Researcher:
Çukuroğlu, Engin

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PhD Student

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Engin

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Çukuroğlu

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Çukuroğlu, Engin

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2010 - 20146

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Now showing 1 - 6 of 6
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    Hot spots in protein-protein interfaces: towards drug discovery
    (Elsevier, 2014) N/A; N/A; Department of Computer Engineering; Department of Chemical and Biological Engineering; Çukuroğlu, Engin; Engin, Hatice Billur; Gürsoy, Attila; Keskin, Özlem; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; N/A; College of Engineering; College of Engineering; N/A; N/A; 8745; 26605
    Identification of drug-like small molecules that alter protein-protein interactions might be a key step in drug discovery. However, it is very challenging to find such molecules that target interface regions in protein complexes. Recent findings indicate that such molecules usually target specifically energetically favored residues (hot spots) in protein protein interfaces. These residues contribute to the stability of protein-protein complexes. Computational prediction of hot spots on bound and unbound structures might be useful to find druggable sites on target interfaces. We review the recent advances in computational hot spot prediction methods in the first part of the review and then provide examples on how hot spots might be crucial in drug design. (C) 2014 Published by Elsevier Ltd.
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    Structural properties of hub proteins
    (IEEE, 2010) Ozkirimli, Elif; N/A; Department of Chemical and Biological Engineering; Keskin, Özlem; Çukuroğlu, Engin; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 26605; N/A
    Protein-protein interaction networks are scale free networks with a few hub proteins that have many interaction partners in the network. In this work, we examined the flexibility of the hubs by using a structural perspective and compared date hubs, which bind their partners at different times, and party hubs, which bind their partners simultaneously, with non hub proteins. The flexibility of the proteins is evaluated using temperature factors. Party hubs are found to be more flexible than date hubs, which in turn are more flexible than non-hub proteins. These may explain how a hub interacts with its partners specifically.
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    Analysis of hot region organization in hub proteins
    (Springer, 2010) N/A; Department of Computer Engineering; Department of Chemical and Biological Engineering; Çukuroğlu, Engin; 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
    Protein interaction maps constructed from binary interactions reveal that some proteins are highly connected to others (acting as hub proteins), whereas some others have a few interactions (at the edges of the map). This paper addresses hub proteins from a structural point: interfaces. It investigates how hot spots are organized in hub proteins (hot regions). We annotate interfaces as the ones between two date-hubs (DD), two party hubs (PP), and two non-hubs (NN). We investigate the physico-chemical properties of these three types of interfaces focusing on the accessible surface area distribution, hot region organization, and amino acid composition differences. Results reveal that there are significant differences between DD and PP interfaces. More of the hot spots are organized into the hot regions in DD interfaces compared to PP ones. A high fraction of the interfaces are covered by hot regions in DD interfaces. There are more distinct hot regions in DDs. Since the same (or overlapping) DD interfaces should be used repeatedly, different hot regions can be used to bind to different partners. Further, these hot region characteristics can be used to predict whether a given hub interface is involved in a DD or a PP interface type with 80% accuracy.
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    PublicationOpen Access
    HotRegion: a database of predicted hot spot clusters
    (Oxford University Press (OUP), 2012) N/A; Department of Computer Engineering; Department of Chemical and Biological Engineering; Çukuroğlu, Engin; Gürsoy, Attila; Keskin, Özlem; PhD Student; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 8745; 26605
    Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot regions are important for the stability of protein complexes, as well as providing specificity to binding sites. We propose a database called HotRegion, which provides the hot region information of the interfaces by using predicted hot spot residues, and structural properties of these interface residues such as pair potentials of interface residues, accessible surface area (ASA) and relative ASA values of interface residues of both monomer and complex forms of proteins. Also, the 3D visualization of the interface and interactions among hot spot residues are provided.
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    PublicationOpen Access
    PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes
    (Oxford University Press (OUP), 2014) Nussinov, Ruth; Department of Computer Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Başpınar, Alper; Çukuroğlu, Engin; Keskin, Özlem; Gürsoy, Attila; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 26605; 8745
    The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein structures, PRISM will provide a structural model of their complex if a matching template interface is available. Users can download the complex structure, retrieve the interface residues and visualize the complex model.
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    PublicationOpen Access
    Non-redundant unique interface structures as templates for modeling protein interactions
    (Public Library of Science, 2014) Nussinov, Ruth; (TBD); Gürsoy, Attila; Çukuroğlu, Engin; Keskin, Özlem; Faculty Member; PhD Student; (TBD); The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; 8745; N/A; 26605
    Improvements in experimental techniques increasingly provide structural data relating to protein-protein interactions. Classification of structural details of protein-protein interactions can provide valuable insights for modeling and abstracting design principles. Here, we aim to cluster protein-protein interactions by their interface structures, and to exploit these clusters to obtain and study shared and distinct protein binding sites. We find that there are 22604 unique interface structures in the PDB. These unique interfaces, which provide a rich resource of structural data of protein-protein interactions, can be used for template-based docking. We test the specificity of these non-redundant unique interface structures by finding protein pairs which have multiple binding sites. We suggest that residues with more than 40% relative accessible surface area should be considered as surface residues in template-based docking studies. This comprehensive study of protein interface structures can serve as a resource for the community. The dataset can be accessed at https://prism.ccbb.ku.edu.tr/piface.