reportedly tolerable to alanine substitution for RNA binding. Secondly, the C-terminal arginine residue of the DHBV Pol TP domain (R183) was shown to be critical for RNA binding, whereas alanine substitution of the corresponding arginine residue of the HBV Pol TP domain (R160) remained able to support RNA encapsidation. Together, these data highlight the divergence between avian and mammalian hepadnaviral Pols with respect to an arginine residue critical for RNA encapsidation.

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Moon, Hee-Jung, Manish Kumar Tiwari, Ranjitha Singh, Yun Chan Kang et Jung-Kul Lee. « Molecular Determinants of the Cofactor Specificity of Ribitol Dehydrogenase, a Short-Chain Dehydrogenase/Reductase ». Applied and Environmental Microbiology 78, n^o 9 (17 février 2012) : 3079–86. http://dx.doi.org/10.1128/aem.07751-11.

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ABSTRACTRibitol dehydrogenase fromZymomonas mobilis(ZmRDH) catalyzes the conversion of ribitol tod-ribulose and concomitantly reduces NAD(P)+to NAD(P)H. A systematic approach involving an initial sequence alignment-based residue screening, followed by a homology model-based screening and site-directed mutagenesis of the screened residues, was used to study the molecular determinants of the cofactor specificity of ZmRDH. A homologous conserved amino acid, Ser156, in the substrate-binding pocket of the wild-type ZmRDH was identified as an important residue affecting the cofactor specificity of ZmRDH. Further insights into the function of the Ser156 residue were obtained by substituting it with other hydrophobic nonpolar or polar amino acids. Substituting Ser156 with the negatively charged amino acids (Asp and Glu) altered the cofactor specificity of ZmRDH toward NAD+(S156D, [kcat/Km,NAD]/[kcat/Km,NADP] = 10.9, whereKm,NADis theKmfor NAD+andKm,NADPis theKmfor NADP+). In contrast, the mutants containing positively charged amino acids (His, Lys, or Arg) at position 156 showed a higher efficiency with NADP+as the cofactor (S156H, [kcat/Km,NAD]/[kcat/Km,NADP] = 0.11). These data, in addition to those of molecular dynamics and isothermal titration calorimetry studies, suggest that the cofactor specificity of ZmRDH can be modulated by manipulating the amino acid residue at position 156.

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Eduljee, Cyrus, Thomas W. Claydon, Vijay Viswanathan, David Fedida et Steven J. Kehl. « SCAM analysis reveals a discrete region of the pore turret that modulates slow inactivation in Kv1.5 ». American Journal of Physiology-Cell Physiology 292, n^o 3 (mars 2007) : C1041—C1052. http://dx.doi.org/10.1152/ajpcell.00274.2006.

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In Kv1.5, protonation of histidine 463 in the S5-P linker (turret) increases the rate of depolarization-induced inactivation and decreases the peak current amplitude. In this study, we examined how amino acid substitutions that altered the physico-chemical properties of the side chain at position 463 affected slow inactivation and then used the substituted cysteine accessibility method (SCAM) to probe the turret region (E456-P468) to determine whether residue 463 was unique in its ability to modulate the macroscopic current. Substitutions at position 463 of small, neutral (H463G and H463A) or large, charged (H463R, H463K, and H463E) side groups accelerated inactivation and induced a dependency of the current amplitude on the external potassium concentration. When cysteine substitutions were made in the distal turret (T462C-P468C), modification with either the positively charged [2-(trimethylammonium)ethyl] methanethiosulfonate bromide (MTSET) or negatively charged sodium (2-sulfonatoethyl) methanethiosulfonate reagent irreversibly inhibited current. This inhibition could be antagonized either by the R487V mutation (homologous to T449V in Shaker) or by raising the external potassium concentration, suggesting that current inhibition by MTS reagents resulted from an enhancement of inactivation. These results imply that protonation of residue 463 does not modulate inactivation solely by an electrostatic interaction with residues near the pore mouth, as proposed by others, and that residue 463 is part of a group of residues within the Kv1.5 turret that can modulate P/C-type inactivation.

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Chen, Mei-Fang, et Tsung-Yu Chen. « Side-chain Charge Effects and Conductance Determinants in the Pore of ClC-0 Chloride Channels ». Journal of General Physiology 122, n^o 2 (28 juillet 2003) : 133–45. http://dx.doi.org/10.1085/jgp.200308844.

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The charge on the side chain of the internal pore residue lysine 519 (K519) of the Torpedo ClC-0 chloride (Cl−) channel affects channel conductance. Experiments that replace wild-type (WT) lysine with neutral or negatively charged residues or that modify the K519C mutant with various methane thiosulfonate (MTS) reagents show that the conductance of the channel decreases when the charge at position 519 is made more negative. This charge effect on the channel conductance diminishes in the presence of a high intracellular Cl− concentration ([Cl−]i). However, the application of high concentrations of nonpermeant ions, such as glutamate or sulfate (SO42−), does not change the conductance, suggesting that the electrostatic effects created by the charge at position 519 are unlikely due to a surface charge mechanism. Another pore residue, glutamate 127 (E127), plays an even more critical role in controlling channel conductance. This negatively charged residue, based on the structures of the homologous bacterial ClC channels, lies 4–5 Å from K519. Altering the charge of this residue can influence the apparent Cl− affinity as well as the saturated pore conductance in the conductance-Cl− activity curve. Amino acid residues at the selectivity filter also control the pore conductance but mutating these residues mainly affects the maximal pore conductance. These results suggest at least two different conductance determinants in the pore of ClC-0, consistent with the most recent crystal structure of the bacterial ClC channel solved to 2.5 Å, in which multiple Cl−-binding sites were identified in the pore. Thus, we suggest that the occupancy of the internal Cl−-binding site is directly controlled by the charged residues located at the inner pore mouth. On the other hand, the Cl−-binding site at the selectivity filter controls the exit rate of Cl− and therefore determines the maximal channel conductance.

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Bäckström, B. Thomas, Barbara T. Hausmann et Ed Palmer. « Signaling Efficiency of the T Cell Receptor Controlled by a Single Amino Acid in the β Chain Constant Region ». Journal of Experimental Medicine 186, n^o 11 (1 décembre 1997) : 1933–38. http://dx.doi.org/10.1084/jem.186.11.1933.

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A single amino acid residue, Gln136, located within the connecting peptide domain of Cβ controls the ability of the α/β TCR to transmit a full signal. TCRs in which this Cβ residue is mutated to Phe, the residue found in TCR-γ, are unresponsive to antigenic ligands. Interestingly, this Cβ residue is either polar or charged in every species studied thus far, including the trout and the skate. In contrast, the analogous residue in Cγ is always hydrophobic. In spite of their compromised antigen responsiveness, the mutant TCR complex contains the CD3-γ, -δ, -ε, and -ζ chains, and undergoes ζ chain phosphorylation and ZAP-70 recruitment. However, the biological response of the mutant TCR could be rescued with a calcium ionophore, implying that mutant TCRs are defective in generating a calcium-mediated signal. The implications of the differences between Cβ and Cγ are considered.

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Bogati, Bikash, Selene F. H. Shore, Thomas D. Nipper, Oana Stoiculescu et Elizabeth M. Fozo. « Charged Amino Acids Contribute to ZorO Toxicity ». Toxins 15, n^o 1 (31 décembre 2022) : 32. http://dx.doi.org/10.3390/toxins15010032.

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Chromosomally encoded toxin-antitoxin systems have been increasingly identified and characterized across bacterial species over the past two decades. Overproduction of the toxin gene results in cell growth stasis or death for the producing cell, but co-expression of its antitoxin can repress the toxic effects. For the subcategory of type I toxin-antitoxin systems, many of the described toxin genes encode a small, hydrophobic protein with several charged residues distributed across the sequence of the toxic protein. Though these charged residues are hypothesized to be critical for the toxic effects of the protein, they have not been studied broadly across different type I toxins. Herein, we mutated codons encoding charged residues in the type I toxin zorO, from the zor-orz toxin-antitoxin system, to determine their impacts on growth inhibition, membrane depolarization, ATP depletion, and the localization of this small protein. The non-toxic variants of ZorO accumulated both in the membrane and cytoplasm, indicating that membrane localization alone is not sufficient for its toxicity. While mutation of a charged residue could result in altered toxicity, this was dependent not only on the position of the amino acid within the protein but also on the residue to which it was converted, suggesting a complex role of charged residues in ZorO-mediated toxicity. A previous study indicated that additional copies of the zor-orz system improved growth in aminoglycosides: within, we note that this improved growth is independent of ZorO toxicity. By increasing the copy number of the zorO gene fused with a FLAG-tag, we were able to detect the protein expressed from its native promoter elements: an important step for future studies of toxin expression and function.

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Friedman, M. L., K. T. Schlueter, T. L. Kirley et H. B. Halsall. « Fluorescence quenching of human orosomucoid. Accessibility to drugs and small quenching agents ». Biochemical Journal 232, n^o 3 (15 décembre 1985) : 863–67. http://dx.doi.org/10.1042/bj2320863.

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The fluorescence behaviour of human orosomucoid was investigated. The intrinsic fluorescence was more accessible to acrylamide than to the slightly larger succinimide, indicating limited accessibility to part of the tryptophan population. Although I- showed almost no quenching, that of Cs+ was enhanced, and suggested a region of negative charge proximal to an emitting tryptophan residue. Removal of more than 90% of sialic acid from the glycan chains led to no change in the Cs+, I-, succinimide or acrylamide quenching, indicating that the negatively charged region originates with the protein core. Quenching as a function of pH and temperature supported this view. The binding of chlorpromazine monitored by fluorescence quenching, in the presence and in the absence of the small quenching probes (above), led to a model of its binding domain on orosomucoid that includes two tryptophan residues relatively shielded from the bulk solvent, with the third tryptophan residue being on the periphery of the domain, or affected allotopically and near the negatively charged field.

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Yadav, Mohini, Manabu Igarashi et Norifumi Yamamoto. « Theoretical insights into the molecular mechanism of I117V mutation in neuraminidase mediated reduction of oseltamivir drug susceptibility in A/H5N1 influenza virus ». PeerJ Physical Chemistry 3 (22 novembre 2021) : e19. http://dx.doi.org/10.7717/peerj-pchem.19.

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The substitution of Ile to Val at residue 117 (I117V) of neuraminidase (NA) reduces the susceptibility of the A/H5N1 influenza virus to oseltamivir (OTV). However, the molecular mechanism by which the I117V mutation affects the intermolecular interactions between NA and OTV has not been fully elucidated. In this study, we performed molecular dynamics (MD) simulations to analyze the characteristic conformational changes that contribute to the reduced binding affinity of NA to OTV after the I117V mutation. The results of MD simulations revealed that after the I117V mutation in NA, the changes in the secondary structure around the mutation site had a noticeable effect on the residue interactions in the OTV-binding site. In the case of the WT NA-OTV complex, the positively charged side chain of R118, located in the β-sheet region, frequently interacted with the negatively charged side chain of E119, which is an amino acid residue in the OTV-binding site. This can reduce the electrostatic repulsion of E119 toward D151, which is also a negatively charged residue in the OTV-binding site, so that both E119 and D151 simultaneously form hydrogen bonds with OTV more frequently, which greatly contributes to the binding affinity of NA to OTV. After the I117V mutation in NA, the side chain of R118 interacted with the side chain of E119 less frequently, likely because of the decreased tendency of R118 to form a β-sheet structure. As a result, the electrostatic repulsion of E119 toward D151 is greater than that of the WT case, making it difficult for both E119 and D151 to simultaneously form hydrogen bonds with OTV, which in turn reduces the binding affinity of NA to OTV. Hence, after the I117V mutation in NA, influenza viruses are less susceptible to OTV because of conformational changes in residues of R118, E119, and D151 around the mutation site and in the binding site.

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Moreau, Adrien, Pascal Gosselin-Badaroudine et Mohamed Chahine. « Molecular biology and biophysical properties of ion channel gating pores ». Quarterly Reviews of Biophysics 47, n^o 4 (novembre 2014) : 364–88. http://dx.doi.org/10.1017/s0033583514000109.

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AbstractThe voltage sensitive domain (VSD) is a pivotal structure of voltage-gated ion channels (VGICs) and plays an essential role in the generation of electrochemical signals by neurons, striated muscle cells, and endocrine cells. The VSD is not unique to VGICs. Recent studies have shown that a VSD regulates a phosphatase. Similarly, Hv1, a voltage-sensitive protein that lacks an apparent pore domain, is a self-contained voltage sensor that operates as an H+ channel.VSDs are formed by four transmembrane helices (S1–S4). The S4 helix is positively charged due to the presence of arginine and lysine residues. It is surrounded by two water crevices that extend into the membrane from both the extracellular and intracellular milieus. A hydrophobic septum disrupts communication between these water crevices thus preventing the permeation of ions. The septum is maintained by interactions between the charged residues of the S4 segment and the gating charge transfer center. Mutating the charged residue of the S4 segment allows the water crevices to communicate and generate gating pore or omega pore. Gating pore currents have been reported to underlie several neuronal and striated muscle channelopathies. Depending on which charged residue on the S4 segment is mutated, gating pores are permeant either at depolarized or hyperpolarized voltages. Gating pores are cation selective and seem to converge toward Eisenmann's first or second selectivity sequences. Most gating pores are blocked by guanidine derivatives as well as trivalent and quadrivalent cations. Gating pores can be used to study the movement of the voltage sensor and could serve as targets for novel small therapeutic molecules.

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Görbitz, Carl Henrik, et Vitthal N. Yadav. « N-(L-2-Aminopentanoyl)-L-phenylalanine dihydrate, a hydrophobic dipeptide with a nonproteinogenic residue ». Acta Crystallographica Section C Crystal Structure Communications 69, n^o 9 (13 août 2013) : 1067–69. http://dx.doi.org/10.1107/s0108270113021914.

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The title dipeptide, better known as L-norvalyl-L-phenylalanine {systematic name: (S)-2-[(S)-2-aminopentanamido]-3-phenylpropanoic acid dihydrate}, C14H20N2O3·2H2O, has a nonproteinogenic N-terminal residue. In the solid state, it takes on a molecular conformation typical for one of the three classes of nanoporous dipeptides, but like two related compounds with a hydrophobic N-terminal residue and a C-terminal L-phenylalanine, it fails to form channels or pores. Instead, the crystal structure is divided into distinct hydrophobic and hydrophilic layers, the latter encompassing cocrystallized water molecules connecting the charged N- and C-terminal groups.

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Gonzalez, Carlos, Santiago Rebolledo, Marta E. Perez et H. Peter Larsson. « Molecular mechanism of voltage sensing in voltage-gated proton channels ». Journal of General Physiology 141, n^o 3 (11 février 2013) : 275–85. http://dx.doi.org/10.1085/jgp.201210857.

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Voltage-gated proton (Hv) channels play an essential role in phagocytic cells by generating a hyperpolarizing proton current that electrically compensates for the depolarizing current generated by the NADPH oxidase during the respiratory burst, thereby ensuring a sustained production of reactive oxygen species by the NADPH oxidase in phagocytes to neutralize engulfed bacteria. Despite the importance of the voltage-dependent Hv current, it is at present unclear which residues in Hv channels are responsible for the voltage activation. Here we show that individual neutralizations of three charged residues in the fourth transmembrane domain, S4, all reduce the voltage dependence of activation. In addition, we show that the middle S4 charged residue moves from a position accessible from the cytosolic solution to a position accessible from the extracellular solution, suggesting that this residue moves across most of the membrane electric field during voltage activation of Hv channels. Our results show for the first time that the charge movement of these three S4 charges accounts for almost all of the measured gating charge in Hv channels.

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Willms, J. Alexander, Rita Beel, Martin L. Schmidt, Christian Mundt et Marianne Engeser. « A new charge-tagged proline-based organocatalyst for mechanistic studies using electrospray mass spectrometry ». Beilstein Journal of Organic Chemistry 10 (28 août 2014) : 2027–37. http://dx.doi.org/10.3762/bjoc.10.211.

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A new 4-hydroxy-L-proline derivative with a charged 1-ethylpyridinium-4-phenoxy substituent has been synthesized with the aim of facilitating mechanistic studies of proline-catalyzed reactions by ESI mass spectrometry. The charged residue ensures a strongly enhanced ESI response compared to neutral unmodified proline. The connection by a rigid linker fixes the position of the charge tag far away from the catalytic center in order to avoid unwanted interactions. The use of a charged catalyst leads to significantly enhanced ESI signal abundances for every catalyst-derived species which are the ones of highest interest present in a reacting solution. The new charged proline catalyst has been tested in the direct asymmetric inverse aldol reaction between aldehydes and diethyl ketomalonate. Two intermediates in accordance with the List–Houk mechanism for enamine catalysis have been detected and characterized by gas-phase fragmentation. In addition, their temporal evolution has been followed using a microreactor continuous-flow technique.

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BERGERON, Eric, Ajoy BASAK, Etienne DECROLY et Nabil G. SEIDAH. « Processing of alpha4 integrin by the proprotein convertases : histidine at position P6 regulates cleavage ». Biochemical Journal 373, n^o 2 (15 juillet 2003) : 475–84. http://dx.doi.org/10.1042/bj20021630.

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The proprotein convertases (PCs) participate in the limited proteolysis of integrin α4 subunit at the H592VISKR597 ↓ ST site (where underlined residues indicate positively charged amino acids important for PC-mediated cleavage and ↓ indicates the cleavage site), since this cleavage is inhibited by the serpin α1-PDX (α1-antitrypsin Portland). Co-expression of α4 with each convertase in LoVo (furin-deficient human colon carcinoma) cells revealed that furin and proprotein convertase 5A (PC5A) are the best pro-α4 convertases. In agreement, processing of endogenous pro-α4 in human lymphoblastoid CEM-T4 cells was enhanced greatly in stable transfectants overexpressing either enzyme. In many leucocyte cell lines, the expression of furin closely correlated with the endogenous processing efficacy, suggesting that furin is a candidate pro-α4 convertase. Mutational analysis showed that replacement of P1 Arg597 with alanine (R597A) abrogated cleavage, whereas the P6 mutant H592R is even better processed by the endogenous convertases of Chinese-hamster ovary CHO-K1 cells. In vitro kinetic studies using synthetic peptides confirmed the importance of a positively charged residue at P6 and showed that wild-type α4 processing is performed best by furin and PC5A at acidic and neutral pHs, respectively. Biosynthetic analysis of pro-α4 and its H592R and H592K mutants in the presence or absence of the weak base, NH4Cl, revealed that the P6 histidine residue renders its processing by furin sensitive to cellular pH. This suggests that pro-α4 cleavage occurs preferentially in acidic compartments. In conclusion, although the accepted furin processing motif is Arg-Xaa-(Lys/Arg)-Arg↓, our data further extend it to include a regulatory histidine residue at P6 in precursors that lack a basic residue at P4.

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Dong, R. P., N. Kamikawaji, N. Toida, Y. Fujita, A. Kimura et T. Sasazuki. « Characterization of T cell epitopes restricted by HLA-DP9 in streptococcal M12 protein. » Journal of Immunology 154, n^o 9 (1 mai 1995) : 4536–45. http://dx.doi.org/10.4049/jimmunol.154.9.4536.

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Abstract Interaction of the HLA-DP9 (DPA1*0201/DPB1*0901) molecule and M protein of serotype 12 (SS95/12) streptococci, a main component of the streptococcal cell wall Ag, has been investigated to decipher peptide-binding capacity and T cell activation in the context of the HLA-DP molecule. Seven antigenic peptides (amino acids 19-25) restricted by the HLA-DP9 molecule were identified in M12 protein, using M12 protein- or peptide-specific T cell lines from naturally exposed individuals. The binding affinity of each peptide to the HLA-DP9 molecule was measured by fluorescence intensity of biotinylated peptides bound to L cell transfectants expressing HLA-DP9, followed by treatment with avidin-fluorescence. Binding of biotinylated peptides to the HLA-DP9 molecule was inhibited by an excess amount of corresponding nonbiotinylated peptides and other nonbiotinylated peptides, indicating that the peptides were bound to the HLA-DP9 molecule at a single binding site. Seven synthetic peptides containing the T cell epitopes restricted by the HLA-DP9 molecule had high binding affinity to the HLA-DP9 molecule. Comparison of the amino acid sequences of truncated analogues that could bind to the HLA-DP9 molecule and/or activate T cells suggested an HLA-DP9-specific binding motif, composed of a positively charged residue (R or K) at position 1, a hydrophobic residue (A, G, or L) at position 6, and another hydrophobic residue (L or V) at position 9. Analysis of single amino acid-substituted analogues suggested that the positively charged amino acid in the motif served as a key anchor residue for binding to the HLA-DP9 molecule, which differs from the binding motif to the HLA-DR molecules.

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Trujillo, Adriana S., Karen H. Hsu, Meera C. Viswanathan, Anthony Cammarato et Sanford I. Bernstein. « The R369 Myosin Residue within Loop 4 Is Critical for Actin Binding and Muscle Function in Drosophila ». International Journal of Molecular Sciences 23, n^o 5 (25 février 2022) : 2533. http://dx.doi.org/10.3390/ijms23052533.

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The myosin molecular motor interacts with actin filaments in an ATP-dependent manner to yield muscle contraction. Myosin heavy chain residue R369 is located within loop 4 at the actin-tropomyosin interface of myosin’s upper 50 kDa subdomain. To probe the importance of R369, we introduced a histidine mutation of that residue into Drosophila myosin and implemented an integrative approach to determine effects at the biochemical, cellular, and whole organism levels. Substituting the similarly charged but bulkier histidine residue reduces maximal actin binding in vitro without affecting myosin ATPase activity. R369H mutants exhibit impaired flight ability that is dominant in heterozygotes and progressive with age in homozygotes. Indirect flight muscle ultrastructure is normal in mutant homozygotes, suggesting that assembly defects or structural deterioration of myofibrils are not causative of reduced flight. Jump ability is also reduced in homozygotes. In contrast to these skeletal muscle defects, R369H mutants show normal heart ultrastructure and function, suggesting that this residue is differentially sensitive to perturbation in different myosin isoforms or muscle types. Overall, our findings indicate that R369 is an actin binding residue that is critical for myosin function in skeletal muscles, and suggest that more severe perturbations at this residue may cause human myopathies through a similar mechanism.

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Pan, Ying, Lei Song et Yuan Hu. « Effect of Calcium Ion Crosslinked Alginate Based Coating on Flame Retardancy of Polyester-Cotton Fabric ». Materials Science Forum 909 (novembre 2017) : 145–50. http://dx.doi.org/10.4028/www.scientific.net/msf.909.145.

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Bio-based and phosphorus-free coating was fabricated by layer-by-layer assembly method to obtain the flame retardant polyester-cotton fabric. For the first time, the modified polyester-cotton fabrics were prepared by utilizing positively charged polyethylenimine and negatively charged alginate together with subsequent crosslinking of calcium ion. Scanning electron microscopy and energy-dispersive X-ray demonstrated that the calcium ion crosslinked coating was successfully constructed on the substrate. The flame retardancy was investigated by horizontal flame test. The fire resistance of SA/PEI-Ca sample was enhanced significantly compared with the pure sample, as evidenced by the obvious reduction (16%) of flame spread rate and complete char residue.

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Ortega, Gabriel, Miguel A. Aguilar, Bishal K. Gautam et Kevin W. Plaxco. « The effect of charged residue substitutions on the thermodynamics of protein‐surface interactions ». Protein Science 30, n^o 12 (8 novembre 2021) : 2408–17. http://dx.doi.org/10.1002/pro.4215.

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Wei, Huiling, Jie Tan, Bingjie Zhou, Xiaotong Guan, Qiaoxian Zhong et Jiaqi Wang. « Charged Residue Implantation Improves the Affinity of a Cross-Reactive Dengue Virus Antibody ». International Journal of Molecular Sciences 23, n^o 8 (11 avril 2022) : 4197. http://dx.doi.org/10.3390/ijms23084197.

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Dengue virus (DENV) has four serotypes that complicate vaccine development. Envelope protein domain III (EDIII) of DENV is a promising target for therapeutic antibody development. One EDIII-specific antibody, dubbed 1A1D-2, cross-reacts with DENV 1, 2, and 3 but not 4. To improve the affinity of 1A1D-2, in this study, we analyzed the previously solved structure of 1A1D-2-DENV2 EDIII complex. Mutations were designed, including A54E and Y105R in the heavy chain, with charges complementary to the epitope. Molecular dynamics simulation was then used to validate the formation of predicted salt bridges. Interestingly, a surface plasmon resonance experiment showed that both mutations increased affinities of 1A1D-2 toward EDIII of DENV1, 2, and 3 regardless of their sequence variation. Results also revealed that A54E improved affinities through both a faster association and slower dissociation, whereas Y105R improved affinities through a slower dissociation. Further simulation suggested that the same mutants interacted with different residues in different serotypes. Remarkably, combination of the two mutations additively improved 1A1D-2 affinity by 8, 36, and 13-fold toward DENV1, 2, and 3, respectively. In summary, this study demonstrated the utility of tweaking antibody-antigen charge complementarity for affinity maturation and emphasized the complexity of improving antibody affinity toward multiple antigens.

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Duraivelan, Kheerthana, Sagarika Dash et Dibyendu Samanta. « An evolutionarily conserved charged residue dictates the specificity of heterophilic interactions among nectins ». Biochemical and Biophysical Research Communications 534 (janvier 2021) : 504–10. http://dx.doi.org/10.1016/j.bbrc.2020.11.052.

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Wible, Barbara A., Maurizio Taglialatela, Eckhard Ficker et Arthur M. Brown. « Gating of inwardly rectifying K+ channels localized to a single negatively charged residue ». Nature 371, n^o 6494 (septembre 1994) : 246–49. http://dx.doi.org/10.1038/371246a0.

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Page, Dana A., et Edgar C. Young. « A Charged Residue in the HCN Channel C-Linker Stabilizes the Open State ». Biophysical Journal 110, n^o 3 (février 2016) : 282a. http://dx.doi.org/10.1016/j.bpj.2015.11.1525.

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Wang, Yunhua, Wenhu Wang, Junxia Lu, Yi Ren, Shaohua Gu, Yi Xie et Zhongxian Huang. « Preparation and characterization of some surface negatively charged residue mutants of cytochrome b5 ». Chinese Science Bulletin 46, n^o 7 (avril 2001) : 555–58. http://dx.doi.org/10.1007/bf02900407.

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Aubin, Chantal N. St, et Paul Linsdell. « Positive Charges at the Intracellular Mouth of the Pore Regulate Anion Conduction in the CFTR Chloride Channel ». Journal of General Physiology 128, n^o 5 (16 octobre 2006) : 535–45. http://dx.doi.org/10.1085/jgp.200609516.

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Many different ion channel pores are thought to have charged amino acid residues clustered around their entrances. The so-called surface charges contributed by these residues can play important roles in attracting oppositely charged ions from the bulk solution on one side of the membrane, increasing effective local counterion concentration and favoring rapid ion movement through the channel. Here we use site-directed mutagenesis to identify arginine residues contributing important surface charges in the intracellular mouth of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl− channel pore. While wild-type CFTR was associated with a linear current–voltage relationship with symmetrical solutions, strong outward rectification was observed after mutagenesis of two arginine residues (R303 and R352) located near the intracellular ends of the fifth and sixth transmembrane regions. Current rectification was dependent on the charge present at these positions, consistent with an electrostatic effect. Furthermore, mutagenesis-induced rectification was more pronounced at lower Cl− concentrations, suggesting that these mutants had a reduced ability to concentrate Cl− ions near the inner pore mouth. R303 and R352 mutants exhibited reduced single channel conductance, especially at negative membrane potentials, that was dependent on the charge of the amino acid residue present at these positions. However, the very low conductance of both R303E and R352E-CFTR could be greatly increased by elevating intracellular Cl− concentration. Modification of an introduced cysteine residue at position 303 by charged methanethiosulfonate reagents reproduced charge-dependent effects on current rectification. Mutagenesis of arginine residues in the second and tenth transmembrane regions also altered channel permeation properties, however these effects were not consistent with changes in channel surface charges. These results suggest that positively charged arginine residues act to concentrate Cl− ions at the inner mouth of the CFTR pore, and that this contributes to maximization of the rate of Cl− ion permeation through the pore.

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Ngo, Son Tung. « Computational Investigations of the Transmembrane Italian-Mutant (E22K) 3A\(\beta_{11 - 40}\) in Aqueous Solution ». Communications in Physics 28, n^o 3 (14 novembre 2018) : 265. http://dx.doi.org/10.15625/0868-3166/28/3/12773.

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The Amyloid beta (Aβ) oligomers are characterized as critical cytotoxic materials in Alzheimer’s disease (AD) pathogenesis. Structural details of transmembrane oligomers are inevitably necessary to design/search potential inhibitor due to treat AD. However, the experimental detections for structural modify of low-order Aβ oligomers are precluded due to the extremely dynamic fluctuation of the oligomers. In this project, the transmembrane Italian-mutant (E22K) 3Aβ11-40 (tmE22K 3Aβ11-40) was extensively investigated upon the temperature replica exchange molecular dynamics (REMD) simulations. The structural changes of the trimer when replacing the negative charged residue E22 by a positively charged residue K were monitored over simulation intervals. The oligomer size was turned to be larger and the increase of β-content was recorded. The momentous gain of intermolecular contacts with DPPC molecules implies that tmE22K 3Aβ11-40 easier self-inserts into the membrane than the WT one. Furthermore, the tighter interaction between constituting monomers was indicated implying that the E22K mutation probably enhances the Aβ fibril formation. The results are in good agreement with experiments that E22K amyloid is self-aggregate faster than the WT form. Details information of tmE22K trimer structure and kinetics probably yield the understanding of AD mechanism.

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Gäde, G. « A unique charged tyrosine-containing member of the adipokinetic hormone/red-pigment-concentrating hormone peptide family isolated and sequenced from two beetle species ». Biochemical Journal 275, n^o 3 (1 mai 1991) : 671–77. http://dx.doi.org/10.1042/bj2750671.

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An identical neuropeptide was isolated from the corpora cardiaca of two beetle species, Melolontha melolontha and Geotrupes stercorosus. Its primary structure was determined by pulsed-liquid-phase sequencing employing Edman chemistry after enzymically deblocking the N-terminal pyroglutamate residue. The C-terminus was also blocked, as indicated by the lack of digestion when the peptide was incubated with carboxypeptidase A. The sequence of this peptide, which is designated Mem-CC, is pGlu-Leu-Asn-Tyr-Ser-Pro-Asp-Trp-NH2. It is a new member of the adipokinetic hormone/red-pigment-concentrating hormone (AKH/RPCH) family of peptides with two unusual structural features: it is charged and contains a tyrosine residue at position 4, where all other family members have a phenylalanine residue. Structure-activity studies in the migratory locust (Locusta migratoria) and the American cockroach (Periplaneta americana) revealed that the peptide was poorly active, owing to its structural uniqueness.

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Lin, Chen-Sheng, Wei-Jing Li, Chih-Yi Liao, Ju-Ying Kan, Szu-Hao Kung, Su-Hua Huang, Hsueh-Chou Lai et Cheng-Wen Lin. « A Reverse Mutation E143K within the PrM Protein of Zika Virus Asian Lineage Natal RGN Strain Increases Infectivity and Cytopathicity ». Viruses 14, n^o 7 (20 juillet 2022) : 1572. http://dx.doi.org/10.3390/v14071572.

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Zika virus (ZIKV) is a positive-sense single-stranded RNA virus in the Flaviviridae, which is classified into two different lineages Asian and African. The outbreak of ZIKV Asian lineage isolates in 2015–2016 is associated with the increase in cases with prenatal microcephaly and Guillain–Barré syndrome, and has sparked attention throughout the world. Genome sequence alignment and the analysis of Asian and African lineage isolates indicate that amino acid changes, particular in positively charged amino acid substitutions in the pr region of prM protein might involve a phenotypic change that links with the global outbreak of ZIKV Asian-lineage. The study generated and characterized the virological properties of wild type and mutants of single-round infectious particles (SRIPs) and infectious clones (i.c.s) of ZIKV Asian-lineage Natal RGN strain, and then identified the function of amino acid substitutions at the positions 139 [Asn139→Ser139 (N139S)] and 143 [Glu143→Lys143 (E143K)] in ZIKV polyproteins (located within the pr region of prM protein) in the infectivity and cytopathogenicity. The E143K SRIP and i.c. of Natal RGN strain exhibited relatively higher levels of cytopathic effect, EGFP reporter, viral RNA and protein synthesis, and virus yield in three types of human cell lines, TE617, SF268 and HMC3, compared to wild type (WT), N139S SRIPs and i.c.s, which displayed more efficiency in replication kinetics. Additionally, E143K Natal RGN i.c. had greater activities of virus attachment and entry, yielded higher titers of intracellular and extracellular virions, and assembled the E proteins near to the plasma membrane in infected cells than the other i.c.s. The results indicate that the positively charged amino acid residue Lys143, a conserved residue in the pr region of prM of ZIKV African lineages, plays a crucial role in viral replication kinetics, including viral attachment, entry, assembly and egress. Thus, the negatively charged amino acid residue Glu143 within the pr region of prM leads to an alteration of the phenotypes, in particular, a lower replication efficiency of ZIKV Asian-lineage isolates with the attenuation of infectivity and cytopathicity.

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Parrish, Jonathan C., J. Guy Guillemette et Carmichael JA Wallace. « A tale of two charges : Distinct roles for an acidic and a basic amino acid in the structure and function of cytochrome c ». Biochemistry and Cell Biology 79, n^o 1 (1 janvier 2001) : 83–91. http://dx.doi.org/10.1139/o00-083.

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Cytochrome c is a small electron transport protein found in the intermembrane space of mitochondria. As it interacts with a number of different physiological partners in a specific fashion, its structure varies little over eukaryotic evolutionary history. Two highly conserved residues found within its sequence are those at positions 13 and 90 (numbering is based on the standard horse cytochrome c); with single exceptions, residue 13 is either Lys or Arg, and residue 90 is either Glu or Asp. There have been conflicting views on the roles to be ascribed to these residues, particularly residue 13, so the functional properties of a number of site-directed mutants of Saccaromyces cerevisiae iso-1 cytochrome c have been examined. Results indicate that the two residues do not interact specifically with each other; however, residue 13 (Arg) is likely to be involved in interactions between cytochrome c and other electro statically oriented physiological partners (intermolecular), whereas residue 90 (Asp) is involved in maintaining the intrinsic structure and stability of cytochrome c (intramolecular). This is supported by molecular dynamics simulations carried out for these mutants where removal of the negative charge at position 90 leads to significant shifts in the conformations of neighboring residues, particularly lysine 86. Both charged residues appear to exert their effects through electrostatics; however, biological activity is significantly more sensitive to substitutions of residue 13 than of residue 90.Key words: cytochrome c, structure-function studies, molecular modelling, surface electrostatics.

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Hall, A., H. Dalbøge, A. Grubb et M. Abrahamson. « Importance of the evolutionarily conserved glycine residue in the N-terminal region of human cystatin C (Gly-11) for cysteine endopeptidase inhibition ». Biochemical Journal 291, n^o 1 (1 avril 1993) : 123–29. http://dx.doi.org/10.1042/bj2910123.

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Human cystatin C variants in which the evolutionarily conserved Gly-11 residue has been replaced by residues with positively charged (Arg), negatively charged (Glu), bulky hydrophobic (Trp), or small (Ser or Ala) side-chains have been produced by site-directed mutagenesis and expression in Escherichia coli. The five variants were isolated and structurally verified. Their inhibitory properties were compared with those of wild-type recombinant cystatin C by determination of the equilibrium constants for dissociation (Ki) of their complexes with the cysteine endopeptidases papain and human cathepsin B and with the cysteine exopeptidase dipeptidyl peptidase I. The Ser-11 and Ala-11 cystatin C variants displayed Ki values for the two endopeptidases that were approx. 20-fold higher than those of wild-type cystatin C, while the corresponding values for the Trp-11. Arg-11 and Glu-11 variants were increased by a factor of about 2000. In contrast, the Ki values for the interactions of all five variants with the exopeptidase differed from that of wild-type cystatin C by a factor of less than 10. Wild-type cystatin C and the Ser-11, Ala-11 and Glu-11 variants were incubated with neutrophil elastase, which in all cases resulted in the rapid hydrolysis of a single peptide bond, between amino acid residues 10 and 11. The Ki values for the interactions with papain of these three N-terminal-decapeptide-lacking cystatin C variants were 20-50 nM, just one order of magnitude higher than the value for N-terminally truncated wild-type cystatin C, which in turn was similar to the corresponding values for the full-length Glu-11, Arg-11 and Trp-11 variants. These data indicate that the crucial feature of the conserved Gly residue in position 11 of wild-type cystatin C is that this residue, devoid of a side-chain, will allow the N-terminal segment of cystatin C to adopt a conformation suitable for interaction with the substrate-binding pockets of cysteine endopeptidases, resulting in high-affinity binding and efficient inhibition. The functional properties of the remaining part of the proteinase contact area, which is built from more C-terminal inhibitor segments, are not significantly affected even when amino acids with bulky or charged side-chains replace the Gly-11 residue of the N-terminal segment.

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Choo, Liza Nuriati Lim Kim, Osumanu Haruna Ahmed, Nik Muhamad Nik Majid et Zakry Fitri Abd Aziz. « Pineapple Residue Ash Reduces Carbon Dioxide and Nitrous Oxide Emissions in Pineapple Cultivation on Tropical Peat Soils at Saratok, Malaysia ». Sustainability 13, n^o 3 (20 janvier 2021) : 1014. http://dx.doi.org/10.3390/su13031014.

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Burning pineapple residues on peat soils before pineapple replanting raises concerns on hazards of peat fires. A study was conducted to determine whether ash produced from pineapple residues could be used to minimize carbon dioxide (CO2) and nitrous oxide (N2O) emissions in cultivated tropical peatlands. The effects of pineapple residue ash fertilization on CO2 and N2O emissions from a peat soil grown with pineapple were determined using closed chamber method with the following treatments: (i) 25, 50, 70, and 100% of the suggested rate of pineapple residue ash + NPK fertilizer, (ii) NPK fertilizer, and (iii) peat soil only. Soils treated with pineapple residue ash (25%) decreased CO2 and N2O emissions relative to soils without ash due to adsorption of organic compounds, ammonium, and nitrate ions onto the charged surface of ash through hydrogen bonding. The ability of the ash to maintain higher soil pH during pineapple growth primarily contributed to low CO2 and N2O emissions. Co-application of pineapple residue ash and compound NPK fertilizer also improves soil ammonium and nitrate availability, and fruit quality of pineapples. Compound NPK fertilizers can be amended with pineapple residue ash to minimize CO2 and N2O emissions without reducing peat soil and pineapple productivity.

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Seica, Ana Filipa Santos, Cristina V. Iancu, Benedikt Pfeilschifter, M. Gregor Madej, Jun-Yong Choe et Petra Hellwig. « Asp22 drives the protonation state of the Staphylococcus epidermidis glucose/H+ symporter ». Journal of Biological Chemistry 295, n^o 45 (28 août 2020) : 15253–61. http://dx.doi.org/10.1074/jbc.ra120.014069.

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The Staphylococcus epidermidis glucose/H+ symporter (GlcPSe) is a membrane transporter highly specific for glucose and a homolog of the human glucose transporters (GLUT, SLC2 family). Most GLUTs and their bacterial counterparts differ in the transport mechanism, adopting uniport and sugar/H+ symport, respectively. Unlike other bacterial GLUT homologs (for example, XylE), GlcPSe has a loose H+/sugar coupling. Asp22 is part of the proton-binding site of GlcPSe and crucial for the glucose/H+ co-transport mechanism. To determine how pH variations affect the proton site and the transporter, we performed surface-enhanced IR absorption spectroscopy on the immobilized GlcPSe. We found that Asp22 has a pKa of 8.5 ± 0.1, a value consistent with that determined previously for glucose transport, confirming the central role of this residue for the transport mechanism of GlcPSe. A neutral replacement of the negatively charged Asp22 led to positive charge displacements over the entire pH range, suggesting that the polarity change of the WT reflects the protonation state of Asp22. We expected that the substitution of the residue Ile105 for a serine, located within hydrogen-bonding distance to Asp22, would change the microenvironment, but the pKa of Asp22 corresponded to that of the WT. A167E mutation, selected in analogy to the XylE, introduced an additional protonatable site and perturbed the protonation state of Asp22, with the latter now exhibiting a pKa of 6.4. These studies confirm that Asp22 is the proton-binding residue in GlcPSe and show that charged residues in its vicinity affect the pKa of glucose/H+ symport.

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Jaglan, Prem S., Byron L. Cox, Thomas S. Arnold, Marc F. Kubicek, Dorothy J. Stuart et Terry J. Gilbertson. « Liquid Chromatographic Determination of Desfuroylceftiofur Metabolite of Ceftiofur as Residue in Cattle Plasma ». Journal of AOAC INTERNATIONAL 73, n^o 1 (1 janvier 1990) : 26–30. http://dx.doi.org/10.1093/jaoac/73.1.26.

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Abstract A liquid chromatographic (LC) method has been developed for the determination of the desfuroylceftiofur metabolite of ceftiofur as a residue in the plasma of animals. Plasma sample in 0.1 M pH 8.7 phosphate buffer containing dithioerythritol is Incubated under nitrogen for 15 min at 50°C. The sample is centrifuged, charged to a C18 cartridge, and washed with 0.1M ammonium acetate. The desfuroylceftiofur residue on the cartridge Is derivatized by adding 0.1M ammonium acetate containing iodoacetamide and letting the cartridge stand in the dark for 30 min. The cartridge is then drained and rinsed, and the desfuroylceftiofur acetamide is eluted with methanol. The mixture is evaporated to dryness, dissolved in pH 10.6 sodium hydroxide, and charged to a SAX cartridge. The derivative is eluted with 2% acetic acid, reduced In volume, and dissolved in mobile phase for liquid chromatography. The LC system includes a C8 column and guard cartridge with UV detection at 254 nm. The gradient mobile phase (flow rate 1 mL/mln) is 0.01M pH 5 ammonium acetate programmed to 29 % methanol-water (60 + 40) in 25 min. Recoveries were 90-100% with a sensitivity of 0.1 ppm or less. The procedure has been applied to the plasma of cattle, rats, horses, pigs, and dogs.

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Redhu, Archana Kumari, Nitesh Kumar Khandelwal, Atanu Banerjee, Alexis Moreno, Pierre Falson et Rajendra Prasad. « pHluorin enables insights into the transport mechanism of antiporter Mdr1 : R215 is critical for drug/H+ antiport ». Biochemical Journal 473, n^o 19 (27 septembre 2016) : 3127–45. http://dx.doi.org/10.1042/bcj20160407.

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Multidrug resistance 1 (MDR1) is a member of the major facilitator superfamily that contributes to MDR of Candida albicans. This antiporter belongs to the drug/H+ antiporter 1 family, pairing the downhill gradient of protons to drug extrusion. Hence, drug efflux from cytosol to extracellular space and the parallel import of H+ towards cytosol are inextricably linked processes. For monitoring the drug/H+ antiporter activity of Mdr1p, we developed a new system, exploiting a GFP variant pHluorin, which changes its fluorescence properties with pH. This enabled us to measure the cytosolic pH correlated to drug efflux. Since protonation of charged residues is a key step in proton movement, we explored the role of all charged residues of the 12 transmembrane segments (TMSs) of Mdr1p in drug/H+ transport by mutational analysis. This revealed that the conserved residue R215, positioned close to the C-terminal end of TMS-4, is critical for drug/H+ antiport, allowing protonation over a range of pH, in contrast with its H215 or K215 variants that failed to transport drugs at basic pH. Mutation of other residues of TMS-4 highlights the role of this TMS in drug transport, as confirmed by in silico modelling of Mdr1p and docking of drugs. The model points to the importance of R215 in proton transport, suggesting that it may adopt two main conformations, one oriented towards the extracellular face and the other towards the centre of Mdr1p. Together, our results not only establish a new system for monitoring drug/H+ transport, but also unveil a positively charged residue critical to Mdr1p function.

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Waelbroeck, M., J. Perret, P. Vertongen, M. Van Craenenbroeck et P. Robberecht. « Identification of secretin, vasoactive intestinal peptide and glucagon binding sites : from chimaeric receptors to point mutations ». Biochemical Society Transactions 30, n^o 4 (1 août 2002) : 437–41. http://dx.doi.org/10.1042/bst0300437.

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We have identified two basic residues that are important for the recognition of secretin and vasoactive intestinal peptide (VIP) by their respective receptors. These two peptides containing an Asp residue at position 3 interacted with an arginine residue in transmembrane helix 2 (TM2) of the receptor, and the lysine residue in extracellular loop 1 (ECL1) stabilized the active receptor conformation induced by the ligand. The glucagon receptor possesses a Lys instead of an Arg in TM2, and an Ile instead of Lys in ECL1; it markedly prefers a Gln side chain in position 3 of the ligand. Our results suggested that, in the wild-type receptor, the Ile side chain prevented access to the TM2 Lys side chain, but oriented the glucagon Gln3 side chain to its proper binding site. In the double mutant, the ECL1 Lys allowed an interaction between negatively charged residues in position 3 of glucagon and the TM2 Arg, resulting in efficient receptor activation by [Asp3]glucagon as well as by glucagon.

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Skerritt, Matthew R., et Donald L. Campbell. « Role of S4 positively charged residues in the regulation of Kv4.3 inactivation and recovery ». American Journal of Physiology-Cell Physiology 293, n^o 3 (septembre 2007) : C906—C914. http://dx.doi.org/10.1152/ajpcell.00167.2007.

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The molecular and biophysical mechanisms by which voltage-sensitive K+ (Kv)4 channels inactivate and recover from inactivation are presently unresolved. There is a general consensus, however, that Shaker-like N- and P/C-type mechanisms are likely not involved. Kv4 channels also display prominent inactivation from preactivated closed states [closed-state inactivation (CSI)], a process that appears to be absent in Shaker channels. As in Shaker channels, voltage sensitivity in Kv4 channels is thought to be conferred by positively charged residues localized to the fourth transmembrane segment (S4) of the voltage-sensing domain. To investigate the role of S4 positive charge in Kv4.3 gating transitions, we analyzed the effects of charge elimination at each positively charged arginine (R) residue by mutation to the uncharged residue alanine (A). We first demonstrated that R290A, R293A, R296A, and R302A mutants each alter basic activation characteristics consistent with positive charge removal. We then found strong evidence that recovery from inactivation is coupled to deactivation, showed that the precise location of the arginine residues within S4 plays an important role in the degree of development of CSI and recovery from CSI, and demonstrated that the development of CSI can be sequentially uncoupled from activation by R296A, specifically. Taken together, these results extend our current understanding of Kv4.3 gating transitions.

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Dementieva, Ekaterina I., Elena A. Fedorchuk, Lubov Yu Brovko, Alexander P. Savitskii et Natalya N. Ugarova. « Fluorescent Properties of Firefly Luciferases and Their Complexes with Luciferin ». Bioscience Reports 20, n^o 1 (1 février 2000) : 21–30. http://dx.doi.org/10.1023/a:1005579016387.

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Fluorescence of luciferases from Luciola mingrelica (single tryptophanresidue, Trp-419) and Photinus pyralis (two tryptophan residues, Trp-417,Trp-426) was studied. Analysis of quenching of tryptophan fluorescenceshowed that the tryptophan residue conserved in all luciferases is notaccessible for charged quenchers, which is explained by the presence ofpositively and negatively charged amino acid residues in the close vicinityto it. An effective energy transfer from tryptophan to luciferin wasobserved during quenching of tryptophan fluorescence of both luciferaseswith luciferin. From the data on the energy transfer, the distance betweenthe luciferin molecule and Trp-417 (419) in the luciferin–luciferasecomplex was calculated: 11–15 Å for P. pyralis and 12–17Å for L. mingrelica luciferases. The role of the conserved Trp residuein the catalysis is discussed.

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