Journal articles: 'Conformational characterization'

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Seidler, Clarissa A., Janik Kokot, Monica L. Fernández-Quintero, and Klaus R. Liedl. "Structural Characterization of Nanobodies during Germline Maturation." Biomolecules 13, no. 2 (February 17, 2023): 380. http://dx.doi.org/10.3390/biom13020380.

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Camelid heavy-chain antibody variable domains (VHH), nanobodies, are the smallest-known functional antibody fragments with high therapeutic potential. In this study, we investigate a VHH binding to hen egg-white lysozyme (HEL). We structurally and dynamically characterized the conformational diversity of four VHH variants to elucidate the antigen-binding process. For two of these antibodies, not only are the dissociation constants known, but also the experimentally determined crystal structures of the VHH in complex with HEL are available. We performed well-tempered metadynamics simulations in combination with molecular dynamics simulations to capture a broad conformational space and to reconstruct the thermodynamics and kinetics of conformational transitions in the antigen-binding site, the paratope. By kinetically characterizing the loop movements of the paratope, we found that, with an increase in affinity, the state populations shift towards the binding competent conformation. The contacts contributing to antigen binding, and those who contribute to the overall stability, show a clear trend towards less variable but more intense contacts. Additionally, these investigated nanobodies clearly follow the conformational selection paradigm, as the binding competent conformation pre-exists within the structural ensembles without the presence of the antigen.

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Paz, Aviv, Derek P. Claxton, Jay Prakash Kumar, Kelli Kazmier, Paola Bisignano, Shruti Sharma, Shannon A. Nolte, et al. "Conformational transitions of the sodium-dependent sugar transporter, vSGLT." Proceedings of the National Academy of Sciences 115, no. 12 (March 5, 2018): E2742—E2751. http://dx.doi.org/10.1073/pnas.1718451115.

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Sodium-dependent transporters couple the flow of Na+ ions down their electrochemical potential gradient to the uphill transport of various ligands. Many of these transporters share a common core structure composed of a five-helix inverted repeat and deliver their cargo utilizing an alternating-access mechanism. A detailed characterization of inward-facing conformations of the Na+-dependent sugar transporter from Vibrio parahaemolyticus (vSGLT) has previously been reported, but structural details on additional conformations and on how Na+ and ligand influence the equilibrium between other states remains unknown. Here, double electron–electron resonance spectroscopy, structural modeling, and molecular dynamics are utilized to deduce ligand-dependent equilibria shifts of vSGLT in micelles. In the absence and presence of saturating amounts of Na+, vSGLT favors an inward-facing conformation. Upon binding both Na+ and sugar, the equilibrium shifts toward either an outward-facing or occluded conformation. While Na+ alone does not stabilize the outward-facing state, gating charge calculations together with a kinetic model of transport suggest that the resting negative membrane potential of the cell, absent in detergent-solubilized samples, may stabilize vSGLT in an outward-open conformation where it is poised for binding external sugars. In total, these findings provide insights into ligand-induced conformational selection and delineate the transport cycle of vSGLT.

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Dong, Qiwen, Kai Wang, Bin Liu, and Xuan Liu. "Characterization and Prediction of Protein Flexibility Based on Structural Alphabets." BioMed Research International 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/4628025.

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Motivation.To assist efforts in determining and exploring the functional properties of proteins, it is desirable to characterize and predict protein flexibilities.Results.In this study, the conformational entropy is used as an indicator of the protein flexibility. We first explore whether the conformational change can capture the protein flexibility. The well-defined decoy structures are converted into one-dimensional series of letters from a structural alphabet. Four different structure alphabets, including the secondary structure in 3-class and 8-class, the PB structure alphabet (16-letter), and the DW structure alphabet (28-letter), are investigated. The conformational entropy is then calculated from the structure alphabet letters. Some of the proteins show high correlation between the conformation entropy and the protein flexibility. We then predict the protein flexibility from basic amino acid sequence. The local structures are predicted by the dual-layer model and the conformational entropy of the predicted class distribution is then calculated. The results show that the conformational entropy is a good indicator of the protein flexibility, but false positives remain a problem. The DW structure alphabet performs the best, which means that more subtle local structures can be captured by large number of structure alphabet letters. Overall this study provides a simple and efficient method for the characterization and prediction of the protein flexibility.

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Siddiqui, Mahtab Z. "Dehydrophenylalanine analogues: conformational characterization." International Journal of Biological Macromolecules 26, no. 1 (October 1999): 17–21. http://dx.doi.org/10.1016/s0141-8130(99)00063-x.

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SENGE, MATHIAS O., INES BISCHOFF, NORA Y. NELSON, and KEVIN M. SMITH. "Synthesis, Reactivity and Structural Chemistry of 5,10,15,20-Tetraalkylporphyrins." Journal of Porphyrins and Phthalocyanines 03, no. 02 (February 1999): 99–116. http://dx.doi.org/10.1002/(sici)1099-1409(199902)3:2<99::aid-jpp109>3.0.co;2-6.

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The synthesis, reactivity and full characterization of a series of meso-tetraalkyl porphyrins and metalloporphyrins with R ≡ n-butyl (6), 2-methyl-propyl (7), isopropyl (8), l-ethyl-propyl (10) and tert-butyl (11) groups are reported. Derivatives of the last of these show considerably bathochromically shifted absorption bands and the crystal structure of Zn ( II )11(pyr) exhibits a severely ruffled macrocycle conformation. Systematic crystallographic studies of the porphyrins showed that the free base porphyrins with R ≡ n-butyl ( H 26), 2-methyl-propyl ( H 27) and 1-ethyl-propyl ( H 210) are planar. A larger conformational variety was found for the metal complexes. While most Ni ( II ) derivatives and Pd ( II )8 showed a ruffled macrocycle conformation with a degree of ruffling exceeding that of meso-unsubstituted porphyrins, both planar and non-planar forms were found for the related Cu ( II ) derivatives. The Zn ( II ) complexes of porphyrins with isopropyl or 1-ethyl-propyl exhibited conformations with variable degree of distortion. Together with comparative structures from the literature, this study provides experimental evidence that considerable conformational flexibility exists for meso-alkylporphyrins with substituents less bulky than tert-butyl groups.

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Dluhy, R. A., D. Moffatt, D. G. Cameron, R. Mendelsohn, and H. H. Mantsch. "Characterization of cooperative conformational transitions by Fourier transform infrared spectroscopy: application to phospholipid binary mixtures." Canadian Journal of Chemistry 63, no. 7 (July 1, 1985): 1925–32. http://dx.doi.org/10.1139/v85-319.

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Temperature-induced cooperative conformational transitions in biopolymers may be examined in aqueous solution by the use of Fourier transform infrared spectroscopy. The transition is described in terms of a two-state model with a fractional population parameter (which describes the degree of transition at various values intermediate between the two limiting cases) that can be generated by a least-squares technique. This procedure allows for calculation of a conformational index without assuming a linear dependence of the infrared parameter on the extent of transition. Calculations based on the Zimm–Bragg theory of cooperative conformational transitions allow thermodynamic quantities to be derived using the conformational index in conjunction with calorimetric measurements.The method is illustrated with data from the gel/liquid-crystalline phase transitions of binary phospholipid vesicles where the use of isotopic substitution allows the conformation of each component of the binary mixture to be independently monitored. The data suggest the coexistence of well-defined structural domains of phospholipid as well as the preferential clustering of one of the lipid components at the interface between the two phases.

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Appendino, G., M. Calleri, G. Chiari, P. Ugliengo, and D. Viterbo. "Conformational characterization of shiromodiol derivatives." Acta Crystallographica Section A Foundations of Crystallography 43, a1 (August 12, 1987): C63. http://dx.doi.org/10.1107/s0108767387083806.

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Takahashi, Ken-ichi, Tosiyuki Noguti, Hironobu Hojo, Tadayasu Ohkubo, and Mitiko G? "Conformational characterization of designed minibarnase." Biopolymers 58, no. 3 (2001): 260–67. http://dx.doi.org/10.1002/1097-0282(200103)58:3<260::aid-bip1003>3.0.co;2-j.

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9

Yuan, Wen, Jessica Bazick, and Joseph Sodroski. "Characterization of the Multiple Conformational States of Free Monomeric and Trimeric Human Immunodeficiency Virus Envelope Glycoproteins after Fixation by Cross-Linker." Journal of Virology 80, no. 14 (July 15, 2006): 6725–37. http://dx.doi.org/10.1128/jvi.00118-06.

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ABSTRACT The human immunodeficiency virus type 1 (HIV-1) gp120 exterior and gp41 transmembrane envelope glycoproteins assemble into trimers on the virus surface that represent potential targets for antibodies. Potent neutralizing antibodies bind the monomeric gp120 glycoprotein with small changes in entropy, whereas unusually large decreases in entropy accompany gp120 binding by soluble CD4 and less potent neutralizing antibodies. The high degree of conformational flexibility in the free gp120 molecule implied by these observations has been suggested to contribute to masking the trimer from antibodies that recognize the gp120 receptor-binding regions. Here we use cross-linking and recognition by antibodies to investigate the conformational states of gp120 monomers and soluble and cell surface forms of the trimeric HIV-1 envelope glycoproteins. The fraction of monomeric and trimeric envelope glycoproteins able to be recognized after fixation was inversely related to the entropic changes associated with ligand binding. In addition, fixation apparently limited the access of antibodies to the V3 loop and gp41-interactive surface of gp120 only in the context of trimeric envelope glycoproteins. The results support a model in which the unliganded monomeric and trimeric HIV-1 envelope glycoproteins sample several different conformations. Depletion of particular fixed conformations by antibodies allowed characterization of the relationships among the conformational states. Potent neutralizing antibodies recognize the greatest number of conformations and therefore can bind the virion envelope glycoproteins more rapidly and completely than weakly neutralizing antibodies. Thus, the conformational flexibility of the HIV-1 envelope glycoproteins creates thermodynamic and kinetic barriers to neutralization by antibodies directed against the receptor-binding regions of gp120.

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Polêto, Marcelo D., Bruno I. Grisci, Marcio Dorn, and Hugo Verli. "ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories." Bioinformatics 36, no. 11 (February 27, 2020): 3576–77. http://dx.doi.org/10.1093/bioinformatics/btaa130.

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Abstract Motivation The conformational space of small molecules can be vast and difficult to assess. Molecular dynamics (MD) simulations of free ligands in solution have been applied to predict conformational populations, but their characterization is often based on clustering algorithms or manual efforts. Results Here, we introduce ConfID, an analytical tool for conformational characterization of small molecules using MD trajectories. The evolution of conformational sampling and population frequencies throughout trajectories is calculated to check for sampling convergence while allowing to map relevant conformational transitions. The tool is designed to track conformational transition events and calculate time-dependent properties for each conformational population detected. Availability and implementation Toolkit and documentation are freely available at http://sbcb.inf.ufrgs.br/confid Contact marcelo.poleto@ufv.br or bigrisci@inf.ufrgs.br Supplementary information Supplementary data are available at Bioinformatics online.

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Mountassif, Driss, Lucien Fabre, Kaustuv Basu, Mihnea Bostina, Slavica Jonic, and Isabelle Rouiller. "Conformational heterogeneity of the AAA ATPase p97 characterized by single particle cryo-EM." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C853. http://dx.doi.org/10.1107/s2053273314091463.

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p97, a member of the AAA (ATPase Associated with various Activities) ATPase family, is essential and centrally involved in a wide variety of cellular processes. Single amino-acid substitutions in p97 have been associated with the severe degenerative disorder of Inclusion Body Myopathy associated with Paget disease of bone and Frontotemporal Dementia (IBMPFD) as well as amytropic leteral sclerosis (ALS). Current models propose that p97 acts as a motor transmitting the energy from the ATPase cycle to conformational changes of substrate protein complexes causing segregation, remodeling or translocation. Mutations at the interface between the N and the D1 domains impact the ATPase activity and the conformation of D2 on the opposite side of the protein complex, suggesting intermolecular communication. Because of limited structural information, the molecular mechanisms on how p97 drives its activities and the molecular basis for transmission of information within the molecule remain elusive. Structural heterogeneity is observed in vitro and is likely relevant for the in vivo biological function of p97. Single particle cryo-EM is the method of choice to study a flexible complex. The technique allows study in solution and also deals with sample heterogeneity by image classification. We have set-up the characterization of the conformational heterogeneity in WT and disease relevant p97 mutant using multi-likelihood classification and Hybrid Electron Microscopy Normal Mode Analysis HEMNMA. The multi-likelihood analysis shows a link between the conformations of the N and D2 domains. HEMNMA allows the analysis of the asymmetry of the conformational changes. Together these studies describe the structural flexibility of p97 and the coupling of the ATPase activity with conformational changes in health and in disease. Study of this model system also allows the development of new methods to understand the conformational heterogeneity of other protein complexes.

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Saxena, Sarika, Satoru Nagatoishi, Daisuke Miyoshi, and Naoki Sugimoto. "Structural and Functional Characterization of RecG Helicase under Dilute and Molecular Crowding Conditions." Journal of Nucleic Acids 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/392039.

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In an ATP-dependent reaction, theEscherichia coliRecG helicase unwinds DNA junctionsin vitro. We present evidence of a unique protein conformational change in the RecG helicase from anα-helix to aβ-strand upon an ATP binding under dilute conditions using circular dichroism (CD) spectroscopy. In contrast, under molecular crowding conditions, theα-helical conformation was stable even upon an ATP binding. These distinct conformational behaviors were observed to be independent of Na+and Mg2+. Interestingly, CD measurements demonstrated that the spectra of a frayed duplex decreased with increasing of the RecG concentration both under dilute and molecular crowding conditions in the presence of ATP, suggesting that RecG unwound the frayed duplex. Our findings raise the possibility that theα-helix andβ-strand forms of RecG are a preactive and an active structure with the helicase activity, respectively.

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Tucker, David F., Jonathan T. Sullivan, Kimberly-Anne Mattia, Christine R. Fisher, Trevor Barnes, Manu N. Mabila, Rona Wilf, et al. "Isolation of state-dependent monoclonal antibodies against the 12-transmembrane domain glucose transporter 4 using virus-like particles." Proceedings of the National Academy of Sciences 115, no. 22 (May 16, 2018): E4990—E4999. http://dx.doi.org/10.1073/pnas.1716788115.

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The insulin-responsive 12-transmembrane transporter GLUT4 changes conformation between an inward-open state and an outward-open state to actively facilitate cellular glucose uptake. Because of the difficulties of generating conformational mAbs against complex and highly conserved membrane proteins, no reliable tools exist to measure GLUT4 at the cell surface, follow its trafficking, or detect the conformational state of the protein. Here we report the isolation and characterization of conformational mAbs that recognize the extracellular and intracellular domains of GLUT4, including mAbs that are specific for the inward-open and outward-open states of GLUT4. mAbs against GLUT4 were generated using virus-like particles to present this complex membrane protein in its native conformation and using a divergent host species (chicken) for immunization to overcome immune tolerance. As a result, the isolated mAbs recognize conformational epitopes on native GLUT4 in cells, with apparent affinities as high as 1 pM and with specificity for GLUT4 across the human membrane proteome. Epitope mapping using shotgun mutagenesis alanine scanning across the 509 amino acids of GLUT4 identified the binding epitopes for mAbs specific for the states of GLUT4 and allowed the comprehensive identification of the residues that functionally control the GLUT4 inward-open and outward-open states. The mAbs identified here will be valuable molecular tools for monitoring GLUT4 structure, function, and trafficking, for differentiating GLUT4 conformational states, and for the development of novel therapeutics for the treatment of diabetes.

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Shehu, Amarda, Lydia E. Kavraki, and Cecilia Clementi. "Multiscale characterization of protein conformational ensembles." Proteins: Structure, Function, and Bioinformatics 76, no. 4 (September 2009): 837–51. http://dx.doi.org/10.1002/prot.22390.

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Qu, Kun, Qiuluan Chen, Katarzyna A. Ciazynska, Banghui Liu, Xixi Zhang, Jingjing Wang, Yujie He, et al. "Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike." PLOS Pathogens 18, no. 7 (July 29, 2022): e1010583. http://dx.doi.org/10.1371/journal.ppat.1010583.

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The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct “S-R/x3” to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked-1 and locked-2 conformations. For the D614G spike, based on which all variants of concern were evolved, only the locked-2 conformation was observed. Analysis of the structures suggests that rigidified domain D in the locked conformations interacts with the hinge to domain C and thereby restrains RBD movement. Structural change in domain D correlates with spike conformational change. We propose that the locked-1 and locked-2 conformations of S are present in the acidic high-lipid cellular compartments during virus assembly and egress. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed or open conformations. The dynamics of this transition can be altered by mutations that modulate domain D structure, as is the case for the D614G mutation, leading to changes in viral fitness. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.

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Qi, Bo, Luran Jiang, Sai An, Wei Chen, and Yu-Fei Song. "Detecting the Subtle Photo-Responsive Conformational Bistability of Monomeric Azobenzene Functionalized Keggin Polyoxometalates by Using Ion-Mobility Mass Spectrometry." Molecules 27, no. 12 (June 19, 2022): 3927. http://dx.doi.org/10.3390/molecules27123927.

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Accurately characterizing the conformational variation of novel molecular assemblies is important but often ignored due to limited characterization methods. Herein, we reported the use of ion-mobility mass spectrometry (IMS/MS) to investigate the conformational changes of four azobenzene covalently functionalized Keggin hybrids (azo-Keggins, compounds 1–4). The as-prepared azo-Keggins showed the general molecular formula of [C16H36N]4[SiW11O40(Si(CH2)3NH–CO(CH2)nO–C6H4N=NC6H4–R)2] (R = H, n = 0 (1); R = NO2, n = 0 (2); R = H, n = 5 (3); R = H, n = 10 (4)). The resultant azo-Keggins maintained stable monomeric states in the gas phase with intact molecular structures. Furthermore, the subtle photo-responsive trans-cis conformational variations of azo-Keggins were clearly revealed by the molecular shape-related collision cross-section value difference ranging from 2.44 Å2 to 6.91 Å2. The longer the alkyl chains linkers were, the larger the conformational variation was. Moreover, for compounds 1 and 2, higher stability in trans-conformation can be observed, while for compounds 3 and 4, bistability can be achieved for both of them.

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Campos-Escamilla, Camila, Dritan Siliqi, Luis A. Gonzalez-Ramirez, Carmen Lopez-Sanchez, Jose Antonio Gavira, and Abel Moreno. "X-ray Characterization of Conformational Changes of Human Apo- and Holo-Transferrin." International Journal of Molecular Sciences 22, no. 24 (December 13, 2021): 13392. http://dx.doi.org/10.3390/ijms222413392.

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Human serum transferrin (Tf) is a bilobed glycoprotein whose function is to transport iron through receptor-mediated endocytosis. The mechanism for iron release is pH-dependent and involves conformational changes in the protein, thus making it an attractive system for possible biomedical applications. In this contribution, two powerful X-ray techniques, namely Macromolecular X-ray Crystallography (MX) and Small Angle X-ray Scattering (SAXS), were used to study the conformational changes of iron-free (apo) and iron-loaded (holo) transferrin in crystal and solution states, respectively, at three different pH values of physiological relevance. A crystallographic model of glycosylated apo-Tf was obtained at 3.0 Å resolution, which did not resolve further despite many efforts to improve crystal quality. In the solution, apo-Tf remained mostly globular in all the pH conditions tested; however, the co-existence of closed, partially open, and open conformations was observed for holo-Tf, which showed a more elongated and flexible shape overall.

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Jablonski, Chet R., and Zhongxin Zhou. "Synthesis, multinuclear NMR, and solution conformation of (η5-indenyl)CoIRfL complexes (L = CO, P-donor)." Canadian Journal of Chemistry 70, no. 10 (October 1, 1992): 2544–51. http://dx.doi.org/10.1139/v92-322.

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The preparation, spectroscopic characterization, and conformational analysis of a series of Co(III) indenyl complexes, (C9H7)CoIRfL (Rf = C3F7, C6F13, L = CO, P-donor), 2–8, are described. I3C and 1H NMR parameters are consistent with a slightly distorted -η5-C9H7 coordination. 1H nuclear Overhauser effect difference (nOed) spectra indicate a preferred solution conformation in which the perfluoroalkyl group is trans to the C3a—C7a ring junction.

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Watanabe, Tokio, Hirokazu Yagi, Saeko Yanaka, Takumi Yamaguchi, and Koichi Kato. "Comprehensive characterization of oligosaccharide conformational ensembles with conformer classification by free-energy landscape via reproductive kernel Hilbert space." Physical Chemistry Chemical Physics 23, no. 16 (2021): 9753–60. http://dx.doi.org/10.1039/d0cp06448c.

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Násztor, Zoltán, János Horváth, and Balázs Leitgeb. "In Silico Conformational Analysis of the Short-Sequence Hypomurocin A Peptides." International Journal of Peptides 2015 (January 28, 2015): 1–6. http://dx.doi.org/10.1155/2015/281065.

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In this theoretical study, a conformational analysis was performed on short-sequence hypomurocin A peptides, in order to identify their characteristic structural properties. For each hypomurocin A molecule, not only the backbone conformations, but also the side-chain conformations were examined. The results indicated that certain tetrapeptide units could be characterized by types I and III β-turn structures, and considering the helical conformations, it could be concluded that the hypomurocin A peptides showed a preference for the 310-helical structure over the α-helical structure. Beside the backbone conformations, the side-chain conformations were investigated, and the preferred rotamer states of the side-chains of amino acids were determined. Furthermore, the occurrence of i←i+3 and i←i+4 intramolecular H-bonds was studied, which could play a role in the structural stabilization of β-turns and helical conformations. On the whole, our theoretical study supplied a comprehensive characterization of the three-dimensional structure of short-sequence hypomurocin A peptides.

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Xie, Tao, Tamjeed Saleh, Paolo Rossi, and Charalampos G. Kalodimos. "Conformational states dynamically populated by a kinase determine its function." Science 370, no. 6513 (October 1, 2020): eabc2754. http://dx.doi.org/10.1126/science.abc2754.

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Protein kinases intrinsically sample a number of conformational states with distinct catalytic and binding activities. We used nuclear magnetic resonance spectroscopy to describe in atomic-level detail how Abl kinase interconverts between an active and two discrete inactive structures. Extensive differences in key structural elements between the conformational states give rise to multiple intrinsic regulatory mechanisms. The findings explain how oncogenic mutants can counteract inhibitory mechanisms to constitutively activate the kinase. Energetic dissection revealed the contributions of the activation loop, the Asp-Phe-Gly (DFG) motif, the regulatory spine, and the gatekeeper residue to kinase regulation. Characterization of the transient conformation to which the drug imatinib binds enabled the elucidation of drug-resistance mechanisms. Structural insight into inactive states highlights how they can be leveraged for the design of selective inhibitors.

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Paiz, Elisia A., Karen A. Lewis, and Steven T. Whitten. "Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins." Molecules 26, no. 3 (January 26, 2021): 634. http://dx.doi.org/10.3390/molecules26030634.

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The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained.

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OLSON, BRIAN, KEVIN MOLLOY, S. FARID HENDI, and AMARDA SHEHU. "GUIDING PROBABILISTIC SEARCH OF THE PROTEIN CONFORMATIONAL SPACE WITH STRUCTURAL PROFILES." Journal of Bioinformatics and Computational Biology 10, no. 03 (June 2012): 1242005. http://dx.doi.org/10.1142/s021972001242005x.

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The roughness of the protein energy surface poses a significant challenge to search algorithms that seek to obtain a structural characterization of the native state. Recent research seeks to bias search toward near-native conformations through one-dimensional structural profiles of the protein native state. Here we investigate the effectiveness of such profiles in a structure prediction setting for proteins of various sizes and folds. We pursue two directions. We first investigate the contribution of structural profiles in comparison to or in conjunction with physics-based energy functions in providing an effective energy bias. We conduct this investigation in the context of Metropolis Monte Carlo with fragment-based assembly. Second, we explore the effectiveness of structural profiles in providing projection coordinates through which to organize the conformational space. We do so in the context of a robotics-inspired search framework proposed in our lab that employs projections of the conformational space to guide search. Our findings indicate that structural profiles are most effective in obtaining physically realistic near-native conformations when employed in conjunction with physics-based energy functions. Our findings also show that these profiles are very effective when employed instead as projection coordinates to guide probabilistic search toward undersampled regions of the conformational space.

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SU, XIAODI. "SURFACE PLASMON RESONANCE SPECTROSCOPY AND QUARTZ CRYSTAL MICROBALANCE STUDY OF PROTEIN-DNA INTERACTIONS IN HORMONE RECEPTOR BIOLOGY." COSMOS 05, no. 01 (May 2009): 79–95. http://dx.doi.org/10.1142/s0219607709000415.

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Surface plasmon resonance (SPR) spectroscopy and quartz crystal microbalance (QCM) are surface sensitive analytical techniques capable of real-time monitoring of biomolecular interactions. In this article we review our past work on the use of these two techniques for studying protein–DNA interactions, exemplified with estrogen receptors (ER) and their response elements (ERE). Various assay schemes have been developed for a comprehensive characterization of ER–ERE interactions in terms of sequence specificity, binding affinity, stoichiometry, ligand effects on binding dynamics and conformational changes in the proteins and DNA. These are all important characteristics underlining the mechanism of ER-mediated gene transcription. With these studies we have made the following demonstrations to describe the advantages of these two techniques, namely (i) SPR technique is superior and more versatile than conventional (electrophoretic mobility shift assay) EMSA for studying protein-DNA interactions; (ii) QCM is an alternative tool for studying conformational changes in protein–DNA complexes and (iii) combinational SPR and QCM analysis provides additional characterization of biomolecular films, e.g. film thickness, water content, and conformation rigidity etc.

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Villain-Simonnet, Agnès, Michel Milas, and Marguerite Rinaudo. "A new bacterial polysaccharide (YAS34). I. Characterization of the conformations and conformational transition." International Journal of Biological Macromolecules 27, no. 1 (March 2000): 65–75. http://dx.doi.org/10.1016/s0141-8130(99)00120-8.

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Lima, Igor, Ambuja Navalkar, Samir K. Maji, Jerson L. Silva, Guilherme A. P. de Oliveira, and Elio A. Cino. "Biophysical characterization of p53 core domain aggregates." Biochemical Journal 477, no. 1 (January 8, 2020): 111–20. http://dx.doi.org/10.1042/bcj20190778.

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Aggregation is the cause of numerous protein conformation diseases. A common facet of these maladies is the transition of a protein from its functional native state into higher order forms, such as oligomers and amyloid fibrils. p53 is an essential tumor suppressor that is prone to such conformational transitions, resulting in its compromised ability to avert cancer. This work explores the biophysical properties of early-, mid-, and late-stage p53 core domain (p53C) aggregates. Atomistic and coarse-grained molecular dynamics (MD) simulations suggest that early- and mid-stage p53C aggregates have a polymorphic topology of antiparallel and parallel β-sheets that localize to the core amyloidogenic sequence. Both topologies involve similar extents of interstrand mainchain hydrogen bonding, while sidechain interactions could play a role in regulating strand orientation. The free energy difference between the antiparallel and parallel states was within statistical uncertainty. Negative stain electron microscopy of mature fibrils shows a wide distribution of fiber widths, indicating that polymorphism may extend to the quaternary structure level. Circular dichroism of the fibrils was indicative of β-sheet rich structures in atypical conformations. The Raman spectrum of aggregated p53C was consistent with a mixture of arranged β-sheets and heterogeneous structural elements, which is compatible with the MD findings of an ordered β-sheet nucleus flanked by disordered structure. Structural polymorphism is a common property of amyloids; however, because certain polymorphs of the same protein can be more harmful than others, going forward it will be pertinent to establish correlations between p53C aggregate structure and pathology.

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Sui, Ming-Yue, Yun Geng, Guang-Yan Sun, and Jian-Ping Wang. "Construction of a 9,9′-bifluorenylidene-based small molecule acceptor materials by screening conformation, steric configuration and repeating unit number: a theoretical design and characterization." J. Mater. Chem. C 5, no. 39 (2017): 10343–52. http://dx.doi.org/10.1039/c7tc03496b.

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The effects of molecular conformations, steric configurations and repeat units on the 99BF-based on photovoltaic properties were designed and compared at the molecular level. As a result, thep-conformational linear of the 4-unit molecule may be a high-performance 99′BF derivative.

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Houde, Damian, Joseph Arndt, Wayne Domeier, Steven Berkowitz, and John R. Engen. "Characterization of IgG1 Conformation and Conformational Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry." Analytical Chemistry 81, no. 7 (April 2009): 2644–51. http://dx.doi.org/10.1021/ac802575y.

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Houde, Damian, Joseph Arndt, Wayne Domeier, Steven Berkowitz, and John R. Engen. "Characterization of IgG1 Conformation and Conformational Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry." Analytical Chemistry 81, no. 14 (July 15, 2009): 5966. http://dx.doi.org/10.1021/ac9009287.

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Price, Nicholas C. "Conformational issues in the characterization of proteins." Biotechnology and Applied Biochemistry 31, no. 1 (February 1, 2000): 29. http://dx.doi.org/10.1042/ba19990102.

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Kamenik, Anna S., Uta Lessel, Julian E. Fuchs, Thomas Fox, and Klaus R. Liedl. "Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization." Journal of Chemical Information and Modeling 58, no. 5 (April 13, 2018): 982–92. http://dx.doi.org/10.1021/acs.jcim.8b00097.

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da Silva, J. E. Pereira, S. I. Córdoba de Torresi, D. L. A. de Faria, and M. L. A. Temperini. "Raman characterization of polyaniline induced conformational changes." Synthetic Metals 101, no. 1-3 (May 1999): 834–35. http://dx.doi.org/10.1016/s0379-6779(98)01300-9.

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Bingle, Wade H., James L. Doran, and William J. Page. "Characterization of the surface layer protein from Azotobacter vinelandii." Canadian Journal of Microbiology 32, no. 2 (February 1, 1986): 112–20. http://dx.doi.org/10.1139/m86-023.

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The regular surface array protein (S protein) of Azotobacter vinelandii was extracted from outer membrane fragments with distilled water and further purified by gel filtration chromatography. The protein was shown to behave anomalously on sodium dodecyl sulfate polyacrylamide gels producing a number of conformational isomers. The amino acid composition of S protein was similar to that of other surface array proteins, particularly in its lack of cysteine. The theoretical monomelic molecular weight of S protein was calculated to be 60 218 based on the total amino acid composition and the apparent molecular weight determined by sodium dodecyl sulfate – polyacrylamide gel electrophoresis. Circular dichroism spectra indicated that S protein was composed of approximately 35% β sheet structure, negligible α helix, with the remainder of the polypeptide backbone aperiodic in nature. The effect of the divalent cations Ca2+ and Mg2+ on the conformation of S protein was examined by circular dichroism spectroscopy; however, no conformational change was detected in response to the presence of these species nor did S-protein monomer aggregate into multimers in the presence of these cations. Purified S-protein monomer was inactive in divalent cation mediated reassembly of the S layer onto the surface of distilled water washed cells. A larger multimeric form present only in fresh preparations appeared to be the active species involved in in vitro reassembly of the A. vinelandii surface array.

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Palermo, Giulia, Yinglong Miao, Ross C. Walker, Martin Jinek, and J. Andrew McCammon. "CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations." Proceedings of the National Academy of Sciences 114, no. 28 (June 26, 2017): 7260–65. http://dx.doi.org/10.1073/pnas.1707645114.

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CRISPR-Cas9 has become a facile genome editing technology, yet the structural and mechanistic features underlying its function are unclear. Here, we perform extensive molecular simulations in an enhanced sampling regime, using a Gaussian-accelerated molecular dynamics (GaMD) methodology, which probes displacements over hundreds of microseconds to milliseconds, to reveal the conformational dynamics of the endonuclease Cas9 during its activation toward catalysis. We disclose the conformational transition of Cas9 from its apo form to the RNA-bound form, suggesting a mechanism for RNA recruitment in which the domain relocations cause the formation of a positively charged cavity for nucleic acid binding. GaMD also reveals the conformation of a catalytically competent Cas9, which is prone for catalysis and whose experimental characterization is still limited. We show that, upon DNA binding, the conformational dynamics of the HNH domain triggers the formation of the active state, explaining how the HNH domain exerts a conformational control domain over DNA cleavage [Sternberg SH et al. (2015) Nature, 527, 110–113]. These results provide atomic-level information on the molecular mechanism of CRISPR-Cas9 that will inspire future experimental investigations aimed at fully clarifying the biophysics of this unique genome editing machinery and at developing new tools for nucleic acid manipulation based on CRISPR-Cas9.

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Gao, Rong, Aindrila Mukhopadhyay, Fang Fang, and David G. Lynn. "Constitutive Activation of Two-Component Response Regulators: Characterization of VirG Activation in Agrobacterium tumefaciens." Journal of Bacteriology 188, no. 14 (July 15, 2006): 5204–11. http://dx.doi.org/10.1128/jb.00387-06.

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ABSTRACT Response regulators are the ultimate modulators in two-component signal transduction pathways. The N-terminal receiver domains generally accept phosphates from cognate histidine kinases to control output. VirG for example, the response regulator of the VirA/VirG two-component system in Agrobacterium tumefaciens, mediates the expression of virulence genes in response to plant host signals. Response regulators have a highly conserved structure and share a similar conformational activation upon phosphorylation, yet the sequence and structural features that determine or perturb the cooperative activation events are ill defined. Here we use VirG and the unique features of the Agrobacterium system to extend our understanding of the response regulator activation. Two previously isolated constitutive VirG mutants, VirGN54D and VirGI77V/D52E, provide the foundation for our studies. In vivo phosphorylation patterns establish that VirGN54D is able to accumulate phosphates from small-molecule phosphate donors, such as acetyl phosphate, while the VirGI77V/D52E allele carries conformational changes mimicking the active conformation. Further structural alterations on these two alleles begin to reveal the changes necessary for response regulator activation.

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Chen, Kun-Lin, Deng Li, Ting-Xuan Lu, and Shu-Wei Chang. "Structural Characterization of the CD44 Stem Region for Standard and Cancer-Associated Isoforms." International Journal of Molecular Sciences 21, no. 1 (January 3, 2020): 336. http://dx.doi.org/10.3390/ijms21010336.

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CD44 is widely expressed in most vertebrate cells, whereas the expression of CD44v6 is restricted to only a few tissues and has been considered to be associated with tumor progression and metastasis. Thus, CD44v6 has been recognized as a promising prognostic biomarker and therapeutic target for various cancers for more than a decade. However, despite many experimental studies, the structural dynamics and differences between CD44s and CD44v6, particularly in their stem region, still remain elusive. Here, a computational study was conducted to address these problems. We found that the stem of CD44s adopted predominantly two conformations, one featuring antiparallel β-sheets and the other featuring parallel β-sheets, whereas the stem of CD44v6 adopted mainly one conformation with relatively highly suppressed β-sheet contents. Moreover, Phe215 was found to be essential in the β-sheets of both CD44s and CD44v6. We finally found intramolecular Phe215–Trp224 hydrogen-bonding interactions and hydrophobic interactions with Phe215 that cooperatively drove conformational differences upon the addition of the v6 region to CD44. Our study elucidated the structural differences between the stem regions of CD44s and CD44v6 and thus can offer useful structural information for drug design to specifically target CD44v6 in promising clinical applications.

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Angulo-Cornejo, Jorge R., Ketty Ayala-León, Gabriel García Herbosa, José V. Cuevas, Virginia Diez, Rainer Richter, Lothar Hennig, and Lothar Beyer. "Synthesis and Structural Characterization of N-[4-(2-Hydroxyethyl)-1,2,4-oxathiazinan-3-ylidene]-benzamide and its Mercury(II) Chloride Adduct." Zeitschrift für Naturforschung B 60, no. 9 (September 1, 2005): 945–50. http://dx.doi.org/10.1515/znb-2005-0906.

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The synthesis of N-[4-(2-hydroxyethyl)-1,2,4-oxathiazinan-3-ylidene]-benzamide (2a) and N-[4- (2-hydroxyethyl)-1,2,4-oxathiazinan-3-ylidene]-2-fluorobenzamide (2b) by oxidation of the corresponding 1,1-bis(2-hydroxyethyl)-3-aroylthioureas with potassium iodate in aqueous solution is reported. Variable temperature 1H NMR spectra of 2a prove that the heterocyclic 1,2,4-(O, S,N) sixmembered ring is involved in a dynamic chair-boat conformational interconversion. Molecular mechanic calculations show that the chair conformation is more stable than the boat conformation by 3.0 kcal/mol. The synthesis of the adduct [(2a)·0.5 HgCl2] 3 as well as the X-ray structural characterization of 2a and 3 are also reported.

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38

Pinto, B. Mario, Blair D. Johnston, Raymond J. Batchelor, Frederick W. B. Einstein, and Ian D. Gay. "Selenium coronands. A novel conformational pair." Canadian Journal of Chemistry 66, no. 11 (November 1, 1988): 2956–58. http://dx.doi.org/10.1139/v88-457.

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The synthesis and characterization of the novel selenium coronands, 1,3,7,9-tetraselenacyclododecane 1a, 1,3,7,9,13,15-hexaselenacyclooctadecane 2a, the corresponding β-gem-dimethyl derivatives 1b, 2b, and 1,5,9,13-tetraselenacyclohexadecane 3, and 1,5,9,13,17,21-hexaselenacyclotetracosane 4 are described. X-ray crystallographic analysis of 1a reveals three independent molecules that exist in two distinct conformations, one molecule having approximate two-fold symmetry together with two molecules (of similar conformation) each having crystallographic [Formula: see text] symmetry. The conformations are denoted as [3333] or [66]. Whereas one resembles that of cyclododecane and tetrathia-12-crown-4 with respect to torsion angles, the other resembles that of tetraoxa-12-crown-4. The solid state CP-MAS 77Se and 13C nmr spectra are interpreted in light of the crystallographic information. Crystal structure: formula Se4C8H16; fw = 428.05; monoclinic, P21/c; Z = 8; a = 15.823(2) Å, b = 5.534(1) Å, c = 27.962(5) Å, β = 92.26(1)°; V = 2446.6 Å3; T = 200 K; R = 0.027 for 2162 observed data (I ≥ 2.5σ(I)).

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Signorelli, Sara, Salvatore Cannistraro, and Anna Rita Bizzarri. "Structural Characterization of the Intrinsically Disordered Protein p53 Using Raman Spectroscopy." Applied Spectroscopy 71, no. 5 (June 23, 2016): 823–32. http://dx.doi.org/10.1177/0003702816651891.

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The intrinsically disordered protein p53 has attracted a strong interest for its important role in genome safeguarding and potential therapeutic applications. However, its disordered character makes difficult a full characterization of p53 structural architecture. A deep knowledge of p53 structural motifs could significantly help the understanding of its functional properties, in connection with its complex binding network. We have applied Raman spectroscopy to investigate the structural composition and the conformational heterogeneity of both full-length p53 and its DNA binding domain (DBD), in different solvent environments. In particular, a careful analysis of the Amide I Raman band, which is highly sensitive to protein secondary structure elements such as α-helices, β-sheets and random coils, has revealed the presence of extended random coils in p53 and predominant β-sheet regions in its DBD. In addition, this analysis has allowed us to explore the ensemble of interchanging conformations in both p53 and its DBD, highlighting a higher conformational heterogeneity in p53 than in its DBD. Furthermore, by applying a principal components analysis, we have identified the principal spectral markers in both p53 and DBD samples. The combination of the two approaches could be insightful for the study of intrinsically disordered proteins, by offering increased versatility and wide application as a label-free, real-time and non-invasive detection method.

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40

Yazdani-Pedram, M., L. Gargallo, and D. Radić. "Polymer conformation and viscometric behaviour—4. Characterization and conformational studies for poly(dibenzyl itaconate)." European Polymer Journal 21, no. 5 (January 1985): 461–65. http://dx.doi.org/10.1016/0014-3057(85)90125-9.

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41

Abou Assi, Hala, Atul K. Rangadurai, Honglue Shi, Bei Liu, Mary C. Clay, Kevin Erharter, Christoph Kreutz, Christopher L. Holley, and Hashim M. Al-Hashimi. "2′-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states." Nucleic Acids Research 48, no. 21 (October 26, 2020): 12365–79. http://dx.doi.org/10.1093/nar/gkaa928.

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Abstract 2′-O-Methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3′-endo conformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of flexible RNAs containing bulges and internal loops. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotides are paired, increasing both the abundance and lifetime of low-populated short-lived excited states by up to 10-fold. The extent of stabilization increased with number of Nm modifications and was also dependent on Mg2+. Through phi-value analysis, the Nm modification also provided rare insights into the structure of the transition state for conformational exchange. Our results suggest that Nm could alter the biological activities of Nm-modified RNAs by modulating their secondary structural ensembles as well as establish the utility of Nm as a tool for the discovery and characterization of RNA excited state conformations.

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Moreau, Vitor Hugo, Alex W. M. Rietveld, and Sergio T. Ferreira. "Persistent Conformational Heterogeneity of Triosephosphate Isomerase: Separation and Characterization of Conformational Isomers in Solution†." Biochemistry 42, no. 50 (December 2003): 14831–37. http://dx.doi.org/10.1021/bi0343572.

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Asakura, Tetsuo, Masanori Endo, Rina Fukuhara, and Yugo Tasei. "13C NMR characterization of hydrated 13C labeled Bombyx mori silk fibroin sponges prepared using glycerin, poly(ethylene glycol diglycidyl ether) and poly(ethylene glycol) as porogens." Journal of Materials Chemistry B 5, no. 11 (2017): 2152–60. http://dx.doi.org/10.1039/c7tb00323d.

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Alekperov, Dzhamil, Tomohiro Shirosaki, Toshihiko Sakurai, Galina Popova, Vyacheslav Kireev, and Hirotaka Ihara. "Synthesis and Conformational Characterization of Oligopeptide–Cyclotriphosphazene Hybrids." Polymer Journal 35, no. 5 (May 2003): 417–21. http://dx.doi.org/10.1295/polymj.35.417.

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45

Chemes, Doly M., Diego J. Alonso de Armiño, Edgardo H. Cutin, and Norma L. Robles. "Conformational properties and spectroscopic characterization of m-chlorosulfinylaniline." Journal of Molecular Structure 1132 (March 2017): 88–94. http://dx.doi.org/10.1016/j.molstruc.2016.11.024.

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46

Czarnota, Gregory J. "Conformational characterization of nucleosome structure by Electron Microscopy." Proceedings, annual meeting, Electron Microscopy Society of America 51 (August 1, 1993): 194–95. http://dx.doi.org/10.1017/s0424820100146813.

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Chromatin structure at the fundamental level of the nucleosome is important in vital cellular processes. Recent biochemical and genetic analyses show that nucleosome structure and structural changes are very active participants in gene expression, facilitating or inhibiting transcription and reflecting the physiological state of the cell. Structural states and transitions for this macromolecular complex, composed of DNA wound about a heterotypic octamer of variously modified histone proteins, have been measured by physico-chemical techniques and by enzyme-accessibility and are recognized to occur with various post-translational modifications, gene activation, transformation and with ionic-environment. In spite of studies which indicate various forms of nucleosome structure, all current x-ray and neutron diffraction studies have consistently resulted in only one structure, suggestive of a static conformation. In contrast, two-dimensional electron microscopy studies and three-dimensional reconstruction techniques have yielded different structures. These fundamental differences between EM and other ultrastructural studies have created a long standing quandary, which I have addressed and resolved using spectroscopic electron microscopy and statistical analyses of nucleosome images in a study of nucleosome structure with ionic environment.

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47

Martin, M. M., P. Plaza, and Y. H. Meyer. "Ultrafast conformational relaxation of triphenylmethane dyes: spectral characterization." Journal of Physical Chemistry 95, no. 23 (November 1991): 9310–14. http://dx.doi.org/10.1021/j100176a051.

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Oellerich, Silke, Hainer Wackerbarth, and Peter Hildebrandt. "Spectroscopic Characterization of Nonnative Conformational States of Cytochromec." Journal of Physical Chemistry B 106, no. 25 (June 2002): 6566–80. http://dx.doi.org/10.1021/jp013841g.

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49

Mathew, Sanyo M., and C. Scott Hartley. "Parento-Phenylene Oligomers: Synthesis, Conformational Behavior, and Characterization." Macromolecules 44, no. 21 (November 8, 2011): 8425–32. http://dx.doi.org/10.1021/ma201866p.

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50

Harper, J. Wade, and Bert L. Vallee. "Conformational characterization of human angiogenin by limited proteolysis." Journal of Protein Chemistry 7, no. 4 (August 1988): 355–63. http://dx.doi.org/10.1007/bf01024885.

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Journal articles on the topic 'Conformational characterization'

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