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Protein folds and functions

Andrew CR Martin, Christine A Orengo, E Gail Hutchinson, Susan Jones, Maria Karmirantzou, Roman A Laskowski, John BO Mitchell, Chiara Taroni, Janet M Thornton
1998 Structure  
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

Jianlin Cheng, Hiroto Saigo, Pierre Baldi
2005 Proteins: Structure, Function, and Bioinformatics  
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

Ratna R Thangudu, Malini Manoharan, N Srinivasan, Frédéric Cadet, R Sowdhamini, Bernard Offmann
2008 BMC Structural Biology  
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

Anubha Dubey
2014 International Journal of Scientific Research in Knowledge  
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

E. Gail Hutchinson, Janet M. Thornton
2008 Protein Science  
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

Bryan J. McCullough, Hayden Eastwood, Dave J. Clark, Nick C. Polfer, Dominic J. Campopiano, Julia A Dorin, Alison Maxwell, Ross J. Langley, John R.W. Govan, Summer L. Bernstein, Michael T. Bowers, Perdita E. Barran
2006 International Journal of Mass Spectrometry  
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

Mateusz Sikora, Joanna I. Sułkowska, Marek Cieplak, Angel Garcia
2009 PLoS Computational Biology  
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

Akhila Melarkode Vattekatte, Nicolas Ken Shinada, Tarun J Narwani, Floriane Noël, Olivier Bertrand, Jean-Philippe Meyniel, Alain Malpertuy, Jean-Christophe Gelly, Frédéric Cadet, Alexandre G de Brevern
2020 PeerJ  
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

Maja Malkowska, Katarzyna Kokoszynska, Magdalena Dymecka, Leszek Rychlewski, Lucjan S Wyrwicz
2013 Virology Journal  
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

Michael Hennig, Johan N. Jansonius, Anke C. Terwisscha van Scheltinga, Bauke W. Dijkstra, Bernhard Schlesier
1995 Journal of Molecular Biology  
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

Malini Manoharan, Kannan Sankar, Bernard Offmann, Sowdhamini Ramanathan
2013 Bioinformatics and Biology Insights  
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

Pawel Dabrowski-Tumanski, Joanna I. Sulkowska
2017 Proceedings of the National Academy of Sciences of the United States of America  
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

Payal Gupta, Prasanta K. Dash
2017 Scientific Reports  
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.  ... 
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

Dimos Goundaroulis, Neslihan Gügümcü, Sofia Lambropoulou, Julien Dorier, Andrzej Stasiak, Louis Kauffman
2017 Polymers  
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

Luke W Guddat, Alan S McAlpine, David Hume, Susan Hamilton, John de Jersey, Jennifer L Martin
1999 Structure  
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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