Статті в журналах: "Β-strand"

1

Zhang, Ning, Shan Gao, Lei Zhang, Jishou Ruan та Tao Zhang. "Statistical Analysis of Terminal Extensions of Protein β-Strand Pairs". Advances in Bioinformatics 2013 (28 січня 2013): 1–7. http://dx.doi.org/10.1155/2013/909436.

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The long-range interactions, required to the accurate predictions of tertiary structures of β-sheet-containing proteins, are still difficult to simulate. To remedy this problem and to facilitate β-sheet structure predictions, many efforts have been made by computational methods. However, known efforts on β-sheets mainly focus on interresidue contacts or amino acid partners. In this study, to go one step further, we studied β-sheets on the strand level, in which a statistical analysis was made on the terminal extensions of paired β-strands. In most cases, the two paired β-strands have different lengths, and terminal extensions exist. The terminal extensions are the extended part of the paired strands besides the common paired part. However, we found that the best pairing required a terminal alignment, and β-strands tend to pair to make bigger common parts. As a result, 96.97% of β-strand pairs have a ratio of 25% of the paired common part to the whole length. Also 94.26% and 95.98% of β-strand pairs have a ratio of 40% of the paired common part to the length of the two β-strands, respectively. Interstrand register predictions by searching interacting β-strands from several alternative offsets should comply with this rule to reduce the computational searching space to improve the performances of algorithms.

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2

KEDARISETTI, KANAKA DURGA, MARCIN J. MIZIANTY, SCOTT DICK, and LUKASZ KURGAN. "IMPROVED SEQUENCE-BASED PREDICTION OF STRAND RESIDUES." Journal of Bioinformatics and Computational Biology 09, no. 01 (February 2011): 67–89. http://dx.doi.org/10.1142/s0219720011005355.

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Accurate identification of strand residues aids prediction and analysis of numerous structural and functional aspects of proteins. We propose a sequence-based predictor, BETArPRED, which improves prediction of strand residues and β-strand segments. BETArPRED uses a novel design that accepts strand residues predicted by SSpro and predicts the remaining positions utilizing a logistic regression classifier with nine custom-designed features. These are derived from the primary sequence, the secondary structure (SS) predicted by SSpro, PSIPRED and SPINE, and residue depth as predicted by RDpred. Our features utilize certain local (window-based) patterns in the predicted SS and combine information about the predicted SS and residue depth. BETArPRED is evaluated on 432 sequences that share low identity with the training chains, and on the CASP8 dataset. We compare BETArPRED with seven modern SS predictors, and the top-performing automated structure predictor in CASP8, the ZHANG-server. BETArPRED provides statistically significant improvements over each of the SS predictors; it improves prediction of strand residues and β-strands, and it finds β-strands that were missed by the other methods. When compared with the ZHANG-server, we improve predictions of strand segments and predict more actual strand residues, while the other predictor achieves higher rate of correct strand residue predictions when under-predicting them.

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3

Terwilliger, Thomas C. "Rapid model building of β-sheets in electron-density maps". Acta Crystallographica Section D Biological Crystallography 66, № 3 (12 лютого 2010): 276–84. http://dx.doi.org/10.1107/s0907444910000302.

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A method for rapidly building β-sheets into electron-density maps is presented. β-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and Cβatoms along the strand averaged over all repeats present in the strand. The β-strands obtained are then assembled into a single atomic model of the β-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 Å. The β-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5 Å resolution in which a third of the residues in β-sheets were built and a structure at 3.8 Å in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5 Å.

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4

Vischer, Henry F., Joke C. M. Granneman, and Jan Bogerd. "Opposite Contribution of Two Ligand-Selective Determinants in the N-Terminal Hormone-Binding Exodomain of Human Gonadotropin Receptors." Molecular Endocrinology 17, no. 10 (October 1, 2003): 1972–81. http://dx.doi.org/10.1210/me.2003-0172.

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Abstract The nine leucine-rich repeat-containing exodomains of the human FSH receptor (hFSH-R) and the human LH/chorionic gonadotropin receptor (hLH-R) harbor molecular determinants that allow the mutually exclusive binding of human FSH (hFSH) and human LH (hLH)/human chorionic gonadotropin (hCG) when these hormones are present in physiological concentrations. Previously, we have shown that the β-strands of hLH-R leucine-rich repeats 3 and 6 can confer full hCG/hLH responsiveness and binding when simultaneously introduced into a hFSH-R background without affecting the receptor’s responsiveness to hFSH. In the present study, we have determined the nature of contribution of each of these two β-strands in conferring hCG/hLH responsiveness to this mutant hFSH-R. Human LH-R β-strand 3 appeared to function as a positive hCG/hLH determinant by increasing the hCG/hLH responsiveness of the hFSH-R. In contrast, mutagenesis of hFSH-R β-strand 6, rather than the introduction of its corresponding hLH-R β-strand, appeared to allow the interaction of hCG/hLH with the hFSH-R. Hence, hFSH-R β-strand 6 functions as a negative determinant and, as such, restrains binding of hCG/hLH to the hFSH-R. Detailed mutagenic analysis revealed that the ability of the hFSH-R to interact with hCG/hLH depends primarily on the identity of two amino acids (Asn104, a positive LH-R determinant, and Lys179 a negative FSH-R determinant) that are situated on the C-terminal ends of β-strands 3 and 6, respectively.

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5

Gao, Yang, Yanxiang Cui, Tara Fox, Shiqiang Lin, Huaibin Wang, Natalia de Val, Z. Hong Zhou, and Wei Yang. "Structures and operating principles of the replisome." Science 363, no. 6429 (January 24, 2019): eaav7003. http://dx.doi.org/10.1126/science.aav7003.

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Visualization in atomic detail of the replisome that performs concerted leading– and lagging–DNA strand synthesis at a replication fork has not been reported. Using bacteriophage T7 as a model system, we determined cryo–electron microscopy structures up to 3.2-angstroms resolution of helicase translocating along DNA and of helicase-polymerase-primase complexes engaging in synthesis of both DNA strands. Each domain of the spiral-shaped hexameric helicase translocates sequentially hand-over-hand along a single-stranded DNA coil, akin to the way AAA+ ATPases (adenosine triphosphatases) unfold peptides. Two lagging-strand polymerases are attached to the primase, ready for Okazaki fragment synthesis in tandem. A β hairpin from the leading-strand polymerase separates two parental DNA strands into a T-shaped fork, thus enabling the closely coupled helicase to advance perpendicular to the downstream DNA duplex. These structures reveal the molecular organization and operating principles of a replisome.

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6

Haworth, Naomi L., та Merridee A. Wouters. "Between-strand disulfides: forbidden disulfides linking adjacent β-strands". RSC Advances 3, № 46 (2013): 24680. http://dx.doi.org/10.1039/c3ra42486c.

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7

HAWORTH, NAOMI L., LINA L. FENG, and MERRIDEE A. WOUTERS. "HIGH TORSIONAL ENERGY DISULFIDES: RELATIONSHIP BETWEEN CROSS-STRAND DISULFIDES AND RIGHT-HANDED STAPLES." Journal of Bioinformatics and Computational Biology 04, no. 01 (February 2006): 155–68. http://dx.doi.org/10.1142/s0219720006001734.

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Redox-active disulfides are capable of being oxidized and reduced under physiological conditions. The enzymatic role of redox-active disulfides in thiol-disulfide reductases is well-known, but redox-active disulfides are also present in non-enzymatic protein structures where they may act as switches of protein function. Here, we examine disulfides linking adjacent β-strands (cross-strand disulfides), which have been reported to be redox-active. Our previous work has established that these cross-strand disulfides have high torsional energies, a quantity likely to be related to the ease with which the disulfide is reduced. We examine the relationship between conformations of disulfides and their location in protein secondary structures. By identifying the overlap between cross-strand disulfides and various conformations, we wish to address whether the high torsional energy of a cross-strand disulfide is sufficient to confer redox activity or whether other factors, such as the presence of the cross-strand disulfide in a strained β-sheet, are required.

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8

Vischer, Henry F., Joke C. M. Granneman та Jan Bogerd. "Identification of Follicle-Stimulating Hormone-Selective β-Strands in the N-Terminal Hormone-Binding Exodomain of Human Gonadotropin Receptors". Molecular Endocrinology 20, № 8 (1 серпня 2006): 1880–93. http://dx.doi.org/10.1210/me.2005-0202.

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Abstract Glycoprotein hormone receptors contain large N-terminal extracellular domains (ECDs) that distinguish these receptors from most other G protein-coupled receptors. Each glycoprotein hormone receptor ECD consists of a curved leucine-rich repeat domain flanked by N- and C-terminal cysteine-rich regions. Selectivity of the different glycoprotein hormone receptors for their cognate hormones is exclusively determined by their ECDs and, in particular, their leucine-rich repeat domain. To identify human (h)FSH-selective determinants we used a gain-of-function mutagenesis strategy in which β-strands of the hLH receptor (hLH-R) were substituted with their hFSH receptor (hFSH-R) counterparts. Introduction of hFSH-R β-strand 1 into hLH-R conferred responsiveness to hFSH, whereas hLH-R mutants harboring one of the other hFSH-R β-strands displayed none or very limited sensitivity to hFSH. However, combined substitution of hFSH-R β-strand 1 and some of the other hFSH-R β-strands further increased the sensitivity of the mutant hLH-R to hFSH. The apparent contribution of multiple hFSH-R β-strands in providing a selective hormone binding interface corresponds well with their position in relation to hFSH as recently determined in the crystal structure of hFSH in complex with part of the hFSH-R ECD.

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9

Chandrasekhar, Srivari, Ambadi Sudhakar, Marelli Udaya Kiran, Bathini Nagendra Babu та Bharatam Jagadeesh. "β-Strand mimetics: formation of bend-strands in oligomers of enantiomeric β-amino acids". Tetrahedron Letters 49, № 52 (грудень 2008): 7368–71. http://dx.doi.org/10.1016/j.tetlet.2008.10.031.

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10

Tsai, James H., Amy Sue Waldman та James S. Nowick. "Two New β-strand Mimics". Bioorganic & Medicinal Chemistry 7, № 1 (січень 1999): 29–38. http://dx.doi.org/10.1016/s0968-0896(98)00225-9.

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11

Singh, Hanuman, Akshay Chenna, Upanshu Gangwar, Julie Borah, Gaurav Goel та V. Haridas. "Bispidine as a β-strand nucleator: from a β-arch to self-assembled cages and vesicles". Chemical Science 12, № 47 (2021): 15757–64. http://dx.doi.org/10.1039/d1sc04860k.

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Bispidine is a versatile scaffold that could be placed either at the terminal or at the middle of the peptide strand for nucleating β-strand structures. These β-strand mimetics self-assemble to single hole submicron cages and vesicles.

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12

Vorberg, Ina, Kaman Chan та Suzette A. Priola. "Deletion of β-Strand and α-Helix Secondary Structure in Normal Prion Protein Inhibits Formation of Its Protease-Resistant Isoform". Journal of Virology 75, № 21 (1 листопада 2001): 10024–32. http://dx.doi.org/10.1128/jvi.75.21.10024-10032.2001.

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ABSTRACT A fundamental event in the pathogenesis of transmissible spongiform encephalopathies (TSE) is the conversion of a normal, proteinase K-sensitive, host-encoded protein, PrP-sen, into its protease-resistant isoform, PrP-res. During the formation of PrP-res, PrP-sen undergoes conformational changes that involve an increase of β-sheet secondary structure. While previous studies in which PrP-sen deletion mutants were expressed in transgenic mice or scrapie-infected cell cultures have identified regions in PrP-sen that are important in the formation of PrP-res, the exact role of PrP-sen secondary structures in the conformational transition of PrP-sen to PrP-res has not yet been defined. We constructed PrP-sen mutants with deletions of the first β-strand, the second β-strand, or the first α-helix and tested whether these mutants could be converted to PrP-res in both scrapie-infected neuroblastoma cells (Sc+-MNB cells) and a cell-free conversion assay. Removal of the second β-strand or the first α-helix significantly altered both processing and the cellular localization of PrP-sen, while deletion of the first β-strand had no effect on these events. However, all of the mutants significantly inhibited the formation of PrP-res in Sc+-MNB cells and had a greatly reduced ability to form protease-resistant PrP in a cell-free assay system. Thus, our results demonstrate that deletion of the β-strands and the first α-helix of PrP-sen can fundamentally affect PrP-res formation and/or PrP-sen processing.

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13

Zhou, Rui, Guanghui Yang, Xuefei Guo, Qiang Zhou, Jianlin Lei та Yigong Shi. "Recognition of the amyloid precursor protein by human γ-secretase". Science 363, № 6428 (10 січня 2019): eaaw0930. http://dx.doi.org/10.1126/science.aaw0930.

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Cleavage of amyloid precursor protein (APP) by the intramembrane protease γ-secretase is linked to Alzheimer’s disease (AD). We report an atomic structure of human γ-secretase in complex with a transmembrane (TM) APP fragment at 2.6-angstrom resolution. The TM helix of APP closely interacts with five surrounding TMs of PS1 (the catalytic subunit of γ-secretase). A hybrid β sheet, which is formed by a β strand from APP and two β strands from PS1, guides γ-secretase to the scissile peptide bond of APP between its TM and β strand. Residues at the interface between PS1 and APP are heavily targeted by recurring mutations from AD patients. This structure, together with that of γ-secretase bound to Notch, reveal contrasting features of substrate binding, which may be applied toward the design of substrate-specific inhibitors.

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14

Huang, Cheng-Hsin, Tong Wai Wong, Chen-Hsu Yu, Jing-Yuan Chang, Shing-Jong Huang, Shou-Ling Huang та Richard P. Cheng. "Swapping the Positions in a Cross-Strand Lateral Ion-Pairing Interaction between Ammonium- and Carboxylate-Containing Residues in a β-Hairpin". Molecules 26, № 5 (3 березня 2021): 1346. http://dx.doi.org/10.3390/molecules26051346.

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Cross-strand lateral ion-pairing interactions are important for antiparallel β-sheet stability. Statistical studies suggested that swapping the position of cross-strand lateral residues should not significantly affect the interaction. Herein, we swapped the position of ammonium- and carboxylate-containing residues with different side-chain lengths in a cross-strand lateral ion-pairing interaction in a β-hairpin. The peptides were analyzed by 2D-NMR. The fraction folded population and folding free energy were derived from the chemical shift data. The ion-pairing interaction energy was derived using double mutant cycle analysis. The general trends for the fraction folded population and interaction energetics remained similar upon swapping the position of the interacting charged residues. The most stabilizing cross-strand interactions were between short residues, similar to the unswapped study. However, the fraction folded populations for most of the swapped peptides were higher compared to the corresponding unswapped peptides. Furthermore, subtle differences in the ion-pairing interaction energy upon swapping were observed, most likely due to the “unleveled” relative positioning of the interacting residues created by the inherent right-handed twist of the structure. These results should be useful for developing functional peptides that rely on lateral ion-pairing interactions across antiparallel β-strands.

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15

TSOI, Pui Yan, та Mengsu YANG. "Kinetic study of various binding modes between human DNA polymerase β and different DNA substrates by surface-plasmon-resonance biosensor". Biochemical Journal 361, № 2 (8 січня 2002): 317–25. http://dx.doi.org/10.1042/bj3610317.

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The interaction of a series of DNA substrates with human DNA polymerase β has been studied in real time by using a surface-plasmon-resonance (SPR) biosensor technique. We have prepared the sensor surfaces comprising different DNA targets, including single-stranded DNA, blunt-end double-stranded DNA, gapped DNA and DNA template—primer duplexes containing various mismatches at different positions. The binding and dissociation of polymerase β at the DNA-modified surfaces was measured in real time, and the kinetics profiles of polymerase—DNA interaction were analysed using various physical models. The results showed that polymerase β binding to single-stranded DNA (KA = 1.25×108M−1; where KA is the equilibrium affinity constant) was thermodynamically more favourable than to blunt-end DNA duplex (KA = 7.56×107M−1) or gapped DNA (KA = 8.53×107M−1), with a single binding mode on each DNA substrate. However, polymerase β bound to DNA template—primer duplexes (15bp with a 35nt overhang) at two sites, presumably one at the single-strand overhang and the other at the 3′-end of the primer. When the DNA duplex was fully matched, most of the polymerase β (83%) bound to the template—primer duplex region. The introduction of different numbers of mismatches near the 3′-end of the primer caused the binding affinity and the fraction of polymerase β bound at the duplex region to decrease 8–58-fold and 15–40%, respectively. On the other hand, the affinity of polymerase β for the single-strand overhang remained unchanged while the fraction bound to the single-strand region increased by 15–40%. The destabilizing effect of the mismatches was due to both a decrease in the rate of binding and an increase in the rate of dissociation for polymerase β.

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16

Juarez-Quintero, Víctor, Antolín Peralta-Castro, Claudia G. Benítez Cardoza, Tom Ellenberger, and Luis G. Brieba. "Structure of an open conformation of T7 DNA polymerase reveals novel structural features regulating primer-template stabilization at the polymerization active site." Biochemical Journal 478, no. 13 (July 16, 2021): 2665–79. http://dx.doi.org/10.1042/bcj20200922.

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The crystal structure of full-length T7 DNA polymerase in complex with its processivity factor thioredoxin and double-stranded DNA in the polymerization active site exhibits two novel structural motifs in family-A DNA polymerases: an extended β-hairpin at the fingers subdomain, that interacts with the DNA template strand downstream the primer-terminus, and a helix-loop-helix motif (insertion1) located between residues 102 to 122 in the exonuclease domain. The extended β-hairpin is involved in nucleotide incorporation on substrates with 5′-overhangs longer than 2 nt, suggesting a role in stabilizing the template strand into the polymerization domain. Our biochemical data reveal that insertion1 of the exonuclease domain makes stabilizing interactions that facilitate proofreading by shuttling the primer strand into the exonuclease active site. Overall, our studies evidence conservation of the 3′–5′ exonuclease domain fold between family-A DNA polymerases and highlight the modular architecture of T7 DNA polymerase. Our data suggest that the intercalating β-hairpin guides the template-strand into the polymerization active site after the T7 primase-helicase unwinds the DNA double helix ameliorating the formation of secondary structures and decreasing the appearance of indels.

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17

Jouanne, Marie, Anne Sophie Voisin-Chiret, Rémi Legay, Sébastien Coufourier, Sylvain Rault та Jana Sopkova-de Oliveira Santos. "β-Strand Mimicry: Exploring Oligothienylpyridine Foldamers". European Journal of Organic Chemistry 2016, № 34 (10 листопада 2016): 5686–96. http://dx.doi.org/10.1002/ejoc.201600882.

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18

Novak, Walter R. P., Basudeb Bhattacharyya, Daniel P. Grilley, and Todd M. Weaver. "Proteolysis of truncated hemolysin A yields a stable dimerization interface." Acta Crystallographica Section F Structural Biology Communications 73, no. 3 (February 21, 2017): 138–45. http://dx.doi.org/10.1107/s2053230x17002102.

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Wild-type and variant forms of HpmA265 (truncated hemolysin A) fromProteus mirabilisreveal a right-handed, parallel β-helix capped and flanked by segments of antiparallel β-strands. The low-salt crystal structures form a dimeric structureviathe implementation of on-edge main-chain hydrogen bonds donated by residues 243–263 of adjacent monomers. Surprisingly, in the high-salt structures of two variants, Y134A and Q125A-Y134A, a new dimeric interface is formedviamain-chain hydrogen bonds donated by residues 203–215 of adjacent monomers, and a previously unobserved tetramer is formed. In addition, an eight-stranded antiparallel β-sheet is formed from the flap regions of crystallographically related monomers in the high-salt structures. This new interface is possible owing to additional proteolysis of these variants after Tyr240. The interface formed in the high-salt crystal forms of hemolysin A variants may mimic the on-edge β-strand positioning used in template-assisted hemolytic activity.

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19

Sasaki, Toshiyuki, та Mikiji Miyata. "Characterization of Hidden Chirality: Two-Fold Helicity in β-Strands". Symmetry 11, № 4 (5 квітня 2019): 499. http://dx.doi.org/10.3390/sym11040499.

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A β-strand is a component of a β-sheet and is an important structural motif in biomolecules. An α-helix has clear helicity, while chirality of a β-strand had been discussed on the basis of molecular twists generated by forming hydrogen bonds in parallel or non-parallel β-sheets. Herein we describe handedness determination of two-fold helicity in a zig-zag β-strand structure. Left- (M) and right-handedness (P) of the two-fold helicity was defined by application of two concepts: tilt-chirality and multi-point approximation. We call the two-fold helicity in a β-strand, whose handedness has been unrecognized and unclarified, as hidden chirality. Such hidden chirality enables us to clarify precise chiral characteristics of biopolymers. It is also noteworthy that characterization of chirality of high dimensional structures like a β-strand and α-helix, referred to as high dimensional chirality (HDC) in the present study, will contribute to elucidation of the possible origins of chirality and homochirality in nature because such HDC originates from not only asymmetric centers but also conformations in a polypeptide chain.

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20

Nowick, James S., Darren L. Holmes, Gilbert Mackin, Glenn Noronha, A. J. Shaka та Eric M. Smith. "An Artificial β-Sheet Comprising a Molecular Scaffold, a β-Strand Mimic, and a Peptide Strand1". Journal of the American Chemical Society 118, № 11 (січень 1996): 2764–65. http://dx.doi.org/10.1021/ja953334a.

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21

Mattice, Wayne L., Eok Lee та Harold A. Scheraga. "Dominance of irregular structures in the formation of intramolecular antiparallel β sheets by homopolyamino acids". Canadian Journal of Chemistry 63, № 1 (1 січня 1985): 140–46. http://dx.doi.org/10.1139/v85-023.

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Анотація:

A matrix formulation of the conformational partition function is used to assess the influence of irregular structures on the formation of intramolecular antiparallel β sheets. An antiparallel sheet is considered to be irregular if any pair of contiguous strands has an unequal number of residues. The regular structures in the model consist of antiparallel sheets in which every strand contains the same number of residues. Aside from a growth parameter t, the model contains two parameters that account for the influence of edge effects. Each tight turn contributes a factor δ, and each residue in the sheet that does not have a partner in a preceding strand contributes a factor τ. When τ < δ = 1, preferred sheets consist of an extremely large number of very short strands. Such sheets resemble those found in cross-β fibers. Irregular structures increase the cooperativity of the formation of cross-β fibers. They cause the fibers that are formed to be longer (have more strands) and thicker (have more residues per strand) than if all antiparallel sheets were regular. A much different result is obtained if end effects are modified so that the antiparallel sheets formed resemble those found in globular proteins. Formation of antiparallel sheets remains cooperative, but irregular sheets now markedly reduce the cooperativity of the transition. At high antiparallel-sheet content, irregular structures cause typical antiparallel sheets to be smaller. The behavior of the conformational partition function shows that irregular structures make the dominant contribution to both transitions. Therefore, formulations that restrict consideration to regular structures may provide a misleading picture of antiparallel-sheet formation.

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22

Lundquist, Karl, Jeremy Bakelar, Nicholas Noinaj, and James C. Gumbart. "C-terminal kink formation is required for lateral gating in BamA." Proceedings of the National Academy of Sciences 115, no. 34 (August 7, 2018): E7942—E7949. http://dx.doi.org/10.1073/pnas.1722530115.

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In Gram-negative bacteria, the outer membrane contains primarily β-barrel transmembrane proteins and lipoproteins. The insertion and assembly of β-barrel outer-membrane proteins (OMPs) is mediated by the β-barrel assembly machinery (BAM) complex, the core component of which is the 16-stranded transmembrane β-barrel BamA. Recent studies have indicated a possible role played by the seam between the first and last β-barrel strands of BamA in the OMP insertion process through lateral gating and a destabilized membrane region. In this study, we have determined the stability and dynamics of the lateral gate through over 12.5 μs of equilibrium simulations and 4 μs of free-energy calculations. From the equilibrium simulations, we have identified a persistent kink in the C-terminal strand and observed spontaneous lateral-gate separation in a mimic of the native bacterial outer membrane. Free-energy calculations of lateral gate opening revealed a significantly lower barrier to opening in the C-terminal kinked conformation; mutagenesis experiments confirm the relevance of C-terminal kinking to BamA structure and function.

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23

Makabe, Koki, Shude Yan, Valentina Tereshko, Grzegorz Gawlak та Shohei Koide. "β-Strand Flipping and Slipping Triggered by Turn Replacement Reveal the Opportunistic Nature of β-Strand Pairing". Journal of the American Chemical Society 129, № 47 (листопад 2007): 14661–69. http://dx.doi.org/10.1021/ja074252c.

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24

KALCHISHKOVA, NIKOLINA, and KONRAD J. BÖHM. "ON THE RELEVANCE OF THE CORE HELIX ALPHA 6 TO KINESIN ACTIVITY GENERATION." Biophysical Reviews and Letters 04, no. 01n02 (April 2009): 63–75. http://dx.doi.org/10.1142/s1793048009000934.

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KIF5A and Eg5 are plus-end directed motor proteins with conserved motor domains. The catalytic cores of both motors comprise a central β-sheet consisting of eight β-strands surrounded by six α-helices. Notwithstanding the high level of similarity in their structural organization, Eg5 moves significantly slower than KIF5A. Recently, we reported that neck linker and neck elements of KIF5A and Eg5 contribute to velocity regulation. As the neck linker of both motors is known to be connected to the catalytic core via helix α6, the question arises if also helix α6 and strand β8 as the last core elements might be involved in velocity regulation. To elucidate the role these structures in kinesin activity generation we constructed KIF5A- and Eg5-based chimeras in which the β8 strand, helix α6, the neck linker, and the neck were interchanged. Additionally, we studied the role of α6 and β8 in ATP hydrolysis and microtubule binding by expression of truncated KIF5A and Eg5 constructs lacking both strand β8 and helix α6, or α6 only. The results obtained suggest that strand β8 and helix α6 are not involved in microtubule-binding, but α6 is an obligate and kinesin type-specific structure required to generate ATPase activity.

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25

Egelund, R., S. Jensen, K. W. Rodenburg, and P. A. Andreasen. "Solvent Effects on Activity and Conformation of Plasminogen Activator Inhibitor-1." Thrombosis and Haemostasis 81, no. 03 (1999): 407–14. http://dx.doi.org/10.1055/s-0037-1614487.

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SummaryWe have studied effects of the solvent composition on the activity and the conformation of human plasminogen activator inhibitor-1 (PAI-1) from HT-1080 fibrosarcoma cells. Non-ionic detergents, including Triton X-100, reduced the inhibitory activity of PAI-1 more than 20-fold at 0° C, but less than 2-fold at 37° C, while glycerol partly prevented the detergent-induced activity-loss at 0° C. The activity-loss was associated with an increase in PAI-1 substrate behaviour. Evaluating the PAI-1 conformation by proteolytic susceptibility of specific peptide bonds, we found that the V8-proteinase susceptibility of the Glu332-Ser333 (P17-P16) bond, part of the hinge between the reactive centre loop (RCL) and β-strand 5A, and the endoproteinase Asp-N susceptibility of several bonds in the β-strand 2A-α-helix E region were increased by detergents at both 0 and 37° C. The susceptibility of the Gln321-Ala322 and the Lys325-Val326 bonds in β-strand 5A to papain and trypsin, respectively, was increased by detergents at 0° C, but not at 37° C, showing a strict correlation between proteinase susceptibility of β-strand 5A and activity-loss at 0° C. Since the β-strand 2A-α-helix E region also showed differential susceptibility to endoproteinase Asp-N in latent, active, and reactive centre-cleaved PAI-1, we propose that a detergent-induced conformational change of the β-strand 2A-α-helix E region influences the movements of β-sheet A, resulting in a cold-induced conformational change of β-strand 5A and thereby an increased substrate behaviour at low temperatures. These results provide new information about the structural basis for serpin substrate behaviour.

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26

Serrano, Pedro, Margaret A. Johnson, Amarnath Chatterjee, Benjamin W. Neuman, Jeremiah S. Joseph, Michael J. Buchmeier, Peter Kuhn, and Kurt Wüthrich. "Nuclear Magnetic Resonance Structure of the Nucleic Acid-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein 3." Journal of Virology 83, no. 24 (October 14, 2009): 12998–3008. http://dx.doi.org/10.1128/jvi.01253-09.

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ABSTRACT The nuclear magnetic resonance (NMR) structure of a globular domain of residues 1071 to 1178 within the previously annotated nucleic acid-binding region (NAB) of severe acute respiratory syndrome coronavirus nonstructural protein 3 (nsp3) has been determined, and N- and C-terminally adjoining polypeptide segments of 37 and 25 residues, respectively, have been shown to form flexibly extended linkers to the preceding globular domain and to the following, as yet uncharacterized domain. This extension of the structural coverage of nsp3 was obtained from NMR studies with an nsp3 construct comprising residues 1066 to 1181 [nsp3(1066-1181)] and the constructs nsp3(1066-1203) and nsp3(1035-1181). A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand β-sheet holding two α-helices of three and four turns that are oriented antiparallel to the β-strands. Two antiparallel two-strand β-sheets and two 310-helices are anchored against the surface of this barrel-like molecular core. Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold.

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27

Rehman, Zahid U., and Bernd H. A. Rehm. "Dual Roles of Pseudomonas aeruginosa AlgE in Secretion of the Virulence Factor Alginate and Formation of the Secretion Complex." Applied and Environmental Microbiology 79, no. 6 (January 18, 2013): 2002–11. http://dx.doi.org/10.1128/aem.03960-12.

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ABSTRACTAlgE is a monomeric 18-stranded β-barrel protein required for secretion of the extracellular polysaccharide alginate inPseudomonas aeruginosa. To assess the molecular mechanism of alginate secretion, AlgE was subjected to site-specific and FLAG epitope insertion mutagenesis. Except for β-strands 6 and 10, epitope insertions into the transmembrane β-strands abolished localization of AlgE to the outer membrane. Interestingly, an epitope insertion into β-strand 10 produced alginate and was only detectable in outer membranes isolated from cells grown on solid media. The deletion of nine C-terminal amino acid residues destabilized AlgE. Replacement of amino acids that constitute the highly electropositive pore constriction showed that individual amino acid residues have a specific function in alginate secretion. Two of the triple mutants (K47E+R353A+R459E and R74E+R362A+R459E) severely reduced alginate production. Mutual stability analysis using thealgEdeletion mutant PDO300ΔalgE(miniCTX) showed the periplasmic alginate biosynthesis proteins AlgK and AlgX were completely destabilized, while the copy number of the inner membrane c-di-GMP receptor Alg44 was reduced. Chromosomal integration ofalgErestored AlgK, AlgX, and Alg44, providing evidence for a multiprotein complex that spans the cell envelope. Periplasmic turn 4 of AlgE was identified as an important region for maintaining the stability of the putative multiprotein complex.

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28

Jacchieri, Saul G. "Study of α-helix to β-strand to β-sheet transitions in amyloid: the role of segregated hydrophobic β-strands". Biophysical Chemistry 74, № 1 (серпень 1998): 23–34. http://dx.doi.org/10.1016/s0301-4622(98)00157-4.

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29

Remaut, Han, та Gabriel Waksman. "Protein–protein interaction through β-strand addition". Trends in Biochemical Sciences 31, № 8 (серпень 2006): 436–44. http://dx.doi.org/10.1016/j.tibs.2006.06.007.

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30

Chaudhuri, Saikat, Manikandan Mohanan, Andreas V. Willems, Jeffery A. Bertke та Nagarjuna Gavvalapalli. "β-Strand inspired bifacial π-conjugated polymers". Chemical Science 10, № 23 (2019): 5976–82. http://dx.doi.org/10.1039/c9sc01724k.

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β-Strand inspired bifacial π-conjugated polymers that are soluble despite the absence of pendant solubilizing chains are reported. Precise tunability of the bifacial monomer height enables control of polymer solubility and intermolecular interactions.

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31

Bhat, Archana S., Lisa N. Kinch та Nick V. Grishin. "β‐Strand ‐mediated interactions of protein domains". Proteins: Structure, Function, and Bioinformatics 88, № 11 (11 липня 2020): 1513–27. http://dx.doi.org/10.1002/prot.25970.

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32

Budyak, Ivan L., Anastasia Zhuravleva та Lila M. Gierasch. "The Role of Aromatic–Aromatic Interactions in Strand–Strand Stabilization of β-Sheets". Journal of Molecular Biology 425, № 18 (вересень 2013): 3522–35. http://dx.doi.org/10.1016/j.jmb.2013.06.030.

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33

Alba, Eva De, Manuel Rico та M. Angeles Jiménez. "The turn sequence directs β- strand alignment in designed β-hairpins". Protein Science 8, № 11 (31 грудня 2008): 2234–44. http://dx.doi.org/10.1110/ps.8.11.2234.

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34

Nowick, James S., Mason Pairish, In Quen Lee, Darren L. Holmes та Joseph W. Ziller. "An Extended β-Strand Mimic for a Larger Artificial β-Sheet". Journal of the American Chemical Society 119, № 23 (червень 1997): 5413–24. http://dx.doi.org/10.1021/ja963843s.

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35

Kikuchi, Nobuaki, Kazuo Fujiwara та Masamichi Ikeguchi. "β‐Strand twisting/bending in soluble and transmembrane β‐barrel structures". Proteins: Structure, Function, and Bioinformatics 86, № 12 (листопад 2018): 1231–41. http://dx.doi.org/10.1002/prot.25576.

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36

Saeed, Muhammad, S. A. Akbar Behjatnia, Shahid Mansoor, Yusuf Zafar, Shahida Hasnain та M. Ali Rezaian. "A Single Complementary-Sense Transcript of a Geminiviral DNA β Satellite Is Determinant of Pathogenicity". Molecular Plant-Microbe Interactions® 18, № 1 (січень 2005): 7–14. http://dx.doi.org/10.1094/mpmi-18-0007.

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Small circular single-stranded DNA satellites, termed DNAβ, have recently been found associated with some geminivirus infections. The DNA β associated with Cotton leaf curl virus is responsible for symptom expression of a devastating disease in Pakistan. Mutagenesis of DNA β revealed that the complementary-sense open reading frame (ORF) βC1 is required for inducing disease symptoms in Nicotiana tabacum. An ORF present on the virion-sense strand βV1 appeared to have no role in pathogenesis. Tobacco plants transformed with a βC1 ORF under the control of the Cauliflower mosaic virus 35S promoter or with a dimeric DNA β exhibited severe disease-like phenotypes, while plants transformed with a mutated version of βC1 appeared normal. Northern blot analysis of RNA from the transgenic plants, using strand-specific probes, identified a single complementary-sense transcript. The transcript carries the full βC1 ORF encoding a 118-amino acid product. It maps to the DNA β at nucleotide position 186 to 563 and contains a polyadenylation signal 18 nt upstream of the stop codon. A TATA box is located 43 nt upstream of the start codon. Our results indicate that βC1 protein is responsible for DNA β-induced disease symptoms.

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37

Werner, Susanne, Karin Vogel-Bachmayr, Britta Hollinderbäumer, and Birgitta M. Wöhrl. "Requirements for Minus-Strand Transfer Catalyzed by Rous Sarcoma Virus Reverse Transcriptase." Journal of Virology 75, no. 21 (November 1, 2001): 10132–38. http://dx.doi.org/10.1128/jvi.75.21.10132-10138.2001.

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ABSTRACT We have examined the specific minus-strand transfer reactions that occur after the synthesis of minus strong-stop DNA and nonspecific strand switching on homopolymeric poly(rA) templates with different types of Rous sarcoma virus (RSV) reverse transcriptases. Three different types of reverse transcriptases can be isolated from virions of RSV: heterodimeric αβ and homodimeric α and β. The mechanism of minus-strand transfer was examined using a model primer-template substrate corresponding to the 5′- and 3′-terminal RNA regions of the RSV genome. The results reveal that the RNase H activity of RSV reverse transcriptases is required for minus-strand transfer. Less than 2% of strand transfer of the extended product is detectable with RNase H-deficient enzymes. We could show that the α homodimer lacking the integrase domain can perform strand transfer almost as efficiently as the αβ and αPol heterodimers. In contrast, the activities of β and Pol for minus-strand transfer are reduced. Furthermore, a two- to fivefold increase in minus-strand transfer activities was observed in the presence of human immunodeficiency virus type 1 nucleocapsid protein.

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38

Leader, David P., та E. James Milner-White. "Identification and characterization of two classes of G1 β-bulge". Acta Crystallographica Section D Structural Biology 77, № 2 (26 січня 2021): 217–23. http://dx.doi.org/10.1107/s2059798320015533.

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In standard β-bulges, a residue in one strand of a β-sheet forms hydrogen bonds to two successive residues (`1' and `2') of a second strand. Two categories, `classic' and `G1' β-bulges, are distinguished by their dihedral angles: 1,2-αRβR (classic) or 1,2-αLβR (G1). It had previously been observed that G1 β-bulges are most often found as components of two quite distinct composite structures, suggesting that a basis for further differentiation might exist. Here, it is shown that two subtypes of G1 β-bulges, G1α and G1β, may be distinguished by their conformation (αR or βR) at residue `0' of the second strand. β-Bulges that are constituents of the composite structure named the β-bulge loop are of the G1α type, whereas those that are constituents of the composite structure named β-link here are of the G1β type. A small proportion of G1β β-bulges, but not G1α β-bulges, occur in other contexts. There are distinctive differences in amino-acid composition and sequence pattern between these two types of G1 β-bulge which may have practical application in protein design.

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39

Hayat, Sikander, Chris Sander, Debora S. Marks та Arne Elofsson. "All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences". Proceedings of the National Academy of Sciences 112, № 17 (9 квітня 2015): 5413–18. http://dx.doi.org/10.1073/pnas.1419956112.

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Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases.

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40

Gruss, Fabian, Franziska Zaehringer, Roman Jakob, Björn Burmann, Sebastian Hiller, and Timm Maier. "A lateral gate for autotransporter and outer membrane protein assembly." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1492. http://dx.doi.org/10.1107/s2053273314085076.

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β-barrel proteins are key functional components of the outer membranes of gram-negative bacteria, mitochondria and plastids. They mediate transport across the membrane, act as receptors and are involved in bacterial pathogenicity. Despite their crucial roles, assembly and membrane insertion of β-barrel outer membrane proteins, which are mediated by β-barrel membrane proteins of the OMP85 family, have remained elusive. The crystal structure of the Escherichia coli OMP85 protein TamA [1], which is involved in autotransporter biogenesis, now provides a novel perspective on β-barrel membrane protein assembly. The protein was crystallized in lipidic phase and microseeding was employed to obtain high-quality 2.3 Å diffraction data. TamA comprises a 16-stranded transmembrane β-barrel and three N-terminal POTRA domains. The barrel is closed at the extracellular face by a conserved lid loop tightly interacting with a conserved lock region on the inner barrel wall. The C-terminal β-strand of the barrel forms an unusual inward kink, which creates a gate for substrate access to the lipid bilayer and weakens lateral inter-strand connection. These structural features immediately suggest a mechanism of autotransporter insertion based on barrel expansion and lateral release. Based on structural conservation of all core elements [2], this mechanism might well be relevant for the entire OMP85 family.

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41

Robinson, Colin W., Carl S. Rye, Nicola E. A. Chessum та Keith Jones. "A model β-sheet interaction and thermodynamic analysis of β-strand mimetics". Organic & Biomolecular Chemistry 13, № 27 (2015): 7402–7. http://dx.doi.org/10.1039/c5ob00886g.

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42

Syud, Faisal A., Heather E. Stanger, Heather Schenck Mortell, Juan F. Espinosa, John D. Fisk, Charles G. Fry та Samuel H. Gellman. "Influence of Strand Number on Antiparallel β-Sheet Stability in Designed Three- and Four-stranded β-Sheets". Journal of Molecular Biology 326, № 2 (лютий 2003): 553–68. http://dx.doi.org/10.1016/s0022-2836(02)01304-9.

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43

Johansson, J. "Membrane properties and amyloid fibril formation of lung surfactant protein C." Biochemical Society Transactions 29, no. 4 (August 1, 2001): 601–6. http://dx.doi.org/10.1042/bst0290601.

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Pulmonary surfactant is essential for respiration and lung host defence and is composed of 80–90% lipids, mainly dipalmitoylphosphatidylcholine (DPPC). Surfactant protein C (SP-C) constitutes 1–2 % of the surfactant mass, and is one of the most hydrophobic peptides yet isolated. SP-C residues 9–34 form an α-helix with a central poly-valine segment, which perfectly matches the thickness of a fluid DPPC bilayer. The palmitoyl groups linked to Cys-5 and Cys-6 of SP-C increase the capacity of the peptide to promote lipid adsorption at an air/liquid interface, and augment the mechanical stability of SP-C/lipid mixtures. SP-C undergoes α-helix → β-sheet transition and forms amyloid fibrils. NMR and MS studies show that the poly-valine helix is kinetically stabilized, and that once it unfolds, formation of β-sheet aggregates is significantly faster than refolding. α-Helix unfolding is accelerated after removal of the palmitoyl groups. Secondary structure prediction of SP-C yields β-strand conformation of the poly-valine part. A database search revealed similar discordance between experimentally determined helices and predicted β-strands for other amyloid-forming proteins, including the prion protein associated with spongiform encephalopathies, and the amyloid-β (Aβ) peptide associated with Alzheimer's disease. For Aβ and SP-C, removal of the helix/strand discordance by residue replacements abrogates fibril formation in vitro.

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44

Derewenda, Zygmunt S., and Urszula Derewenda. "Relationships among serine hydrolases: evidence for a common structural motif in triacylglyceride lipases and esterases." Biochemistry and Cell Biology 69, no. 12 (December 1, 1991): 842–51. http://dx.doi.org/10.1139/o91-125.

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A detailed analysis of the highly refined (1.9 Å resolution) molecular model of the fungal (Rhizomucor miehei) triglyceride lipase reveals a unique conformation of the oligopeptide containing the active serine (Ser 144) residue. It consists of a six-residue β-strand (strand 4 of the central sheet), a four-residue turn of type II′ with serine in the ε conformation, and a buried α-helix packed in a parallel way against strands 4 and 5 of the central β-pleated sheet. It is shown that the invariant glycines in positions (1) and (5) of the so-called lipase consensus sequence (G-X-S-X-G) are in extended and helical conformations, respectively, and that they are conserved owing to the steric restrictions imposed on these residues by the packing stereochemistry of this β-εSer-α motif, and not by secondary structure requirements, as is the case in serine proteinases. Sequence homologies indicate that this unique motif is likely to be found in serine esterases and other lipases, indicating a possible evolutionary link of these families of hydrolytic enzymes.Key words: serine proteinases, lipases, esterases, protein crystallography, protein structure.

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45

Falnes, Pål Ø., Magnus E. Jakobsson, Erna Davydova, Angela Ho та Jędrzej Małecki. "Protein lysine methylation by seven-β-strand methyltransferases". Biochemical Journal 473, № 14 (12 липня 2016): 1995–2009. http://dx.doi.org/10.1042/bcj20160117.

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Lysine methylation is an important post-translational protein modification, and a number of novel lysine-specific protein methyltransferases belonging to the seven-β-strand methyltransferase family have recently been discovered. This article provides a comprehensive review of this group of enzymes.

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46

Wingren, Christer, Allen B. Edmundson та Carl A. K. Borrebaeck. "Designing proteins to crystallize through β-strand pairing". Protein Engineering, Design and Selection 16, № 4 (квітень 2003): 255–64. http://dx.doi.org/10.1093/proeng/gzg038.

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47

Hammond, Ming C., Baruch Z. Harris, Wendell A. Lim та Paul A. Bartlett. "β Strand Peptidomimetics as Potent PDZ Domain Ligands". Chemistry & Biology 13, № 12 (грудень 2006): 1247–51. http://dx.doi.org/10.1016/j.chembiol.2006.11.010.

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48

Boumendjel, Ahcene, John C. Roberts, Essa Hu, Peter V. Pallai та Julius Rebek. "Design and Asymmetric Synthesis of β-Strand Peptidomimetics". Journal of Organic Chemistry 61, № 13 (січень 1996): 4434–38. http://dx.doi.org/10.1021/jo9522771.

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49

Pehere, Ashok D., та Andrew D. Abell. "New β-Strand Templates Constrained by Huisgen Cycloaddition". Organic Letters 14, № 5 (16 лютого 2012): 1330–33. http://dx.doi.org/10.1021/ol3002199.

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50

German, Elizabeth A., Jonathan E. Ross, Peter C. Knipe, Michaela F. Don, Sam Thompson та Andrew D. Hamilton. "β-Strand Mimetic Foldamers Rigidified through Dipolar Repulsion". Angewandte Chemie 127, № 9 (19 січня 2015): 2687–90. http://dx.doi.org/10.1002/ange.201410290.

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