51
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Konc J, Janezic D. ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins. Nucleic Acids Res 2012; 40:W214-21. [PMID: 22600737 PMCID: PMC3394329 DOI: 10.1093/nar/gks435] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The ProBiS web server is a web server for detection of structurally similar binding sites in the PDB and for local pairwise alignment of protein structures. In this article, we present a new version of the ProBiS web server that is 10 times faster than earlier versions, due to the efficient parallelization of the ProBiS algorithm, which now allows significantly faster comparison of a protein query against the PDB and reduces the calculation time for scanning the entire PDB from hours to minutes. It also features new web services, and an improved user interface. In addition, the new web server is united with the ProBiS-Database and thus provides instant access to pre-calculated protein similarity profiles for over 29 000 non-redundant protein structures. The ProBiS web server is particularly adept at detection of secondary binding sites in proteins. It is freely available at http://probis.cmm.ki.si/old-version, and the new ProBiS web server is at http://probis.cmm.ki.si.
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Affiliation(s)
- Janez Konc
- National Institute of Chemistry, Ljubljana, Slovenia
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52
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Vankayala SL, Hargis JC, Woodcock HL. Unlocking the binding and reaction mechanism of hydroxyurea substrates as biological nitric oxide donors. J Chem Inf Model 2012; 52:1288-97. [PMID: 22519847 DOI: 10.1021/ci300035c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydroxyurea is the only FDA approved treatment of sickle cell disease. It is believed that the primary mechanism of action is associated with the pharmacological elevation of nitric oxide in the blood; however, the exact details of this are still unclear. In the current work, we investigate the atomic level details of this process using a combination of flexible-ligand/flexible-receptor virtual screening coupled with energetic analysis that decomposes interaction energies. Utilizing these methods, we were able to elucidate the previously unknown substrate binding modes of a series of hydroxyurea analogs to hemoglobin and the concomitant structural changes of the enzyme. We identify a backbone carbonyl that forms a hydrogen bond with bound substrates. Our results are consistent with kinetic and electron paramagnetic resonance (EPR) measurements of hydroxyurea-hemoglobin reactions, and a full mechanism is proposed that offers new insights into possibly improving substrate binding and/or reactivity.
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Affiliation(s)
- Sai Lakshmana Vankayala
- Department of Chemistry and Center for Molecular Diversity in Drug Design, Discovery, and Delivery, University of South Floridar, Tampa, Florida 33620, USA
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53
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Affiliation(s)
- Maria Kontoyianni
- Department
of Pharmaceutical Sciences and §Department of Psychology, Southern Illinois University Edwardsville, Edwardsville,
Illinois 62026, United States
| | - Christopher B. Rosnick
- Department
of Pharmaceutical Sciences and §Department of Psychology, Southern Illinois University Edwardsville, Edwardsville,
Illinois 62026, United States
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54
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Konc J, Cesnik T, Konc JT, Penca M, Janežič D. ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. J Chem Inf Model 2012; 52:604-12. [PMID: 22268964 PMCID: PMC3287116 DOI: 10.1021/ci2005687] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
ProBiS-Database is a searchable repository of precalculated
local
structural alignments in proteins detected by the ProBiS algorithm
in the Protein Data Bank. Identification of functionally important
binding regions of the protein is facilitated by structural similarity
scores mapped to the query protein structure. PDB structures that
have been aligned with a query protein may be rapidly retrieved from
the ProBiS-Database, which is thus able to generate hypotheses concerning
the roles of uncharacterized proteins. Presented with uncharacterized
protein structure, ProBiS-Database can discern relationships between
such a query protein and other better known proteins in the PDB. Fast
access and a user-friendly graphical interface promote easy exploration
of this database of over 420 million local structural alignments.
The ProBiS-Database is updated weekly and is freely available online
at http://probis.cmm.ki.si/database.
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Affiliation(s)
- Janez Konc
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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55
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Daminelli S, Haupt VJ, Reimann M, Schroeder M. Drug repositioning through incomplete bi-cliques in an integrated drug–target–disease network. Integr Biol (Camb) 2012; 4:778-88. [DOI: 10.1039/c2ib00154c] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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56
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Guo F, Li SC, Wang L. Protein-protein binding sites prediction by 3D structural similarities. J Chem Inf Model 2011; 51:3287-94. [PMID: 22077765 DOI: 10.1021/ci200206n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Identifying the location of binding sites on proteins is of fundamental importance for a wide range of applications including molecular docking, de novo drug design, structure identification, and comparison of functional sites. In this paper, we develop an efficient approach for finding binding sites between proteins. Our approach consists of four steps: local sequence alignment, protein surface detection, 3D structure comparison, and candidate binding site selection. A comparison of our method with the LSA algorithm shows that the binding sites predicted by our method are somewhat closer to the actual binding sites in the protein-protein complexes. The software package is available at http://sites.google.com/site/guofeics/pro-bs for noncommercial use.
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Affiliation(s)
- Fei Guo
- School of Computer Science and Technology, Shandong University, Jinan 250101, Shandong, China
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57
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Liu JY, Li Z, Li H, Zhang JT. Critical residue that promotes protein dimerization: a story of partially exposed Phe25 in 14-3-3σ. J Chem Inf Model 2011; 51:2612-25. [PMID: 21870863 DOI: 10.1021/ci200212y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many proteins exist and function as oligomers. While hydrophobic interactions have been recognized as the major driving force for oligomerization, detailed molecular mechanisms for the assembly are unknown. Here, we used 14-3-3σ as a model protein and investigated the role of hydrophobic residues at the dimeric interface using MD simulations and coimmunoprecipitations. We found that a half-exposed and half-buried residue in the interface, Phe(25), plays a more important role in promoting homodimerization than the hydrophobic core residues by organizing both favorable hydrophobic and hydrophilic interactions. Phe(25) is critical in packing and stabilizing hydrophobic core residues. We conclude that the structural stability of hydrophobic cores is critical for a stable homodimer complex and this stable property can be bestowed by residues outside of hydrophobic core. The important organizing activity of Phe(25) for homodimerization of 14-3-3σ originates from its unique physical location, rigidity, size, and hydrophobicity. Thus, hydrophobic residues that are not deeply buried at the oligomeric interface may play important but different roles from the buried core residues and they may promote oligomerization by organizing co-operativity of core and other residues for favorable hydrophobic and electrostatic interactions.
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Affiliation(s)
- Jing-Yuan Liu
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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58
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Singh T, Biswas D, Jayaram B. AADS--an automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors. J Chem Inf Model 2011; 51:2515-27. [PMID: 21877713 DOI: 10.1021/ci200193z] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report here a robust automated active site detection, docking, and scoring (AADS) protocol for proteins with known structures. The active site finder identifies all cavities in a protein and scores them based on the physicochemical properties of functional groups lining the cavities in the protein. The accuracy realized on 620 proteins with sizes ranging from 100 to 600 amino acids with known drug active sites is 100% when the top ten cavity points are considered. These top ten cavity points identified are then submitted for an automated docking of an input ligand/candidate molecule. The docking protocol uses an all atom energy based Monte Carlo method. Eight low energy docked structures corresponding to different locations and orientations of the candidate molecule are stored at each cavity point giving 80 docked structures overall which are then ranked using an effective free energy function and top five structures are selected. The predicted structure and energetics of the complexes agree quite well with experiment when tested on a data set of 170 protein-ligand complexes with known structures and binding affinities. The AADS methodology is implemented on an 80 processor cluster and presented as a freely accessible, easy to use tool at http://www.scfbio-iitd.res.in/dock/ActiveSite_new.jsp .
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Affiliation(s)
- Tanya Singh
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
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59
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Yeturu K, Chandra N. PocketAlign a novel algorithm for aligning binding sites in protein structures. J Chem Inf Model 2011; 51:1725-36. [PMID: 21662242 DOI: 10.1021/ci200132z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physics.iisc.ernet.in/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.
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Affiliation(s)
- Kalidas Yeturu
- Bioinformatics Centre, Indian Institute of Science, Bangalore-560012, India
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60
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Musiani F, Bellucci M, Ciurli S. Model Structures of Helicobacter pylori UreD(H) Domains: A Putative Molecular Recognition Platform. J Chem Inf Model 2011; 51:1513-20. [DOI: 10.1021/ci200183n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Matteo Bellucci
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
- Center for Magnetic Resonance (CERM), University of Florence, Florence, Italy
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61
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Virtual screening for potential inhibitors of bacterial MurC and MurD ligases. J Mol Model 2011; 18:1063-72. [PMID: 21667288 DOI: 10.1007/s00894-011-1139-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 05/25/2011] [Indexed: 12/24/2022]
Abstract
Mur ligases are bacterial enzymes involved in the cytoplasmic steps of peptidoglycan biosynthesis and are viable targets for antibacterial drug discovery. We have performed virtual screening for potential ATP-competitive inhibitors targeting MurC and MurD ligases, using a protocol of consecutive hierarchical filters. Selected compounds were evaluated for inhibition of MurC and MurD ligases, and weak inhibitors possessing dual inhibitory activity have been identified. These compounds represent new scaffolds for further optimisation towards multiple Mur ligase inhibitors with improved inhibitory potency.
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62
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Moll M, Bryant DH, Kavraki LE. The LabelHash Server and Tools for substructure-based functional annotation. Bioinformatics 2011; 27:2161-2. [DOI: 10.1093/bioinformatics/btr343] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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63
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Parca L, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M. Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. Nucleic Acids Res 2011; 39:W278-82. [PMID: 21622655 PMCID: PMC3125782 DOI: 10.1093/nar/gkr389] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phosfinder is a web server for the identification of phosphate binding sites in protein structures. Phosfinder uses a structural comparison algorithm to scan a query structure against a set of known 3D phosphate binding motifs. Whenever a structural similarity between the query protein and a phosphate binding motif is detected, the phosphate bound by the known motif is added to the protein structure thus representing a putative phosphate binding site. Predicted binding sites are then evaluated according to (i) their position with respect to the query protein solvent-excluded surface and (ii) the conservation of the binding residues in the protein family. The server accepts as input either the PDB code of the protein to be analyzed or a user-submitted structure in PDB format. All the search parameters are user modifiable. Phosfinder outputs a list of predicted binding sites with detailed information about their structural similarity with known phosphate binding motifs, and the conservation of the residues involved. A graphical applet allows the user to visualize the predicted binding sites on the query protein structure. The results on a set of 52 apo/holo structure pairs show that the performance of our method is largely unaffected by ligand-induced conformational changes. Phosfinder is available at http://phosfinder.bio.uniroma2.it.
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Affiliation(s)
- Luca Parca
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy
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64
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Zhang T, Liu LA, Lewis DFV, Wei DQ. Long-Range Effects of a Peripheral Mutation on the Enzymatic Activity of Cytochrome P450 1A2. J Chem Inf Model 2011; 51:1336-46. [DOI: 10.1021/ci200112b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tao Zhang
- State Key Laboratory of Microbial Metabolism (Shanghai Jiao Tong University), Luc Montagnier Biomedical Research Institute, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai Minhang District, China 200240
| | - Limin Angela Liu
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States 98109
| | - David F. V. Lewis
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, U.K
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism (Shanghai Jiao Tong University), Luc Montagnier Biomedical Research Institute, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai Minhang District, China 200240
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65
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Pacios LF, Tordesillas L, Palacín A, Sánchez-Monge R, Salcedo G, Díaz-Perales A. LocaPep: Localization of Epitopes on Protein Surfaces Using Peptides from Phage Display Libraries. J Chem Inf Model 2011; 51:1465-73. [DOI: 10.1021/ci200059c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Luis F. Pacios
- Department Biotecnología, ETSI Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Leticia Tordesillas
- Department Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Arantxa Palacín
- Department Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Rosa Sánchez-Monge
- Department Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Gabriel Salcedo
- Department Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Araceli Díaz-Perales
- Department Biotecnología, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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66
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Carl N, Konc J, Vehar B, Janezic D. Protein-protein binding site prediction by local structural alignment. J Chem Inf Model 2011; 50:1906-13. [PMID: 20919700 DOI: 10.1021/ci100265x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Generalization of an earlier algorithm has led to the development of new local structural alignment algorithms for prediction of protein-protein binding sites. The algorithms use maximum cliques on protein graphs to define structurally similar protein regions. The search for structural neighbors in the new algorithms has been extended to all the proteins in the PDB and the query protein is compared to more than 60,000 proteins or over 300,000 single-chain structures. The resulting structural similarities are combined and used to predict the protein binding sites. This study shows that the location of protein binding sites can be predicted by comparing only local structural similarities irrespective of general protein folds.
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Affiliation(s)
- Nejc Carl
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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67
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Škedelj V, Tomašić T, Mašič LP, Zega A. ATP-binding site of bacterial enzymes as a target for antibacterial drug design. J Med Chem 2011; 54:915-29. [PMID: 21235241 DOI: 10.1021/jm101121s] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Veronika Škedelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
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