Academic literature on the topic 'Residue conservation; Protein folding'
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Journal articles on the topic "Residue conservation; Protein folding"
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de Haard, H. J., B. Kazemier, A. van der Bent, P. Oudshoorn, P. Boender, B. van Gemen, J. W. Arends, and H. R. Hoogenboom. "Absolute conservation of residue 6 of immunoglobulin heavy chain variable regions of class IIA is required for correct folding." Protein Engineering Design and Selection 11, no. 12 (December 1, 1998): 1267–76. http://dx.doi.org/10.1093/protein/11.12.1267.
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Liu, Xinsheng, Jing Li, Wanlin Guo, and Wei Wang. "A new method for quantifying residue conservation and its applications to the protein folding nucleus." Biochemical and Biophysical Research Communications 351, no. 4 (December 2006): 1031–36. http://dx.doi.org/10.1016/j.bbrc.2006.10.157.
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Sergel, Theresa A., Lori W. McGinnes, and Trudy G. Morrison. "Mutations in the Fusion Peptide and Adjacent Heptad Repeat Inhibit Folding or Activity of the Newcastle Disease Virus Fusion Protein." Journal of Virology 75, no. 17 (September 1, 2001): 7934–43. http://dx.doi.org/10.1128/jvi.75.17.7934-7943.2001.
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ABSTRACT Paramyxovirus fusion proteins have two heptad repeat domains, HR1 and HR2, which have been implicated in the fusion activity of the protein. Peptides with sequences from these two domains form a six-stranded coiled coil, with the HR1 sequences forming a central trimer (K. A. Baker, R. E. Dutch, R. A. Lamb, and T. S. Jardetzky, Mol. Cell 3:309–319, 1999; X. Zhao, M. Singh, V. N. Malashkevich, and P. S. Kim, Proc. Natl. Acad. Sci. USA 97:14172–14177, 2000). We have extended our previous mutational analysis of the HR1 domain of the Newcastle disease virus fusion protein, focusing on the role of the amino acids forming the hydrophobic core of the trimer, amino acids in the “a” and “d” positions of the helix from amino acids 123 to 182. Both conservative and nonconservative point mutations were characterized for their effects on synthesis, stability, proteolytic cleavage, and surface expression. Mutant proteins expressed on the cell surface were characterized for fusion activity by measuring syncytium formation, content mixing, and lipid mixing. We found that all mutations in the “a” position interfered with proteolytic cleavage and surface expression of the protein, implicating the HR1 domain in the folding of the F protein. However, mutation of five of seven “d” position residues had little or no effect on surface expression but, with one exception at residue 175, did interfere to various extents with the fusion activity of the protein. One of these “d” mutations, at position 154, interfered with proteolytic cleavage, while the rest of the mutants were cleaved normally. That most “d” position residues do affect fusion activity argues that a stable HR1 trimer is required for formation of the six-stranded coiled coil and, therefore, optimal fusion activity. That most of the “d” position mutations do not block folding suggests that formation of the core trimer may not be required for folding of the prefusion form of the protein. We also found that mutations within the fusion peptide, at residue 128, can interfere with folding of the protein, implicating this region in folding of the molecule. No characterized mutation enhanced fusion.
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Toofanny, Rudesh D., Sara Calhoun, Amanda L. Jonsson, and Valerie Daggett. "Shared unfolding pathways of unrelated immunoglobulin-like β-sandwich proteins." Protein Engineering, Design and Selection 32, no. 7 (July 2019): 331–45. http://dx.doi.org/10.1093/protein/gzz040.
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Abstract The Dynameomics project contains native state and unfolding simulations of 807 protein domains, where each domain is representative of a different metafold; these metafolds encompass ~97% of protein fold space. There is a long-standing question in structural biology as to whether proteins in the same fold family share the same folding/unfolding characteristics. Using molecular dynamics simulations from the Dynameomics project, we conducted a detailed study of protein unfolding/folding pathways for 5 protein domains from the immunoglobulin (Ig)-like β-sandwich metafold (the highest ranked metafold in our database). The domains have sequence similarities ranging from 4 to 15% and are all from different SCOP superfamilies, yet they share the same overall Ig-like topology. Despite having very different amino acid sequences, the dominant unfolding pathway is very similar for the 5 proteins, and the secondary structures that are peripheral to the aligned, shared core domain add variability to the unfolding pathway. Aligned residues in the core domain display consensus structure in the transition state primarily through conservation of hydrophobic positions. Commonalities in the obligate folding nucleus indicate that insights into the major events in the folding/unfolding of other domains from this metafold may be obtainable from unfolding simulations of a few representative proteins.
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Michnick, Stephen W., and Eugene Shakhnovich. "A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies." Folding and Design 3, no. 4 (August 1998): 239–51. http://dx.doi.org/10.1016/s1359-0278(98)00035-2.
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Larson, Stefan M., Ingo Ruczinski, Alan R. Davidson, David Baker, and Kevin W. Plaxco. "Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation." Journal of Molecular Biology 316, no. 2 (February 2002): 225–33. http://dx.doi.org/10.1006/jmbi.2001.5344.
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Jain, Rohit, Khaja Muneeruddin, Jeremy Anderson, Michael J. Harms, Scott A. Shaffer, and C. Robert Matthews. "A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family." Proceedings of the National Academy of Sciences 118, no. 17 (April 19, 2021): e2019571118. http://dx.doi.org/10.1073/pnas.2019571118.
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The amino acid sequences of proteins have evolved over billions of years, preserving their structures and functions while responding to evolutionary forces. Are there conserved sequence and structural elements that preserve the protein folding mechanisms? The functionally diverse and ancient (βα)1–8 TIM barrel motif may answer this question. We mapped the complex six-state folding free energy surface of a ∼3.6 billion y old, bacterial indole-3-glycerol phosphate synthase (IGPS) TIM barrel enzyme by equilibrium and kinetic hydrogen–deuterium exchange mass spectrometry (HDX-MS). HDX-MS on the intact protein reported exchange in the native basin and the presence of two thermodynamically distinct on- and off-pathway intermediates in slow but dynamic equilibrium with each other. Proteolysis revealed protection in a small (α1β2) and a large cluster (β5α5β6α6β7) and that these clusters form cores of stability in Ia and Ibp. The strongest protection in both states resides in β4α4 with the highest density of branched aliphatic side chain contacts in the folded structure. Similar correlations were observed previously for an evolutionarily distinct archaeal IGPS, emphasizing a key role for hydrophobicity in stabilizing common high-energy folding intermediates. A bioinformatics analysis of IGPS sequences from the three superkingdoms revealed an exceedingly high hydrophobicity and surprising α-helix propensity for β4, preceded by a highly conserved βα-hairpin clamp that links β3 and β4. The conservation of the folding mechanisms for archaeal and bacterial IGPS proteins reflects the conservation of key elements of sequence and structure that first appeared in the last universal common ancestor of these ancient proteins.
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Cagiada, Matteo, Kristoffer E. Johansson, Audrone Valanciute, Sofie V. Nielsen, Rasmus Hartmann-Petersen, Jun J. Yang, Douglas M. Fowler, Amelie Stein, and Kresten Lindorff-Larsen. "Understanding the Origins of Loss of Protein Function by Analyzing the Effects of Thousands of Variants on Activity and Abundance." Molecular Biology and Evolution 38, no. 8 (March 29, 2021): 3235–46. http://dx.doi.org/10.1093/molbev/msab095.
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Abstract Understanding and predicting how amino acid substitutions affect proteins are keys to our basic understanding of protein function and evolution. Amino acid changes may affect protein function in a number of ways including direct perturbations of activity or indirect effects on protein folding and stability. We have analyzed 6,749 experimentally determined variant effects from multiplexed assays on abundance and activity in two proteins (NUDT15 and PTEN) to quantify these effects and find that a third of the variants cause loss of function, and about half of loss-of-function variants also have low cellular abundance. We analyze the structural and mechanistic origins of loss of function and use the experimental data to find residues important for enzymatic activity. We performed computational analyses of protein stability and evolutionary conservation and show how we may predict positions where variants cause loss of activity or abundance. In this way, our results link thermodynamic stability and evolutionary conservation to experimental studies of different properties of protein fitness landscapes.
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Kagami, Luciano Porto, Gabriele Orlando, Daniele Raimondi, Francois Ancien, Bhawna Dixit, Jose Gavaldá-García, Pathmanaban Ramasamy, Joel Roca-Martínez, Konstantina Tzavella, and Wim Vranken. "b2bTools: online predictions for protein biophysical features and their conservation." Nucleic Acids Research 49, W1 (May 31, 2021): W52—W59. http://dx.doi.org/10.1093/nar/gkab425.
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Abstract We provide integrated protein sequence-based predictions via https://bio2byte.be/b2btools/. The aim of our predictions is to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular dynamics approaches. Upload of a FASTA file or text input of a sequence provides integrated predictions from DynaMine backbone and side-chain dynamics, conformational propensities, and derived EFoldMine early folding, DisoMine disorder, and Agmata β-sheet aggregation. These predictions, several of which were previously not available online, capture ‘emergent’ properties of proteins, i.e. the inherent biophysical propensities encoded in their sequence, rather than context-dependent behaviour (e.g. final folded state). In addition, upload of a multiple sequence alignment (MSA) in a variety of formats enables exploration of the biophysical variation observed in homologous proteins. The associated plots indicate the biophysical limits of functionally relevant protein behaviour, with unusual residues flagged by a Gaussian mixture model analysis. The prediction results are available as JSON or CSV files and directly accessible via an API. Online visualisation is available as interactive plots, with brief explanations and tutorial pages included. The server and API employ an email-free token-based system that can be used to anonymously access previously generated results.
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Malleshappa Gowder, Shambhu, Jhinuk Chatterjee, Tanusree Chaudhuri, and Kusum Paul. "Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of Proteins." Scientific World Journal 2014 (2014): 1–7. http://dx.doi.org/10.1155/2014/971258.
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The analysis of protein structures provides plenty of information about the factors governing the folding and stability of proteins, the preferred amino acids in the protein environment, the location of the residues in the interior/surface of a protein and so forth. In general, hydrophobic residues such as Val, Leu, Ile, Phe, and Met tend to be buried in the interior and polar side chains exposed to solvent. The present work depends on sequence as well as structural information of the protein and aims to understand nature of hydrophobic residues on the protein surfaces. It is based on the nonredundant data set of 218 monomeric proteins. Solvent accessibility of each protein was determined using NACCESS software and then obtained the homologous sequences to understand how well solvent exposed and buried hydrophobic residues are evolutionarily conserved and assigned the confidence scores to hydrophobic residues to be buried or solvent exposed based on the information obtained from conservation score and knowledge of flanking regions of hydrophobic residues. In the absence of a three-dimensional structure, the ability to predict surface accessibility of hydrophobic residues directly from the sequence is of great help in choosing the sites of chemical modification or specific mutations and in the studies of protein stability and molecular interactions.
Dissertations / Theses on the topic "Residue conservation; Protein folding"
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Livingstone, Craig David. "Pattern recognition and protein structure prediction from aligned amino acid sequences." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297307.
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Valdar, William Seth Jermy. "Residue conservation in the prediction of protein-protein interfaces." Thesis, University College London (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246927.
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Chan, Pedro. "A computational investigation of solubility, functionality and the adaptation in subcellular compartments of proteins." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/a-computational-investigation-of-solubility-functionality-and-the-adaptation-in-subcellular-compartments-of-proteins(29ba40c2-0e8b-459a-803b-529da885289a).html.
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A cell is considered to be the smallest unit of life. It carries out a variety of biochemical reactions through the activities of proteins and protein enzymes. In order to perform functions, proteins must be in their native folded state together with the correct environmental conditions. A slight change in pH or temperature could cause disruption to the electrostatic interactions within the protein, thus leading to conformational change and the loss of activity. Studies have shown that solubility could be enhanced by increasing the number of charges on the protein surface. And from the studies of extremophiles, we learned that the presence of non-polar aromatic residues could be a key for thermostable proteins. Thus, charges are important to determine the function and adaptation of proteins.Over the decades, large amount of protein sequence and structure information relating to molecular biology has been produced. By employing algorithms, computational and statistical techniques, it is possible to analyse these data to solve biological problems. Often these investigations are based mainly on sequences since their numbers outstrip the number of available structures. However, adding structures would allow us to investigate problems such as the relationship between charges, sequence, structure and functions, which is the aim of this study.In this thesis, the relationships between proteins and function were examined by various electrostatic features derived from charges and also geometric properties from structures. One interesting finding is that the averaged value of pH of maximum stability of proteins within a subcellular location was highly correlated to the pH of that subcellular compartment, which was due to pKas (of histidines), and their locations on the proteins. We also found that the size of the largest non-charged patch on the protein surface correlates with solubility and provides a predictor with a maximum accuracy of 76%. The use of novel charge-based methods shows little improvement in distinguishing between enzymes and non-enzymes. However, the method of using real charges with grid size of 1 angstrom has paved a way into the idea of using charges and dipoles pattern from enzyme active site to distinguish different enzymes. Finally, a web-tool for displaying conserved residues on 3D protein structure is made available to the public for identifying residues that may be of functional importance.
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Carstensen, Linn [Verfasser], and Reinhard [Akademischer Betreuer] Sterner. "Conservation of the folding mechanism between a thermostable (βα)8-barrel enzyme, its evolutionary relatives, and ancestral precursors generated by protein design / Linn Carstensen. Betreuer: Reinhard Sterner." Regensburg : Universitätsbibliothek Regensburg, 2012. http://d-nb.info/1027850332/34.
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Huang, Yu-Wen, and 黃郁文. "On the relationship between structural packing and residue conservation in protein-protein interfaces." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/h5q83x.
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博士國立交通大學
生物資訊及系統生物研究所
105
Proteins interact with other proteins to perform their biological functions. Thus, the knowledge of protein-protein interfaces is valuable in understanding molecular mechanisms. Recently, we have observed that structural packing profiles of proteins have moderate correlations with their corresponding conservation profiles. However, some proteins were found to have low correlations between these two profiles, where structural packing profiles of the proteins were computed using a weighted contact number (WCN) model with the structures of single proteins. To better understand the characteristics in protein-protein interfaces, we explored the relationship between structural packing and residue conservation in protein-protein interfaces from 344 non-homologous subunits of 328 enzymes complexes. These subunits compose three datasets: Set I, Set A, and Set B. In Set A, catalytic sites of complexes are in the interfaces and consist of residues from multiple subunits; in Set B, catalytic sites of complexes are not in the interfaces and consist of residues from single subunits. We found that interface residues in three datasets tend to have high WCN scores (i.e., low structural packing). However, interface residues of Set B tend to have high conservation scores (i.e., lowly conserved). The tendency is different from those of the other datasets. This could be that complexes of Set B have weaker functional and structural constraints on their evolutionary processes than those of the other datasets in the condition that the enzymatic functions of the complexes are maintained. Surprisingly, the results show that the interface residues have distinct distributions of differences between the WCN scores and the conservation scores from the non-interface residues. Also, the WCN scores of the interface residues tend to be higher than their corresponding conservation scores. Furthermore, using a difference between a WCN score and a conservation score of a residue to detect the protein-protein interfaces, noteworthy sensitivity was obtained. This study provides interface properties in structural packing and residue conservation and elucidates the relationship between the structural packing and the residue conservation in interfaces of individual subunits.
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Lin, Yu-Feng, and 林玉鳳. "On the relationship between protein structures, packing density, and residue conservation of protein domains." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/3f7uch.
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博士國立交通大學
生物資訊及系統生物研究所
105
During evolution, substitutions at individual residues within amino acid sequences arise under the constraints of structure folding, protein function, and the protein–protein interactions. Amino acid sequences generally fold into unique, stable, and well-ordered conformations so that the resulting proteins can carry out their specific functions. As such, residues that are important for function and structural stabilization are generally highly conserved in terms of both sequence and structure. Recent studies have discussed the structural constraints imparted by site-specific substitutions, and amino acid sequence conservation was found to correlate with solvent accessibility and the local packing density such as weighted contact number. The relationship between sequence conservation, site-specific substitution rates derived from multiple sequence alignment, and the weighted contact number, local packing density derived from three-dimensional structure, revealed that the evolution constraint of protein sequence and structure properties were correlated. In this study, we assessed the relationship between the packing density profiles drawn out from similar protein domain structures in SCOP superfamily with the relationship of remote homologs, and the results showed that similar structures had similar weighted contact number profiles, and demonstrated that the packing density profiles could reflect the structural constraints. Then, we compared the site-specific substitution rate profiles of two proteins and their structures, and the results showed that similar conservation profiles could be linked to similar structures. The evolution constraints of protein sequence and structure were not only related to each other in a protein, but also were interrelated in different proteins. The protein sequence and structure restricted by evolution constraints lead to that the binding regions tend to be conserved in sequence and structure and the interacting residues involved are usually in close three-dimensional space. In this study, we analyzed the protein structure, local packing density and residue constitute of metal ion-binding sites, including Ca2+, Cu2+, Cu+, Fe3+, Fe2+, Mg2+, Mn2+, Zn2+, Cd2+, Ni2+, Hg2+, and Co2+. The analysis of local packing density of metal ion-binding sites revealed that the metal ion-binding sites tend to be more crowded in proteins. Our result showed that the distributions of local packing density of metal ion-binding residues were distinct from those of non-metal ion-binding residues. The results showed that there were distinct different binding patterns of these twelve kinds of metal ion-binding sites, indicating the conservation of structure and sequence in metal ion-binding residues. According to the conserved patterns of structure and residue, we further developed a method to predict the metal ion-binding residues and build the model of metal ions docking by using fragment transformation method, and built up the MIB server (Metal Ion Binding sites prediction and docking server, http://bioinfo.cmu.edu.tw/MIB/) for not only twelve metal ion–binding sites prediction but also metal ions docking.
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Chen, Ya-Ping, and 陳雅萍. "Analyzing the Impacts of Sequence Conservation on Protein RNA-binding Residue Prediction." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/21582511879129142405.
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碩士國立臺灣大學
工程科學及海洋工程學研究所
99
Protein-RNA interactions play a vital role in many stages of gene expression such as pre-mRNA synthesis, mRNA splicing and translation. It is generally believed that binding domains or binding motifs enable RNA-binding proteins to recognize their target RNA. Since the corresponding nucleic acid type and the structure level recognized can be quite diverse, predicting RNA-binding residues from primary structure of proteins is indeed a challenging task. In this thesis, we continue the work of ProteRNA and develop two classifiers, namely support vector machine (SVM) and random forests (RF), with the predicted protein disorder added as a new feature descriptor. For the post-processing procedure, we build a discriminator in order to improve the pattern quality by distinguishing RNA-binding residues from other functionally important ones in conserved regions. When considering the dataset preparation effects and variance in binding sites, the two classifiers achieve Matthew’s correlation coefficient (MCC) of 0.5288 and 0.4698 using five-fold cross-validation. Our approach outperforms other predictors which provide online service. Testing on the independent test dataset, the SVM model achieves an accuracy of 92.12%, sensitivity of 38.10%, specificity of 97.47%, precision of 59.89%, F-score of 0.4657 and MCC of 0.4381, while the RF model ranks second only to SVM, it achieves an accuracy of 90.08%, sensitivity of 34.47%, specificity of 95.59%, precision of 43.62%, F-score of 0.3851 and MCC of 0.3346. We observe the measure trend in machine learning methods for datasets based on different sequence identities, and discuss the origin of performance increment and bottleneck. We find out that the homologous sequence, or even remote homologous in the same dataset as query sequence will probably make prediction result closer to the distribution of real binding sites. Besides, a method that identifies the nearest neighbor by sequence alignment and determines its binding residues accordingly may perform better than machine learning methods trained on PSSM in some cases. Nevertheless, when dealing with novel protein sequences, the excellent performance of machine learning methods shows great generalization ability.
Book chapters on the topic "Residue conservation; Protein folding"
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Neumaier, Arnold, Stefan Dallwig, Waltraud Huyer, and Hermann Schichl. "New Techniques for the Construction of Residue Potentials for Protein Folding." In Computational Molecular Dynamics: Challenges, Methods, Ideas, 212–24. Berlin, Heidelberg: Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-642-58360-5_12.
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Hinck, A. P., and W. F. Walkenhorst. "NMR and Mutagenesis Investigations of a Model Cis: Trans Peptide tsomerization Reaction: Xaa116-Pro117of Staphylococcal Nuclease and its Role in Protein Stability and Folding." In Biological NMR Spectroscopy. Oxford University Press, 1997. http://dx.doi.org/10.1093/oso/9780195094688.003.0016.
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The slow rates of peptide bond isomerization in imino acids and the substantial population of the cis peptide bond isomer in Xaa-Pro linkages in peptides were first recognized in NMR studies of proline-containing model compounds (Maia et al., 1971). The important role of this isomerization in protein stability and folding (reviewed by Kim and Baldwin, 1982, 1990; Schmid, 1993) were recognized several years later (Brandts et al., 1975) and the biological relevance of this process was substantiated by the discovery of a ubiquitous enzyme that catalyzes Xaa-Pro peptide bond isomerization (Fischer et al., 1984, 1989; Takahashi et al., 1989). The strict evolutionary conservation of some prolyl residues and the observation that the kinetics of interconversion between alternative functional forms of some systems is consistent with the time scale of proline isomerization suggest that proline isomerization may play a wide role in protein structure and function. Suggestive examples include the sodium pump of Escherichia coli, the disulfide isomerase/thioredoxin class of enzymes, concanavalin A, and bovine prothrornbin fragment I (Brown et al., 1977; Marsh et al, 1979; Dunker, 1982; Brandland Deber, 1986; Langsetmo et al, 1989). NMR spectroscopy is one of the most suitable tools for studying this isomerization reaction. The rates generally are slow on the time scale of NMR chemical shifts but, in favorable cases, are comparable to longitudinal relaxation rates so that the isomerization process can be investigated by chemical exchange spectroscopy. NMR data obtained on calbindin D9k (Chazin et al., 1989), insulin (Higgins et al., 1988), and staphylococcal nuclease (nuclease) as discussed below have shown that each exists in solution under native conditions as a mixture of slowly exchanging conformers. The fact that dynamic molecular heterogeneity in nuclease was first observed in the laboratory of Oleg Jardetzky, as manifested by splitting of the histidyl 1H ε1 resonance from His46 in one-dimensional 1H NMR spectra recorded at 100 MHz (Markley et al., 1970), makes this topic particularly appropriate to a volume celebrating his scientific contributions.
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Royo, Miriam, and George Barany. "Preparation and handling of peptides containing methionine and cysteine." In Fmoc Solid Phase Peptide Synthesis. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780199637256.003.0008.
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Among the genetically encoded amino acid residues, methionine (Met) and cysteine (Cys) are special because they each contain an atom of sulphur. The present chapter describes how these residues are incorporated into peptides in the context of an Fmoc/tBu solid-phase synthesis strategy, as well as further considerations once the synthetic peptide is released from the support. Of added interest, some manipulations of Cys are advantageously performed at the level of the assembled peptide-resin, prior to cleavage. Many of the aspects discussed here also carry over to the preparation of peptides using a Boc/Bzl strategy. The major problems associated with management of Met reflect the susceptibility of the thioether to alkylation and oxidation. One of the merits of the Fmoc/tBu strategy, in contrast to Boc/Bzl, is that in the former strategy Met is usually introduced without recourse to a protecting group for the thioether side-chain. As documented in this chapter, a proper understanding of acidolytic cleavage conditions and the availability of selective procedures to reverse any inadvertent oxidation are likely to lead to success in obtaining homogeneous peptides containing Met. Management of Cys provides additional significant challenges. For some targets, Cys is required with its side-chain in the free thiol form, whereas for other targets, an even number of Cys residues pair with each other via disulphide linkage(s) to provide cystine residue(s). Disulphide bridges play an important role in the folding and structural stabilization of many natural peptides and proteins, and their artificial introduction into natural or designed peptides is a useful approach to improve biological activities/specificities and stabilities. Furthermore, use of a disulphide bridge is a preferred method to conjugate peptides to protein carriers for increasing the response in immuno-logical studies, to link two separate chains for developing discontinuous epitopes, and to generate active site models. This chapter describes Cys protecting groups, how they are removed to provide either free thiols or disulphides directly, and various strategies and practical considerations to minimize side reactions and maximize formation of the desired products. The thioether side-chain of Met is subject to alkylation and oxidation side reactions, either during the synthetic process or during subsequent handling of the Met-containing peptide.
Conference papers on the topic "Residue conservation; Protein folding"
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Maiti, Shyantani, and Pralay Mitra. "Protein Design Assisted Residue Conservation and Functional Stability Analysis for Bacterial Chemotaxis." In 2018 International Conference on Bioinformatics and Systems Biology (BSB). IEEE, 2018. http://dx.doi.org/10.1109/bsb.2018.8770546.
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Hwang, Wonmuk, and Matthew J. Lang. "Mechanism of Force Generation in Kinesin Motility." In ASME 2007 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2007. http://dx.doi.org/10.1115/sbc2007-175543.
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Conventional kinesin is a dimeric motor protein that uses adenosine triphosphate (ATP) to walk processively along the microtubule. Although its nucleotide dependent conformational switching and binding of the neck linker (NL) on the motor head are known to be key events in kinesin motility, the basic mechanism by which it amplifies a small conformational change upon ATP binding to generate the force of the walking stroke has not been known. We combined structural analysis with a set of molecular dynamics simulations to identify the 9-residue long N-terminal region, which we named the ‘cover strand’ (CS), as an additional element essential for kinesin’s power stroke. It operates by differentially forming a β-sheet with NL when ATP binds, whereby the ‘cover-neck bundle’ (CNB) has an inherent conformational bias that drives NL into its binding pocket on the motor head. After the initial stroke, the later half of NL, starting with the ‘asparagine latch’ in the middle, forms specific bonds with the motor head to ensure tight binding. We constructed the force map generated by CNB, which showed a forward bias in agreement with single molecule motility measurements. Our result is consistent with other experimental observations, including the estimated stall force and the transverse anisotropy. The novel mechanism of force generation by the dynamic folding of CNB appears to hold in various kinesin families, and elucidates the economy in the design principle of the smallest known processive motor.
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Pannekoek, H., M. Linders, J. Keijer, H. Veerman, H. Van Heerikhuizen, and D. J. Loskutoff. "THE STRUCTURE OF THE HUMAN ENDOTHELIAL PLASMINOGEN ACTIVATOR INHIBITOR (PAI-1) GENE: NON-RANDOM POSITIONING OF INTRONS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644767.
Full textAbstract:
The endothelium plays a crucial role in the regulation of the fibrinolytic process, since it synthesizes and secretes tissue-type plasminogen activator (t-PA) as well as the fast-acting plasminogen activator inhibitor (PAI-1). Molecular cloning of full-length PAI-1 cDNA, employing a human endothelial cDNA expression library, and a subsequent determination of the complete nucleotide sequence, allowed a prediction of the amino-acid sequence of the PAI-1 glycoprotein. It was observed that the amino-acid sequence is significantly homologous to those of members of the serine protease inhibitor ("Serpin") family, e.g. αl-antitrypsin and antithrombin III. Serpins are regulators of various processes, such as coagulation, inflammatory reactions, complement activation and share a common functional principle and a similar structure, indicative for a common primordial gene. The intron-exon arrangement of Serpin genes may provide a record for the structure of a primordial gene. A comparison of the location of introns among members of the Serpin family reveals that some introns are indeed present at identical or almost identical positions, however in many other cases there is no correspondence between the intron positions among different Serpin genes.Obviously, more data on the chromosomal gene structure of members of this family are required to formulate a scheme for the evolutionary creation of the Serpins. To that end, we have established the number and the precise location of the introns in the PAI-1 gene and have compared these data with those reported on other Serpin genes. For that purpose a human genomic cosmid DNA library of about 340.000 independent colonies was screened with radiolabelled full-length PAI-1 cDNA as probe. Two clones were found which contain the entire PAI-1 gene. Restriction site mapping, electron microscopic inspection of heteroduplexes and nucleotide sequence analysis demonstrate that the PAI-1 gene comprises about 12.2kilo basepairs and consists of nine exons and eight introns. Intron-exon boundaries are all in accord with the "GT-AG" rule, including a cryptic acceptor splice site found in intron 7. Furthermore, it is observed that intron 3 of the PAI-1 gene occupies an identical position as intron E of chicken ovalbumin and intron E of the ovalbumin-related gene Y. The location of the other seven introns is unrelated to the known location of introns in the genes encoding the Serpins, rat angiotensin, chicken ovalbumin (and gene Y), human antithrombin III and human al-antitrypsin. The 3' untranslated region of the PAI-1 gene is devoid of introns, indicating that the two mRNA species detected in cultured endothelial cells which share an identical 5' untranslated segment and codogenic region, but differ in the length of the 3' untranslated region, arise by alternative polyadenylation. An extrapolation of the position of the introns to the amino-acid sequence of PAI-1, and adaption of the view that the subdomain structure of the Serpins is analogous, shows that the introns of PAI-1 are non-randomly distributed. Except for intron 7, the position of the other seven introns corresponds with randon-coil regions of the protein or with the borders of β-sheets and a-helices. Extrapolation of the position of introns in the genes of other Serpins to their respective amino-acid sequences and subdomain structures also reveals a preference for random-coil regions and borders of subdomains. These observations are reminiscent of an evolutionary model, called "intron sliding", that accounts for variations in surface loops of the same protein in different species by aberrant splicing (Craik et al., Science 220 (1983) 1125). The preferential presence of introns in gene segments, encoding these variable regions, and absence in regions determining the general folding of these proteins would explain conservation of the structure during the evolution of those genes.