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Protein folds and functions
1998
Structure
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Conclusions: The availability of structural classification data has enabled this novel overview analysis. ...
These distributions have been examined in the light of protein function and bound ligand. ...
Whereas the presence of a disulphide bridge (which can be derived directly from the coordinates) is a reliable indicator of extracellular location, the absence of a disulphide bridge does not necessarily ...
doi:10.1016/s0969-2126(98)00089-6
pmid:9687369
fatcat:xujs6rt6g5d4nmtdbxiwz7prvi
Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching
2005
Proteins: Structure, Function, and Bioinformatics
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Here, we develop new methods for predicting disulphide bridges in proteins. We first build a large curated data set of proteins containing disulphide bridges to extract relevant statistics. ...
The formation of disulphide bridges between cysteines plays an important role in protein folding, structure, function, and evolution. ...
Thus, it is desirable to be able to classify protein chains into those containing disulphide bridges and those that are entirely devoid of disulphide bridges (chain classification). ...
doi:10.1002/prot.20787
pmid:16320312
fatcat:56kz2wser5fadf6lauphnhicky
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families
2008
BMC Structural Biology
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NS and RS thank the authorities of Université de La Réunion for their visiting professorships. We thank Dr. Alexandre G. de Brevern for useful comments. ...
bridge topology even when their connectivity differs [29] . ...
regard to the SCOP classification of proteins. left handed and right handed conformations. ...
doi:10.1186/1472-6807-8-55
pmid:19111067
pmcid:PMC2628669
fatcat:5doak4gplbhx3l6mpvbblfv2be
The Prediction of Disulphide Bonding in HIV and other lenti-viruses by Machine Learning Techniques
2014
International Journal of Scientific Research in Knowledge
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Hence by different algorithms of WEKA classifier J48 predicts better classification with an accuracy of 89.6104%. ...
The introduction of disulphide bonds into proteins is an important mechanism by which they have evolved and are evolving. ...
The first is the protein chain classification: to classify if the protein contains disulfide bridge(s) or not, the second is the residue classification: to predict the bonding state of cysteines, the third ...
doi:10.12983/ijsrk-2014-p0057-0066
fatcat:hth4d4ocpfh65iiwtqrzu5dyty
PROMOTIF-A program to identify and analyze structural motifs in proteins
2008
Protein Science
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and $-loops; disulphide bridges; and main-chain hydrogen bonding patterns. ...
PROMOTIF creates postscript files showing the examples of each type of motif in the protein, and a summary page. ...
Only the signs of the x values were used in the classification of the disulphide bridges. ...
doi:10.1002/pro.5560050204
pmid:8745398
pmcid:PMC2143354
fatcat:tqcnurl7gjhgthzysf7vurdm5e
Characterisation of DEFB107 by mass spectrometry: Lessons from an anti-antimicrobial defensin
2006
International Journal of Mass Spectrometry
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With the use of molecular modelling, we have generated candidate geometries to discern the influence of disulphide bridging on the overall tertiary structure of DEFB107. ...
mapping respectively, and despite possessing three disulphide bridges, it does not fit the -defensin canonical motif. ...
of Chemistry at the University of Edinburgh. ...
doi:10.1016/j.ijms.2006.01.054
fatcat:3scxbs7vnzhv5g2wmkhia6ctge
Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
2009
PLoS Computational Biology
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New types of potent force clamps are discovered. They involve disulphide bridges and, in particular, cysteine slipknots. ...
A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17 134 proteins as described by a structure-based model. ...
Acknowledgments The idea of making surveys of proteins using Go-like models arose in a very stimulating discussion with J. M. Fernandez in 2005. More recent discussions and suggestions by M. ...
doi:10.1371/journal.pcbi.1000547
pmid:19876372
pmcid:PMC2759523
fatcat:6i4taencvrcgdm42mjhu6m3j7q
Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction
2020
PeerJ
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In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed. ...
An elaborate summary of various studies proposing structural models of VHH domains showed diversity in the algorithms used. ...
Using a recent classification of disulphide bridges (Schmidt, Ho & Hogg, 2006 ) (see Material and Methods section and Figs. ...
doi:10.7717/peerj.8408
pmid:32185102
pmcid:PMC7061911
fatcat:ovj42chiq5gxrpc7cnaucky244
Alphaherpesvirinae and Gammaherpesvirinae glycoprotein L and CMV UL130 originate from chemokines
2013
Virology Journal
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The process of herpesvirus transmission is mediated by a range of proteins, one of which is glycoprotein L (gL). ...
We conclude that the further understanding of the function of viral chemokine-like proteins in Herpesviridae infection may lead to development of novel prophylactic and therapeutic treatment. ...
The conserved topology is a result of the presence of two cysteine bridges (see Figure 1 ). ...
doi:10.1186/1743-422x-10-1
pmid:23279912
pmcid:PMC3598415
fatcat:ym622c4drvd3vnzn2meoilckfm
Crystal Structure of Concanavalin B at 1.65 Å Resolution. An "Inactivated" Chitinase from Seeds ofCanavalia ensiformis
1995
Journal of Molecular Biology
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Biophysical The structure consists of a single domain with a (b/a) 8 topology. ...
This extended loop is unusual for the (b/a) 8 topology, 9747 AG Groningen but appears in a similar conformation in the structures of the seed protein The Netherlands narbonin and several chitinases as ...
Acknowledgement We thank Professor Kasper Kirschner for discussions and critical reading of the manuscript. ...
doi:10.1006/jmbi.1995.0614
pmid:7490746
fatcat:7hoeubemvfcj7a566exoqbcwlu
Association of Putative Members to Family of Mosquito Odorant Binding Proteins: Scoring Scheme Using Fuzzy Functional Templates and Cys Residue Positions
2013
Bioinformatics and Biology Insights
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The algorithm described here uses a scheme for the classification of odorant binding proteins on the basis of functional residues and Cys-pairing. ...
The cysteine-based scoring scheme not only helps in unambiguously identifying families like odorant binding proteins (OBPs), but also aids in their classification at the subfamily level with reliable accuracy ...
Acknowledgements Malini Manoharan was supported by an international PhD fellowship from Conseil Regional de La Reunion in the framework of the joint dual- ...
doi:10.4137/bbi.s11096
pmid:23908587
pmcid:PMC3728099
fatcat:x6pb46455rdeviir3rrnz7xb5y
Topological knots and links in proteins
2017
Proceedings of the National Academy of Sciences of the United States of America
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The classification of these proteins according to their topological complexity, sequence similarity, and biological function is shown in Datasets S1 and S2, and exemplary linked protein are shown in Fig ...
We relate topological properties of these proteins to their function and stability and show that the link topology is characteristic of eukaryotes only. ...
The classification of these proteins according to their topological complexity, sequence similarity, and biological function is shown in Datasets S1 and S2, and exemplary linked protein are shown in Fig ...
doi:10.1073/pnas.1615862114
pmid:28280100
pmcid:PMC5380043
fatcat:njbt2adurjb7do4zm5u22gmpme
Molecular details of secretory phospholipase A2 from flax (Linum usitatissimum L.) provide insight into its structure and function
2017
Scientific Reports
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Physiochemical properties of both the sPLA 2 s revealed they are thermostable proteins requiring di-valent cations for optimum activity.While, structural analysis of both the proteins revealed deviations ...
Structural analysis of flax sPLA 2 s revealed that secondary structure of both the proteins are dominated by α-helix followed by random coils. ...
Financial support in the form of research scholarship to P.G. is acknowledged. www.nature.com/scientificreports/ ...
doi:10.1038/s41598-017-10969-9
pmid:28894144
pmcid:PMC5593939
fatcat:y73nznmoobb7xlrxix2ojtguly
Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids
2017
Polymers
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Further, we present a purely topological model for classifying open protein chains by also taking into account any bridge involving the backbone. ...
Moreover, we demonstrate that our topological model for bonded proteins is robust enough to distinguish all types of lassos in proteins. ...
Until now there has been no purely topological way to study the entanglement of an open protein chain that takes also into account the possible bridges (e.g., disulphide bridges) that may appear in the ...
doi:10.3390/polym9090444
pmid:30965745
pmcid:PMC6418563
fatcat:ielvsykat5akdcpobfxdvq562m
Crystal structure of mammalian purple acid phosphatase
1999
Structure
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Conclusions: Despite less than 15% sequence identity, the protein fold resembles that of the catalytic domain of plant purple acid phosphatase and some serine/threonine protein phosphatases. ...
The internal symmetry suggests that the binuclear centre evolved as a result of the combination of mononuclear ancestors. ...
JLM was the recipient of an ARC Queen Elizabeth II Fellowship. ...
doi:10.1016/s0969-2126(99)80100-2
pmid:10425678
fatcat:sjhkulzrhnd2dpbcl3adrzdvoe
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