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Characterizing oriented protein structural sites using biochemical properties

S C Bagley, L Wei, C Cheng, R B Altman
1995 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
To facilitate the analysis of such protein sites, we have developed a computer system for analyzing the spatial distributions of biochemical properties around a site.  ...  A protein site is a region of a three-dimensional protein structure with a distinguishing functional or structural role.  ...  Conclusion This paper has presented a method for characterizing protein sites using biochemical properties tested for statistical significance against an explicit control group of nonsites.  ... 
pmid:7584427 fatcat:2ywtt2noozff7dz6i2r7moim2m

The published 3D structure of the VDAC channel: native or not?

Marco Colombini
2009 TIBS -Trends in Biochemical Sciences. Regular ed  
As it was refolded from inclusion bodies, the protein used to obtain the 3D structures might not be in the native conformation.  ...  To obtain enough protein for the characterization, the authors of each paper expressed VDAC in Escherichia coli and then refolded the protein from inclusion bodies.  ...  Once a set of sites were characterized as being either type 1 or type 2 sites, double cysteine mutant proteins were constructed using only the known sites.  ... 
doi:10.1016/j.tibs.2009.05.001 pmid:19647437 fatcat:64hau7ckdbhb7lreqtklpi2wtq

Catalytic cycle ofPlasmodium falciparumlactate dehydrogenase

A. Hadfield, C. Limpkin, J. Read, C. Shammas, D. Shoemark, R. Tranter, L. Brady
2004 Acta Crystallographica Section A Foundations of Crystallography  
Their catalytic pathway in the lights of biochemical characterization is very different to the yeast CCP.  ...  Yeast cytochrome c peroxidase (CCP) is the most used paradigm of this class of enzymes, having been extensively characterized [1] . Bacterial CCP are the subject of these studies.  ...  Their catalytic pathway in the lights of biochemical characterization is very different to the yeast CCP.  ... 
doi:10.1107/s0108767304099659 fatcat:loqkxp22cbbancqer6kfakclum

Exploring the Catalytic Significant Residues of Serine Protease Using Substrate-Enriched Residues and a Peptidase Inhibitor

Zahoor Khan, Maryam Shafique, Amir Zeb, Nusrat Jabeen, Sehar Afshan Naz, Arif Zubair
2021 Microbiology and Biotechnology Letters  
The primary sequence was analyzed using ProtParam, SignalP, and Phyre2 tools to investigate biochemical properties, signal peptide, and secondary structure, respectively.  ...  This study was designed to investigate the biochemical properties, critical residues, and the catalytic potential of alkaline serine protease using in-silico approaches.  ...  Material and Methods Primary structure and biochemical properties As the 3D structure of alkaline serine protease (ASP) from Bacillus tequilensis was not available in Protein Data Bank (PDB), thus, the  ... 
doi:10.48022/mbl.2009.09012 fatcat:gt4lcgyrhzgqvmfzypccggmdwy

Conserved features in the active site of nonhomologous serine proteases

Steven C. Bagley, Russ B. Altman
1996 Folding & design  
We have used a computer program to study the properties that are shared by four serine protease active sites with no overall structural or sequence homology.  ...  It is not clear, though, the degree to which these protease families share common biochemical and biophysical properties.  ...  SJ Remington provided the coordinates for the crystal structure of wheat serine carboxypeptidase bound to chymostatin.  ... 
doi:10.1016/s1359-0278(96)00052-1 pmid:9080183 fatcat:nfwwa36qrramlm7ojpk65urbw4

Structure and Function of Human Erythrocyte Pyruvate Kinase

Giovanna Valentini, Laurent R. Chiarelli, Riccardo Fortin, Manuela Dolzan, Alessandro Galizzi, Donald J. Abraham, Changqing Wang, Paola Bianchi, Alberto Zanella, Andrea Mattevi
2002 Journal of Biological Chemistry  
The mutations target distinct regions of RPK structure, including domain interfaces and catalytic and allosteric sites.  ...  Characterization of mutant proteins may serve as a valuable tool to assist with diagnosis and genetic counseling.  ...  Here, we describe the first crystal structure of recombinant RPK and the biochemical characterization of eight mutants found in patients subjected to clinical follow-up. These TCTTCC.  ... 
doi:10.1074/jbc.m202107200 pmid:11960989 fatcat:bq6jirafcrdaxkvjhc25dhjpji

ViewFeature: Integrated Feature Analysis and Visualization

D. R. Banatao, C. C. Huang, P. C. Babbitt, R. B. Altman, T. E. Klein
2000 Biocomputing 2001  
We are, however, able to differentiate between the metal-binding sites of α/β barrels and those of other metal-binding proteins.  ...  Through the use of ViewFeature, we have found that the C-terminal domain of the enolase superfamily does not differ at the scaffold level from metal-binding α/β barrels.  ...  To better orient the user in 3-dimensional space, ViewFeature provides visualization of the specific spherical volume for a volume/property pair oriented around a specific site.  ... 
doi:10.1142/9789814447362_0025 fatcat:j4hfv743gvegrca4bvmr3swogu

New findings about human dipeptidyl peptidase III based on mutations found in cancer

M. Matovina, D. Agić, M. Abramić, S. Matić, Z. Karačić, S. Tomić
2017 RSC Advances  
In this work we investigated the role of two highly conserved residues in the peptidase family M49, whose mutations G313W and R510W were detected in human cancer, using combined experimental and computational  ...  Acknowledgements The work has been supported by Croatian Science Foundation under the project "7235 Flexibility, activity and structure correlations in the dipeptidyl peptidase III family" and by UKF grant  ...  Results and discussion Biochemical properties of h.DPP III mutants We puried and biochemically characterized two recombinant protein mutants of h.DPP III, G313W and R510W, that were found in lung adenocarcinoma  ... 
doi:10.1039/c7ra02642k fatcat:sqgbjj4bqbcerk3jv7huyp4pta

Characteristics and concepts of dynamic hub proteins in DNA processing machinery from studies of RPA

Norie Sugitani, Walter J. Chazin
2015 Progress in Biophysics and Molecular Biology  
Here, we introduce a number of key characteristics and concepts, including the modularity of the proteins, linkage of weak binding sites, direct competition between sites, and allostery, using the well  ...  These modular proteins contain flexible linkers of various lengths, which enable changes in the spatial distribution of the globular domains (architecture) that harbor their essential biochemical functions  ...  Research on DNA processing machinery in our laboratory is supported by operating and center grants from the US National Institutes of Health (RO1 GM65484, PO1 CA092584, RO1 ES016561, P30 ES00267, P30 CA068485  ... 
doi:10.1016/j.pbiomolbio.2014.12.001 pmid:25542993 pmcid:PMC4417437 fatcat:4f32cumyzbcird3hhy3dd6ie5y

High precision protein functional site detection using 3D convolutional neural networks

2018 Bioinformatics  
Pre-defined biochemical features emphasize certain aspects of protein properties while ignoring others, and therefore may fail to capture critical information in complex protein sites.  ...  However, the choice of protein structural representation is critical.  ...  This work also used the XStream computational resource, supported by the National Science Foundation Major Research Instrumentation program (ACI-1429830).  ... 
doi:10.1093/bioinformatics/bty813 pmid:31051039 pmcid:PMC6499237 fatcat:xgn3shpwu5gfzbyj7kygnqmigq

Structural characterization of bacterial cytochrome c peroxidases in different redox states: insights on activation and catalytic mechanisms

A. Echalier, G. W. Pettigrew, V. Fülöp
2004 Acta Crystallographica Section A Foundations of Crystallography  
Their catalytic pathway in the lights of biochemical characterization is very different to the yeast CCP.  ...  Yeast cytochrome c peroxidase (CCP) is the most used paradigm of this class of enzymes, having been extensively characterized [1] . Bacterial CCP are the subject of these studies.  ... 
doi:10.1107/s0108767304099660 fatcat:ul6y5rpinzbjjo6qm73nptnozu

Engineering functional protein interfaces for immunologically modified field effect transistor (ImmunoFET) by molecular genetic means

E. Eteshola, M. T Keener, M. Elias, J. Shapiro, L. J Brillson, B. Bhushan, S. C. Lee
2008 Journal of the Royal Society Interface  
We use protein engineering approaches to engineer the sensing interface of biochemically modified field effect transistor sensors (BioFET).  ...  In addition, we have developed a protein engineering technology (scanning circular permutagenesis) that allows us to alter protein topography to manipulate the position of functional domains of the protein  ...  Surfaces were biochemically characterized using enzyme-linked immunosorbent assay to demonstrate the specific affinity properties.  ... 
doi:10.1098/rsif.2007.1107 pmid:17580287 pmcid:PMC2605506 fatcat:5bukwjpslfdfdfny4pww3bhszq

Solid state NMR and protein–protein interactions in membranes

Yimin Miao, Timothy A Cross
2013 Current Opinion in Structural Biology  
dynamics, and high-resolution structure for these proteins.  ...  Protein-protein interactions can also benefit from this solid state NMR capability to characterize membrane proteins in a native-like environment.  ...  of the conductance domain (residues 22-62has the same conductance properties as the full length protein) of this channel has been characterized by ssNMR using a combination of orientational and distance  ... 
doi:10.1016/j.sbi.2013.08.004 pmid:24034903 pmcid:PMC3855169 fatcat:ojvia4xmojeobf2rdfhpv7ha3e

Structural and Biochemical Analysis of a Unique Phosphatase from Bdellovibrio bacteriovorus Reveals Its Structural and Functional Relationship with the Protein Tyrosine Phosphatase Class of Phytase

Robert J. Gruninger, John Thibault, Michael J. Capeness, Robert Till, Steven C. Mosimann, R. Elizabeth Sockett, Brent L. Selinger, Andrew L. Lovering, Paul Hoskisson
2014 PLoS ONE  
The structure reveals that Bd1204 has the smallest and least electropositive active site of all characterized PTPLPs to date yet possesses a unique substrate specificity characterized by a strict preference  ...  Bd1204 is both structurally and mechanistically related to the PTP-like phytase (PTPLP) class of enzymes and possesses a number of unique properties not observed in any other PTPLPs characterized to date  ...  These unique biochemical properties of Bd1204 call for a reevaluation of the basis of substrate specificity within this everexpanding group of proteins.  ... 
doi:10.1371/journal.pone.0094403 pmid:24718691 pmcid:PMC3981807 fatcat:4pajybccjfbnbmdjrldwqkk7o4

Unusual properties of the cytochrome P450 superfamily

D. C. Lamb, M. R. Waterman
2013 Philosophical Transactions of the Royal Society of London. Biological Sciences  
These novel properties expand our appreciation of the broad view of P450 structure and function, and generate curiosity concerning the evolution of P450s.  ...  In some cases, structural properties, previously not found in P450s, can lead to enzymatic activities impacting the biological function of organisms containing these enzymes; whereas, in other cases, the  ...  The structural resolution of further catalytically active eukaryotic CPRs and their biochemical characterization will address this question.  ... 
doi:10.1098/rstb.2012.0434 pmid:23297356 pmcid:PMC3538423 fatcat:5cgxetj6jrgmzlpe4fxpunr6ki
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