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Now showing 1 - 5 of 5
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    PublicationOpen Access
    Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions
    (Wiley, 2017) Department of Chemical and Biological Engineering; Hacısüleyman, Aysima; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; N/A; 179997
    A fast and approximate method of generating allosteric communication landscapes in proteins is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but an ensemble of pathways is possible. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations should be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. By this approach, residues that should be manipulated to control protein activity may be determined. This should be of great importance for allosteric drug design and for understanding the effects of mutations on function. The model is applied to determine allosteric communication in three proteins, Ubiquitin, Pyruvate Kinase, and the PDZ domain. Predictions are in agreement with molecular dynamics simulations and experimental evidence.
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    Combining protein-protein interaction networks with structures
    (Cell Press, 2009) Nussinov, Ruth; N/A; Department of Computer Engineering; Department of Chemical and Biological Engineering; Kar, Gözde; Gürsoy, Attila; Keskin, Özlem; PhD Student; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 8745; 26605
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    Phosphoproteomic changes in red blood cell membranes by Adenylyl cyclase/Protein kinase A signaling pathway and their roles on the mechanical stress responses of red blood cells
    (Ios Press, 2021) N/A; N/A; N/A; N/A; Uğurel, Elif; Çilek, Neslihan; Göksel, Evrim; Yalçın, Özlem; Researcher; PhD Student; PhD Student; Faculty Member; School of Medicine; Graduate School of Health Sciences; Graduate School of Health Sciences; School of Medicine; N/A; N/A; N/A; 218440
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    PublicationOpen Access
    PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps (corrigendum)
    (International Union of Crystallography, 2018) Nussinov, Ruth; Department of Chemical and Biological Engineering; Kuzu, Güray; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; N/A; 26605; 8745
    A revised Table 6 and Supporting Information are provided for the article by Kuzu et al. [(2016 ), Acta Cryst. D72, 1137-1148].
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    Purification and characterization of a type III photolyase from caulobacter crescentus
    (Amer Chemical Soc, 2008) Öztürk, Nuri; Kao, Ya-Ting; Selby, Christopher P.; Kavakli, I. Halil; Partch, Carrie L.; Zhong, Dongping; Sancar, Aziz; Department of Chemical and Biological Engineering; Kavaklı, İbrahim Halil; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40319
    The photolyase/cryptochrome family is a large family of flavoproteins that encompasses DNA repair proteins, photolyases, and cryptochromes that regulate blue-light-dependent growth and development in plants, and light-dependent and light-independent circadian clock setting in animals. Phylogenetic analysis has revealed a new class of the family, named type III photolyase, which cosegregates with plant cryptochromes. Here we describe the isolation and characterization of a type III photolyase from Caulobacter crescentus. Spectroscopic analysis shows that the enzyme contains both the methenyl tetrahydrofolate photoantenna and the FAD catalytic cofactor. Biochemical analysis shows that it is a bona fide photolyase that repairs cyclobutane pyrimidine dimers. Mutation of an active site Trp to Arg disrupts FAD binding with no measurable effect on MTHF binding. Using enzyme preparations that contain either both chromophores or only folate, we were able to determine the efficiency and rate of transfer of energy from MTHF to FAD.