301
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Aeluri M, Chamakuri S, Dasari B, Guduru SKR, Jimmidi R, Jogula S, Arya P. Small Molecule Modulators of Protein–Protein Interactions: Selected Case Studies. Chem Rev 2014; 114:4640-94. [DOI: 10.1021/cr4004049] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Madhu Aeluri
- Dr. Reddy’s Institute
of Life Sciences (DRILS), University of Hyderabad Campus Gachibowli, Hyderabad 500046, India
| | - Srinivas Chamakuri
- Dr. Reddy’s Institute
of Life Sciences (DRILS), University of Hyderabad Campus Gachibowli, Hyderabad 500046, India
| | - Bhanudas Dasari
- Dr. Reddy’s Institute
of Life Sciences (DRILS), University of Hyderabad Campus Gachibowli, Hyderabad 500046, India
| | - Shiva Krishna Reddy Guduru
- Dr. Reddy’s Institute
of Life Sciences (DRILS), University of Hyderabad Campus Gachibowli, Hyderabad 500046, India
| | - Ravikumar Jimmidi
- Dr. Reddy’s Institute
of Life Sciences (DRILS), University of Hyderabad Campus Gachibowli, Hyderabad 500046, India
| | - Srinivas Jogula
- Dr. Reddy’s Institute
of Life Sciences (DRILS), University of Hyderabad Campus Gachibowli, Hyderabad 500046, India
| | - Prabhat Arya
- Dr. Reddy’s Institute
of Life Sciences (DRILS), University of Hyderabad Campus Gachibowli, Hyderabad 500046, India
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302
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Prediction of multi-type membrane proteins in human by an integrated approach. PLoS One 2014; 9:e93553. [PMID: 24676214 PMCID: PMC3968155 DOI: 10.1371/journal.pone.0093553] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/05/2014] [Indexed: 11/29/2022] Open
Abstract
Membrane proteins were found to be involved in various cellular processes performing various important functions, which are mainly associated to their types. However, it is very time-consuming and expensive for traditional biophysical methods to identify membrane protein types. Although some computational tools predicting membrane protein types have been developed, most of them can only recognize one kind of type. Therefore, they are not as effective as one membrane protein can have several types at the same time. To our knowledge, few methods handling multiple types of membrane proteins were reported. In this study, we proposed an integrated approach to predict multiple types of membrane proteins by employing sequence homology and protein-protein interaction network. As a result, the prediction accuracies reached 87.65%, 81.39% and 70.79%, respectively, by the leave-one-out test on three datasets. It outperformed the nearest neighbor algorithm adopting pseudo amino acid composition. The method is anticipated to be an alternative tool for identifying membrane protein types. New metrics for evaluating performances of methods dealing with multi-label problems were also presented. The program of the method is available upon request.
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303
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Reuter C, Kleczka M, de Mazancourt S, Neudörfl JM, Kühne R, Schmalz HG. Stereoselective Synthesis of Proline-Derived Dipeptide Scaffolds (ProM-3 and ProM-7) Rigidified in a PPII Helix Conformation. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301875] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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304
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Using a combined computational-experimental approach to predict antibody-specific B cell epitopes. Structure 2014; 22:646-57. [PMID: 24631463 DOI: 10.1016/j.str.2014.02.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/23/2014] [Accepted: 02/01/2014] [Indexed: 11/22/2022]
Abstract
Antibody epitope mapping is crucial for understanding B cell-mediated immunity and required for characterizing therapeutic antibodies. In contrast to T cell epitope mapping, no computational tools are in widespread use for prediction of B cell epitopes. Here, we show that, utilizing the sequence of an antibody, it is possible to identify discontinuous epitopes on its cognate antigen. The predictions are based on residue-pairing preferences and other interface characteristics. We combined these antibody-specific predictions with results of cross-blocking experiments that identify groups of antibodies with overlapping epitopes to improve the predictions. We validate the high performance of this approach by mapping the epitopes of a set of antibodies against the previously uncharacterized D8 antigen, using complementary techniques to reduce method-specific biases (X-ray crystallography, peptide ELISA, deuterium exchange, and site-directed mutagenesis). These results suggest that antibody-specific computational predictions and simple cross-blocking experiments allow for accurate prediction of residues in conformational B cell epitopes.
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305
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Cukuroglu E, Gursoy A, Nussinov R, Keskin O. Non-redundant unique interface structures as templates for modeling protein interactions. PLoS One 2014; 9:e86738. [PMID: 24475173 PMCID: PMC3903793 DOI: 10.1371/journal.pone.0086738] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 12/18/2013] [Indexed: 01/16/2023] Open
Abstract
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 http://prism.ccbb.ku.edu.tr/piface.
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Affiliation(s)
- Engin Cukuroglu
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
| | - Ruth Nussinov
- National Cancer Institute, Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey
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306
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Doi T, Yoshida M, Ohsawa K, Shin-ya K, Takagi M, Uekusa Y, Yamaguchi T, Kato K, Hirokawa T, Natsume T. Total synthesis and characterization of thielocin B1 as a protein–protein interaction inhibitor of PAC3 homodimer. Chem Sci 2014. [DOI: 10.1039/c3sc53237b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We have characterized the inhibition of the protein–protein interaction of the homodimer of proteasome assembling chaperone (PAC) 3 with thielocin B1.
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Affiliation(s)
- Takayuki Doi
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578, Japan
| | - Masahito Yoshida
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578, Japan
| | - Kosuke Ohsawa
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST)
- Tokyo 135-0064, Japan
| | - Motoki Takagi
- Biomedicinal Information Research Center (BIRC)
- Japan Biological Informatics Consortium (JBIC)
- Tokyo 135-0064, Japan
| | - Yoshinori Uekusa
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science
- National Institutes of Natural Sciences
- Okazaki, Japan
- Graduate School of Pharmaceutical Sciences
- Nagoya City University
| | - Takumi Yamaguchi
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science
- National Institutes of Natural Sciences
- Okazaki, Japan
- Graduate School of Pharmaceutical Sciences
- Nagoya City University
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science
- National Institutes of Natural Sciences
- Okazaki, Japan
- Graduate School of Pharmaceutical Sciences
- Nagoya City University
| | - Takatsugu Hirokawa
- Computational Biology Research Center (CBRC)
- National Institute of Advanced Industrial Science and Technology (AIST)
- Tokyo 135-0064, Japan
| | - Tohru Natsume
- National Institute of Advanced Industrial Science and Technology (AIST)
- Tokyo 135-0064, Japan
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307
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Blanco MA, Sahin E, Robinson AS, Roberts CJ. Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation. J Phys Chem B 2013; 117:16013-28. [PMID: 24289039 DOI: 10.1021/jp409300j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semiquantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work (Grüenberger et al., J. Phys. Chem. B 2013, 117, 763), this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental value of B22 as a function of solution ionic strength for α-chymotrypsinogen A and γD-Crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependence on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino-acids/surface patches that form interprotein contacts at conditions that favor dimerization of gD-Crys. The resulting regions agree with previously found aggregation-prone sites, as well as suggesting new ones that may be important.
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Affiliation(s)
- Marco A Blanco
- Department of Chemical and Biomolecular Engineering and Center for Molecular and Engineering Thermodynamics, University of Delaware , Newark, Delaware 19176, United States
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308
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Minhas FUAA, Geiss BJ, Ben-Hur A. PAIRpred: partner-specific prediction of interacting residues from sequence and structure. Proteins 2013; 82:1142-55. [PMID: 24243399 DOI: 10.1002/prot.24479] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 11/04/2013] [Accepted: 11/09/2013] [Indexed: 11/10/2022]
Abstract
We present a novel partner-specific protein-protein interaction site prediction method called PAIRpred. Unlike most existing machine learning binding site prediction methods, PAIRpred uses information from both proteins in a protein complex to predict pairs of interacting residues from the two proteins. PAIRpred captures sequence and structure information about residue pairs through pairwise kernels that are used for training a support vector machine classifier. As a result, PAIRpred presents a more detailed model of protein binding, and offers state of the art accuracy in predicting binding sites at the protein level as well as inter-protein residue contacts at the complex level. We demonstrate PAIRpred's performance on Docking Benchmark 4.0 and recent CAPRI targets. We present a detailed performance analysis outlining the contribution of different sequence and structure features, together with a comparison to a variety of existing interface prediction techniques. We have also studied the impact of binding-associated conformational change on prediction accuracy and found PAIRpred to be more robust to such structural changes than existing schemes. As an illustration of the potential applications of PAIRpred, we provide a case study in which PAIRpred is used to analyze the nature and specificity of the interface in the interaction of human ISG15 protein with NS1 protein from influenza A virus. Python code for PAIRpred is available at http://combi.cs.colostate.edu/supplements/pairpred/.
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309
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Ahmed MH, Habtemariam M, Safo MK, Scarsdale JN, Spyrakis F, Cozzini P, Mozzarelli A, Kellogg GE. Unintended consequences? Water molecules at biological and crystallographic protein–protein interfaces. Comput Biol Chem 2013; 47:126-41. [DOI: 10.1016/j.compbiolchem.2013.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/27/2013] [Accepted: 08/27/2013] [Indexed: 01/31/2023]
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310
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Madeira PP, Bessa A, Teixeira MA, Álvares-Ribeiro L, Aires-Barros MR, Rodrigues AE, Zaslavsky BY. Study of organic compounds–water interactions by partition in aqueous two-phase systems. J Chromatogr A 2013; 1322:97-104. [DOI: 10.1016/j.chroma.2013.10.085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/24/2013] [Accepted: 10/26/2013] [Indexed: 01/07/2023]
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311
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Murugan RN, Ahn M, Lee WC, Kim HY, Song JH, Cheong C, Hwang E, Seo JH, Shin SY, Choi SH, Park JE, Bang JK. Exploring the binding nature of pyrrolidine pocket-dependent interactions in the polo-box domain of polo-like kinase 1. PLoS One 2013; 8:e80043. [PMID: 24223211 PMCID: PMC3819306 DOI: 10.1371/journal.pone.0080043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/26/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Over the years, a great deal of effort has been focused on the design and synthesis of potent, linear peptide inhibitors targeting the polo-like kinase 1 (Plk1), which is critically involved in multiple mitotic processes and has been established as an adverse prognostic marker for tumor patients. Plk1 localizes to its intracellular anchoring sites via its polo-box domain, and inhibiting the Plk1 polo-box domain has been considered as an approach to circumvent the specificity problems associated with inhibiting the conserved adenosine triphosphate-binding pocket. The polo-box domain consists of two different binding regions, such as the unique, broader pyrrolidine-binding pocket and the conserved, narrow, Tyr-rich hydrophobic channel, among the three Plk polo-box domains (Plks 1-3), respectively. Therefore, the studies that provide insights into the binding nature of the unique, broader pyrrolidine-binding pocket might lead to the development of selective Plk1-inhibitory compounds. METHODOLOGY/PRINCIPAL FINDINGS In an attempt to retain the monospecificity by targeting the unique, broader pyrrolidine-binding pocket, here, for the first time, a systematic approach was undertaken to examine the structure-activity relationship of N-terminal-truncated PLHSpTM derivatives, to apply a site-directed ligand approach using bulky aromatic and non-aromatic systems, and to characterize the binding nature of these analogues using X-ray crystallographic studies. We have identified a new mode of binding interactions, having improved binding affinity and retaining the Plk1 polo-box domain specificity, at the pyrrolidine-binding pocket. Furthermore, our data revealed that the pyrrolidine-binding pocket was very specific to recognize a short and bulky hydrophobic ligand like adamantane, whereas the Tyr-rich hydrophobic channel was specific with lengthy and small hydrophobic groups. CONCLUSION/SIGNIFICANCE The progress made using our site-directed ligands validated this approach to specifically direct the ligand into the unique pyrrolidine-binding region, and it extends the applicability of the strategy for discovering selective protein-protein interaction inhibitors.
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Affiliation(s)
- Ravichandran N. Murugan
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Mija Ahn
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Woo Cheol Lee
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Hye-Yeon Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Jung Hyun Song
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Chaejoon Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Eunha Hwang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Ji-Hyung Seo
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Song Yub Shin
- Department of Bio-Materials, Graduate School and Department of Cellular & Molecular Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Sun Ho Choi
- Dong-A ST, Research Laboratories, YongIn, Gyeonggi-do, Republic of Korea
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeong Kyu Bang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
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312
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Chaurasia S, Pieraccini S, De Gonda R, Conti S, Sironi M. Molecular insights into the stabilization of protein–protein interactions with small molecule: The FKBP12–rapamycin–FRB case study. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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313
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Góngora-Benítez M, Tulla-Puche J, Albericio F. Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics. Chem Rev 2013; 114:901-26. [DOI: 10.1021/cr400031z] [Citation(s) in RCA: 388] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miriam Góngora-Benítez
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Judit Tulla-Puche
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
- Department
of Organic Chemistry, University of Barcelona, Barcelona, 08028 Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
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314
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Perato S, Fogha J, Sebban M, Voisin-Chiret AS, Sopkova-de Oliveira Santos J, Oulyadi H, Rault S. Conformation Control of Abiotic α-Helical Foldamers. J Chem Inf Model 2013; 53:2671-80. [DOI: 10.1021/ci400365y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Serge Perato
- Normandie Université, France
- UNICAEN, CERMN (Centre d’Etudes
et de Recherche sur
le Médicament de Normandie UPRES EA 4258-FR CNRS 3038 INC3M,
Bd Becquerel), F-14032 Caen, France
| | - Jade Fogha
- Normandie Université, France
- UNICAEN, CERMN (Centre d’Etudes
et de Recherche sur
le Médicament de Normandie UPRES EA 4258-FR CNRS 3038 INC3M,
Bd Becquerel), F-14032 Caen, France
| | - Muriel Sebban
- Université de Rouen, COBRA-UMR 6014, Rue Lucien
Tesnières, F-76821 Mont-Saint-Aignan, France
| | - Anne Sophie Voisin-Chiret
- Normandie Université, France
- UNICAEN, CERMN (Centre d’Etudes
et de Recherche sur
le Médicament de Normandie UPRES EA 4258-FR CNRS 3038 INC3M,
Bd Becquerel), F-14032 Caen, France
| | - Jana Sopkova-de Oliveira Santos
- Normandie Université, France
- UNICAEN, CERMN (Centre d’Etudes
et de Recherche sur
le Médicament de Normandie UPRES EA 4258-FR CNRS 3038 INC3M,
Bd Becquerel), F-14032 Caen, France
| | - Hassan Oulyadi
- Université de Rouen, COBRA-UMR 6014, Rue Lucien
Tesnières, F-76821 Mont-Saint-Aignan, France
| | - Sylvain Rault
- Normandie Université, France
- UNICAEN, CERMN (Centre d’Etudes
et de Recherche sur
le Médicament de Normandie UPRES EA 4258-FR CNRS 3038 INC3M,
Bd Becquerel), F-14032 Caen, France
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315
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Fornili A, Pandini A, Lu HC, Fraternali F. Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles. J Chem Theory Comput 2013; 9:5127-5147. [PMID: 24250278 PMCID: PMC3827836 DOI: 10.1021/ct400486p] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Indexed: 12/13/2022]
Abstract
![]()
The
ability to interact with different partners is one of the most
important features in proteins. Proteins that bind a large number
of partners (hubs) have been often associated with intrinsic disorder.
However, many examples exist of hubs with an ordered structure, and
evidence of a general mechanism promoting promiscuity in ordered proteins
is still elusive. An intriguing hypothesis is that promiscuous binding
sites have specific dynamical properties, distinct from the rest of
the interface and pre-existing in the protein isolated state. Here,
we present the first comprehensive study of the intrinsic dynamics
of promiscuous residues in a large protein data set. Different computational
methods, from coarse-grained elastic models to geometry-based sampling
methods and to full-atom Molecular Dynamics simulations, were used
to generate conformational ensembles for the isolated proteins. The
flexibility and dynamic correlations of interface residues with a
different degree of binding promiscuity were calculated and compared
considering side chain and backbone motions, the latter both on a
local and on a global scale. The study revealed that (a) promiscuous
residues tend to be more flexible than nonpromiscuous ones, (b) this
additional flexibility has a higher degree of organization, and (c)
evolutionary conservation and binding promiscuity have opposite effects
on intrinsic dynamics. Findings on simulated ensembles were also validated
on ensembles of experimental structures extracted from the Protein
Data Bank (PDB). Additionally, the low occurrence of single nucleotide
polymorphisms observed for promiscuous residues indicated a tendency
to preserve binding diversity at these positions. A case study on
two ubiquitin-like proteins exemplifies how binding promiscuity in
evolutionary related proteins can be modulated by the fine-tuning
of the interface dynamics. The interplay between promiscuity and flexibility
highlighted here can inspire new directions in protein–protein
interaction prediction and design methods.
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Affiliation(s)
- Arianna Fornili
- Randall Division of Cell and Molecular Biophysics, King's College London , New Hunt's House, London SE1 1UL, United Kingdom
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316
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Podgornaia AI, Casino P, Marina A, Laub MT. Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling. Structure 2013; 21:1636-47. [PMID: 23954504 DOI: 10.1016/j.str.2013.07.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 06/25/2013] [Accepted: 07/03/2013] [Indexed: 02/01/2023]
Abstract
Two-component signal transduction systems typically involve a sensor histidine kinase that specifically phosphorylates a single, cognate response regulator. This protein-protein interaction relies on molecular recognition via a small set of residues in each protein. To better understand how these residues determine the specificity of kinase-substrate interactions, we rationally rewired the interaction interface of a Thermotoga maritima two-component system, HK853-RR468, to match that found in a different two-component system, Escherichia coli PhoR-PhoB. The rewired proteins interacted robustly with each other, but no longer interacted with the parent proteins. Analysis of the crystal structures of the wild-type and mutant protein complexes and a systematic mutagenesis study reveal how individual mutations contribute to the rewiring of interaction specificity. Our approach and conclusions have implications for studies of other protein-protein interactions and protein evolution and for the design of novel protein interfaces.
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Affiliation(s)
- Anna I Podgornaia
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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317
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Wu F, Minteer SD. Fluorescence Characterization of Co-immobilization-Induced Multi-Enzyme Aggregation in a Polymer Matrix Using Förster Resonance Energy Transfer (FRET): Toward the Metabolon Biomimic. Biomacromolecules 2013; 14:2739-49. [DOI: 10.1021/bm400569k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Fei Wu
- Departments of Chemistry
and Materials Science and
Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Shelley D. Minteer
- Departments of Chemistry
and Materials Science and
Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
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318
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Piatek MJ, Schramm MC, Burra DD, binShbreen A, Jankovic BR, Chowdhary R, Archer JA, Bajic VB. Simplified method for predicting a functional class of proteins in transcription factor complexes. PLoS One 2013; 8:e68857. [PMID: 23874789 PMCID: PMC3709904 DOI: 10.1371/journal.pone.0068857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 06/05/2013] [Indexed: 12/24/2022] Open
Abstract
Background Initiation of transcription is essential for most of the cellular responses to environmental conditions and for cell and tissue specificity. This process is regulated through numerous proteins, their ligands and mutual interactions, as well as interactions with DNA. The key such regulatory proteins are transcription factors (TFs) and transcription co-factors (TcoFs). TcoFs are important since they modulate the transcription initiation process through interaction with TFs. In eukaryotes, transcription requires that TFs form different protein complexes with various nuclear proteins. To better understand transcription regulation, it is important to know the functional class of proteins interacting with TFs during transcription initiation. Such information is not fully available, since not all proteins that act as TFs or TcoFs are yet annotated as such, due to generally partial functional annotation of proteins. In this study we have developed a method to predict, using only sequence composition of the interacting proteins, the functional class of human TF binding partners to be (i) TF, (ii) TcoF, or (iii) other nuclear protein. This allows for complementing the annotation of the currently known pool of nuclear proteins. Since only the knowledge of protein sequences is required in addition to protein interaction, the method should be easily applicable to many species. Results Based on experimentally validated interactions between human TFs with different TFs, TcoFs and other nuclear proteins, our two classification systems (implemented as a web-based application) achieve high accuracies in distinguishing TFs and TcoFs from other nuclear proteins, and TFs from TcoFs respectively. Conclusion As demonstrated, given the fact that two proteins are capable of forming direct physical interactions and using only information about their sequence composition, we have developed a completely new method for predicting a functional class of TF interacting protein partners with high precision and accuracy.
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Affiliation(s)
- Marek J. Piatek
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
| | - Michael C. Schramm
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
| | - Dharani D. Burra
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
| | - Abdulaziz binShbreen
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
| | - Boris R. Jankovic
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
| | - Rajesh Chowdhary
- Biomedical Informatics Research Center, MCRF, Marshfield Clinic, Marshfield, Wisconsin, United States of America
| | - John A.C. Archer
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
- * E-mail:
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319
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Qian W, Park JE, Liu F, Lee KS, Burke TR. Effects on polo-like kinase 1 polo-box domain binding affinities of peptides incurred by structural variation at the phosphoamino acid position. Bioorg Med Chem 2013; 21:3996-4003. [PMID: 22743087 PMCID: PMC3462889 DOI: 10.1016/j.bmc.2012.05.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/03/2012] [Accepted: 05/15/2012] [Indexed: 01/31/2023]
Abstract
Protein-protein interactions (PPIs) mediated by the polo-box domain (PBD) of polo-like kinase 1 (Plk1) serve important roles in cell proliferation. Critical elements in the high affinity recognition of peptides and proteins by PBD are derived from pThr/pSer-residues in the binding ligands. However, there has been little examination of pThr/pSer mimetics within a PBD context. Our current paper compares the abilities of a variety of amino acid residues and derivatives to serve as pThr/pSer replacements by exploring the role of methyl functionality at the pThr β-position and by replacing the phosphoryl group by phosphonic acid, sulfonic acid and carboxylic acids. This work sheds new light on structure activity relationships for PBD recognition of phosphoamino acid mimetics.
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Affiliation(s)
- Wenjian Qian
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, U. S. A
| | - Jung-Eun Park
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Fa Liu
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, U. S. A
| | - Kyung S. Lee
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U. S. A
| | - Terrence R. Burke
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, U. S. A
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320
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Raj M, Bullock BN, Arora PS. Plucking the high hanging fruit: a systematic approach for targeting protein-protein interactions. Bioorg Med Chem 2013; 21:4051-7. [PMID: 23267671 PMCID: PMC3622812 DOI: 10.1016/j.bmc.2012.11.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 11/08/2012] [Accepted: 11/14/2012] [Indexed: 10/27/2022]
Abstract
Development of specific ligands for protein targets that help decode the complexities of protein-protein interaction networks is a key goal for the field of chemical biology. Despite the emergence of powerful in silico and experimental high-throughput screening strategies, the discovery of synthetic ligands that selectively modulate protein-protein interactions remains a challenge for bioorganic and medicinal chemists. This Perspective discusses emerging principles for the rational design of PPI inhibitors. Fundamentally, the approach seeks to adapt nature's protein recognition principles for the design of suitable secondary structure mimetics.
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Affiliation(s)
- Monika Raj
- Department of Chemistry, New York University, NY 10003, USA
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321
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Inhibition of α-helix-mediated protein-protein interactions using designed molecules. Nat Chem 2013; 5:161-73. [PMID: 23422557 DOI: 10.1038/nchem.1568] [Citation(s) in RCA: 572] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 01/07/2013] [Indexed: 12/21/2022]
Abstract
Inhibition of protein-protein interactions (PPIs) represents a significant challenge because it is unclear how they can be effectively and selectively targeted using small molecules. Achieving this goal is critical given the defining role of these interactions in biological processes. A rational approach to inhibitor design based on the secondary structure at the interface is the focus of much research, and different classes of designed ligands have emerged, some of which effectively and selectively disrupt targeted PPIs. This Review discusses the relevance of PPIs and, in particular, the importance of α-helix-mediated PPIs to chemical biology and drug discovery with a focus on designing inhibitors, including constrained peptides, foldamers and proteomimetic-derived ligands. In doing so, key challenges and major advances in developing generic approaches for the elaboration of PPI inhibitors are highlighted. The challenges faced in developing such ligands as drug leads--and how criteria applied to these may differ from conventional small-molecule drugs--are summarized.
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322
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Heurich M, Altintas Z, Tothill IE. Computational design of peptide ligands for ochratoxin A. Toxins (Basel) 2013; 5:1202-18. [PMID: 23793075 PMCID: PMC3717777 DOI: 10.3390/toxins5061202] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/13/2013] [Accepted: 06/13/2013] [Indexed: 11/21/2022] Open
Abstract
In this paper, we describe a peptide library designed by computational modelling and the selection of two peptide sequences showing affinity towards the mycotoxin, ochratoxin A (OTA). A virtual library of 20 natural amino acids was used as building blocks to design a short peptide library against ochratoxin A template using the de novo design program, LeapFrog, and the dynamic modelling software, FlexiDock. Peptide sequences were ranked according to calculated binding scores in their capacity to bind to ochratoxin A. Two high scoring peptides with the sequences N'-Cys-Ser-Ile-Val-Glu-Asp-Gly-Lys-C' (octapeptide) and N'-Gly-Pro-Ala-Gly-Ile-Asp-Gly-Pro-Ala-Gly-Ile-Arg-Cys-C' (13-mer) were selected for synthesis from the resulting database. These synthesized peptides were characterized using a microtitre plate-based binding assay and a surface plasmon resonance biosensor (Biacore 3000). The binding assay confirmed that both de novo designed peptides did bind to ochratoxin A in vitro. SPR analysis confirmed that the peptides bind to ochratoxin A, with calculated K(D) values of ~15.7 μM (13-mer) and ~11.8 μM (octamer). The affinity of the peptides corresponds well with the molecular modelling results, as the 13-mer peptide affinity is about 1.3-times weaker than the octapeptide; this is in accordance with the binding energy values modelled by FlexiDock. This work illustrates the potential of using computational modelling to design a peptide sequence that exhibits in vitro binding affinity for a small molecular weight toxin.
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Affiliation(s)
| | | | - Ibtisam E. Tothill
- Cranfield Health, Cranfield University, Cranfield, Bedfordshire MK43 0AL, England, UK; E-Mail: (Z.A.)
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323
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Kunik V, Ofran Y. The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops. Protein Eng Des Sel 2013; 26:599-609. [DOI: 10.1093/protein/gzt027] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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324
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Kuzu G, Gursoy A, Nussinov R, Keskin O. Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. J Proteome Res 2013; 12:2641-53. [PMID: 23590674 PMCID: PMC3685852 DOI: 10.1021/pr400006k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular functions are performed through protein-protein interactions; therefore, identification of these interactions is crucial for understanding biological processes. Recent studies suggest that knowledge-based approaches are more useful than "blind" docking for modeling at large scales. However, a caveat of knowledge-based approaches is that they treat molecules as rigid structures. The Protein Data Bank (PDB) offers a wealth of conformations. Here, we exploited an ensemble of the conformations in predictions by a knowledge-based method, PRISM. We tested "difficult" cases in a docking-benchmark data set, where the unbound and bound protein forms are structurally different. Considering alternative conformations for each protein, the percentage of successfully predicted interactions increased from ~26 to 66%, and 57% of the interactions were successfully predicted in an "unbiased" scenario, in which data related to the bound forms were not utilized. If the appropriate conformation, or relevant template interface, is unavailable in the PDB, PRISM could not predict the interaction successfully. The pace of the growth of the PDB promises a rapid increase of ensemble conformations emphasizing the merit of such knowledge-based ensemble strategies for higher success rates in protein-protein interaction predictions on an interactome scale. We constructed the structural network of ERK interacting proteins as a case study.
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Affiliation(s)
- Guray Kuzu
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. National Cancer Institute, Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
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325
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Guven Maiorov E, Keskin O, Gursoy A, Nussinov R. The structural network of inflammation and cancer: merits and challenges. Semin Cancer Biol 2013; 23:243-51. [PMID: 23712403 DOI: 10.1016/j.semcancer.2013.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 05/16/2013] [Indexed: 12/14/2022]
Abstract
Inflammation, the first line of defense against pathogens can contribute to all phases of tumorigenesis, including tumor initiation, promotion and metastasis. Within this framework, the Toll-like receptor (TLR) pathway plays a central role in inflammation and cancer. Although extremely useful, the classical representation of this, and other pathways in the cellular network in terms of nodes (proteins) and edges (interactions) is incomplete. Structural pathways can help complete missing parts of such diagrams: they demonstrate in detail how signals coming from different upstream pathways merge and propagate downstream, how parallel pathways compensate each other in drug resistant mutants, how multi-subunit signaling complexes form and in particular why they are needed and how they work, how allosteric events can control these proteins and their pathways, and intricate details of feedback loops and how kick in. They can also explain the mechanisms of some oncogenic SNP mutations. Constructing structural pathways is a challenging task. Here, our goal is to provide an overview of inflammation and cancer from the structural standpoint, focusing on the TLR pathway. We use the powerful PRISM (PRotein Interactions by Structural Matching) tool to reveal important structural information of interactions in and within key orchestrators of the TLR pathway, such as MyD88.
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Affiliation(s)
- Emine Guven Maiorov
- Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istanbul, Turkey.
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326
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Prabhakaran P, Barnard A, Murphy NS, Kilner CA, Edwards TA, Wilson AJ. Aromatic Oligoamide Foldamers with a “Wet Edge” as Inhibitors of the α-Helix-Mediated p53-hDM2 Protein-Protein Interaction. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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327
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Tsai CJ, Nussinov R. The molecular basis of targeting protein kinases in cancer therapeutics. Semin Cancer Biol 2013; 23:235-42. [PMID: 23651790 DOI: 10.1016/j.semcancer.2013.04.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 04/25/2013] [Indexed: 10/26/2022]
Abstract
In this paper, we provide an overview of targeted anticancer therapies with small molecule kinase inhibitors. First, we discuss why a single constitutively active kinase emanating from a variety of aberrant genetic alterations is capable of transforming a normal cell, leading it to acquire the hallmarks of a cancer cell. To draw attention to the fact that kinase inhibition in targeted cancer therapeutics differs from conventional cytotoxic chemotherapy, we exploit a conceptual framework explaining why suppressed kinase activity will selectively kill only the so-called oncogene 'addicted' cancer cell, while sparing the healthy cell. Second, we introduce the protein kinase superfamily in light of its common active conformation with precisely positioned structural elements, and the diversified auto-inhibitory conformations among the kinase families. Understanding the detailed activation mechanism of individual kinases is essential to relate the observed oncogenic alterations to the elevated constitutively active state, to identify the mechanism of consequent drug resistance, and to guide the development of the next-generation inhibitors. To clarify the vital importance of structural guidelines in studies of oncogenesis, we explain how somatic mutations in EGFR result in kinase constitutive activation. Third, in addition to the common theme of secondary (acquired) mutations that prevent drug binding from blocking a signaling pathway which is hijacked by the aberrant activated kinase, we discuss scenarios of drug resistance and relapse by compensating lesions that bypass the inactivated pathway in a vertical or horizontal fashion. Collectively, these suggest that the future challenge of cancer therapy with small molecule kinase inhibitors will rely on the discovery of distinct combinations of optimized drugs to target individual subtypes of different cancers.
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Affiliation(s)
- Chung-Jung Tsai
- Basic Science Program, SAIC-Frederick, Inc., National Cancer Institute, Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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328
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Yao X, Ji C, Xie D, Zhang JZH. Interaction specific binding hotspots in Endonuclease colicin-immunity protein complex from MD simulations. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4877-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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329
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Wilson AJ, Ault JR, Filby MH, Philips HIA, Ashcroft AE, Fletcher NC. Protein destabilisation by ruthenium(II) tris-bipyridine based protein-surface mimetics. Org Biomol Chem 2013; 11:2206-12. [PMID: 23411505 PMCID: PMC3731202 DOI: 10.1039/c3ob26251k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Highly functionalised ruthenium(II) tris-bipyridine receptor 1 which acts as a selective sensor for equine cytochrome c (cyt c) is shown to destabilise the native protein conformation by around 25 °C. Receptors 2 and 3 do not exert this effect confirming the behaviour is a specific effect of molecular recognition between 1 and cyt c, whilst the absence of a destabilising effect on 60% acetylated cyt c demonstrates the behaviour of 1 to be protein specific. Molecular recognition also modifies the conformational properties of the target protein at room temperature as evidenced by ion-mobility spectrometry (IMS) and accelerated trypsin proteolysis.
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Affiliation(s)
- Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom.
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330
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Papaleo E, Renzetti G, Invernizzi G, Ásgeirsson B. Dynamics fingerprint and inherent asymmetric flexibility of a cold-adapted homodimeric enzyme. A case study of the Vibrio alkaline phosphatase. Biochim Biophys Acta Gen Subj 2013; 1830:2970-80. [DOI: 10.1016/j.bbagen.2012.12.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 01/31/2023]
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331
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Murphy NS, Prabhakaran P, Azzarito V, Plante JP, Hardie MJ, Kilner CA, Warriner SL, Wilson AJ. Solid-phase methodology for synthesis of O-alkylated aromatic oligoamide inhibitors of α-helix-mediated protein-protein interactions. Chemistry 2013; 19:5546-50. [PMID: 23508712 PMCID: PMC3743211 DOI: 10.1002/chem.201204098] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Indexed: 01/18/2023]
Abstract
Rapid access to rigid rods: A method is described for the synthesis of 3-O-alkylated aromatic oligobenzamide foldamers that could be used for assembly of libraries of α-helix mimetic inhibitors of protein-protein interactions (see scheme; Fmoc=9-fluorenylmethoxycarbonyl).
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Affiliation(s)
- Natasha S Murphy
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK
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332
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Luo Q, Hamer R, Reinert G, Deane CM. Local network patterns in protein-protein interfaces. PLoS One 2013; 8:e57031. [PMID: 23520460 PMCID: PMC3592891 DOI: 10.1371/journal.pone.0057031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 01/21/2013] [Indexed: 11/25/2022] Open
Abstract
Protein-protein interfaces hold the key to understanding protein-protein interactions. In this paper we investigated local interaction network patterns beyond pair-wise contact sites by considering interfaces as contact networks among residues. A contact site was defined as any residue on the surface of one protein which was in contact with a residue on the surface of another protein. We labeled the sub-graphs of these contact networks by their amino acid types. The observed distributions of these labeled sub-graphs were compared with the corresponding background distributions and the results suggested that there were preferred chemical patterns of closely packed residues at the interface. These preferred patterns point to biological constraints on physical proximity between those residues on one protein which were involved in binding to residues which were close on the interacting partner. Interaction interfaces were far from random and contain information beyond pairs and triangles. To illustrate the possible application of the local network patterns observed, we introduced a signature method, called iScore, based on these local patterns to assess interface predictions. On our data sets iScore achieved 83.6% specificity with 82% sensitivity.
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Affiliation(s)
- Qiang Luo
- Department of Management, College of Information Systems and Management, National University of Defense Technology, Changsha, Hunan, PR China.
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333
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Walter P, Metzger J, Thiel C, Helms V. Predicting where small molecules bind at protein-protein interfaces. PLoS One 2013; 8:e58583. [PMID: 23505538 PMCID: PMC3591369 DOI: 10.1371/journal.pone.0058583] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 02/07/2013] [Indexed: 11/25/2022] Open
Abstract
Small molecules that bind at protein-protein interfaces may either block or stabilize protein-protein interactions in cells. Thus, some of these binding interfaces may turn into prospective targets for drug design. Here, we collected 175 pairs of protein-protein (PP) complexes and protein-ligand (PL) complexes with known three-dimensional structures for which (1) one protein from the PP complex shares at least 40% sequence identity with the protein from the PL complex, and (2) the interface regions of these proteins overlap at least partially with each other. We found that those residues of the interfaces that may bind the other protein as well as the small molecule are evolutionary more conserved on average, have a higher tendency of being located in pockets and expose a smaller fraction of their surface area to the solvent than the remaining protein-protein interface region. Based on these findings we derived a statistical classifier that predicts patches at binding interfaces that have a higher tendency to bind small molecules. We applied this new prediction method to more than 10 000 interfaces from the protein data bank. For several complexes related to apoptosis the predicted binding patches were in direct contact to co-crystallized small molecules.
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Affiliation(s)
- Peter Walter
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Jennifer Metzger
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Christoph Thiel
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- * E-mail:
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334
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A synthetic nanomaterial for virus recognition produced by surface imprinting. Nat Commun 2013; 4:1503. [PMID: 23422671 DOI: 10.1038/ncomms2529] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/21/2013] [Indexed: 01/07/2023] Open
Abstract
Major stumbling blocks in the production of fully synthetic materials designed to feature virus recognition properties are that the target is large and its self-assembled architecture is fragile. Here we describe a synthetic strategy to produce organic/inorganic nanoparticulate hybrids that recognize non-enveloped icosahedral viruses in water at concentrations down to the picomolar range. We demonstrate that these systems bind a virus that, in turn, acts as a template during the nanomaterial synthesis. These virus imprinted particles then display remarkable selectivity and affinity. The reported method, which is based on surface imprinting using silica nanoparticles that act as a carrier material and organosilanes serving as biomimetic building blocks, goes beyond simple shape imprinting. We demonstrate the formation of a chemical imprint, comparable to the formation of biosilica, due to the template effect of the virion surface on the synthesis of the recognition material.
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335
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Andorf CM, Honavar V, Sen TZ. Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PLoS One 2013; 8:e56833. [PMID: 23431393 PMCID: PMC3576370 DOI: 10.1371/journal.pone.0056833] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 01/16/2013] [Indexed: 02/01/2023] Open
Abstract
Background Protein-protein interactions are critical to elucidating the role played by individual proteins in important biological pathways. Of particular interest are hub proteins that can interact with large numbers of partners and often play essential roles in cellular control. Depending on the number of binding sites, protein hubs can be classified at a structural level as singlish-interface hubs (SIH) with one or two binding sites, or multiple-interface hubs (MIH) with three or more binding sites. In terms of kinetics, hub proteins can be classified as date hubs (i.e., interact with different partners at different times or locations) or party hubs (i.e., simultaneously interact with multiple partners). Methodology Our approach works in 3 phases: Phase I classifies if a protein is likely to bind with another protein. Phase II determines if a protein-binding (PB) protein is a hub. Phase III classifies PB proteins as singlish-interface versus multiple-interface hubs and date versus party hubs. At each stage, we use sequence-based predictors trained using several standard machine learning techniques. Conclusions Our method is able to predict whether a protein is a protein-binding protein with an accuracy of 94% and a correlation coefficient of 0.87; identify hubs from non-hubs with 100% accuracy for 30% of the data; distinguish date hubs/party hubs with 69% accuracy and area under ROC curve of 0.68; and SIH/MIH with 89% accuracy and area under ROC curve of 0.84. Because our method is based on sequence information alone, it can be used even in settings where reliable protein-protein interaction data or structures of protein-protein complexes are unavailable to obtain useful insights into the functional and evolutionary characteristics of proteins and their interactions. Availability We provide a web server for our three-phase approach: http://hybsvm.gdcb.iastate.edu.
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Affiliation(s)
- Carson M. Andorf
- Department of Computer Science, Iowa State University, Ames, Iowa, United States of America
| | - Vasant Honavar
- Department of Computer Science, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America
| | - Taner Z. Sen
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America
- United States Department of Agriculture-Agriculture Research Service Corn Insects and Crop Genetics Research Unit, Ames, Iowa, United States of America
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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336
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Sanders JM, Wampole ME, Thakur ML, Wickstrom E. Molecular determinants of epidermal growth factor binding: a molecular dynamics study. PLoS One 2013; 8:e54136. [PMID: 23382875 PMCID: PMC3554757 DOI: 10.1371/journal.pone.0054136] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 12/10/2012] [Indexed: 12/22/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of therapeutics targeting EGF ligands or the receptor itself.
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Affiliation(s)
- Jeffrey M. Sanders
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Matthew E. Wampole
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Mathew L. Thakur
- Department of Radiology, Thomas Jefferson Medical College, Philadelphia, Pennsylvania, United States of America
- Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Eric Wickstrom
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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337
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Yonamine Y, Yoshimatsu K, Lee SH, Hoshino Y, Okahata Y, Shea KJ. Polymer nanoparticle-protein interface. Evaluation of the contribution of positively charged functional groups to protein affinity. ACS APPLIED MATERIALS & INTERFACES 2013; 5:374-379. [PMID: 23259461 DOI: 10.1021/am302404q] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cationic-functionalized polymer nanoparticles (NPs) show strikingly distinct affinities to proteins depending on the nature of the cationic functional group. N-Isopropylacrylamide (NIPAm) polymer NPs incorporating three types of positively charged functional groups (guanidinium, primary amino, and quaternary ammonium groups) were prepared by precipitation polymerization. The affinities to fibrinogen, a protein with an isoelectric point (pI) of 5.5, were compared using UV-vis spectrometry and a quartz crystal microbalance (QCM). Guanidinium-containing NPs showed the highest affinity to fibrinogen. The observation is attributed to strong, specific interactions with carboxylate groups on the protein surface. The affinity of the positively charged NPs to proteins with a range of pIs revealed that protein-NP affinity is due to a combination of ionic, hydrogen bonding, and hydrophobic interactions. Protein affinity can be modulated by varying the composition of these functional monomers in the acrylamide NPs. Engineered NPs containing the guanidinium group with hydrophobic and hydrogen bonding functional groups were used in an affinity precipitation for the selective separation of fibrinogen from a plasma protein mixture. Circular dichroism (CD) revealed that the protein was not denatured in the process of binding or release.
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Affiliation(s)
- Yusuke Yonamine
- Department of Chemistry, University of California Irvine, Irvine, California 92697, USA
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338
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González-González JS, Padilla-Martínez II, García-Báez EV, Franco-Hernández O, Martínez-Martínez FJ. Helical supramolecular assembly of N2,N2')bis[3-(morpholin-4-yl)propyl]-N1,N1'-(1,2-phenylene)dioxalamide dimethyl sulfoxide monosolvate. Acta Crystallogr C 2013; 69:66-9. [PMID: 23282917 DOI: 10.1107/s010827011204365x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 10/22/2012] [Indexed: 11/10/2022] Open
Abstract
In the title compound, C(24)H(36)N(6)O(6)·C(2)H(6)OS, the carbonyl groups are in an antiperiplanar conformation, with O=C-C=O torsion angles of 178.59 (15) and -172.08 (16)°. An intramolecular hydrogen-bonding pattern is depicted by four N-H...O interactions, which form two adjacent S(5)S(5) motifs, and an N-H...N interaction, which forms an S(6) ring motif. Intermolecular N-H...O hydrogen bonding and C-H...O soft interactions allow the formation of a meso-helix. The title compound is the first example of a helical 1,2-phenylenedioxalamide. The oxalamide traps one molecule of dimethyl sulfoxide through N-H...O hydrogen bonding. C-H...O soft interactions give rise to the two-dimensional structure.
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Affiliation(s)
- Juan Saulo González-González
- Instituto de Farmacobiologia, Universidad de la Cañada, Carretera Teotitlán-San Antonio Nanahuatipan Km 1.7 s/n, Paraje Titlacuatitla, CP 68540, Teotitlán de Flores Magon, Oaxaca, Mexico
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339
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Corrada D, Morra G, Colombo G. Investigating allostery in molecular recognition: insights from a computational study of multiple antibody-antigen complexes. J Phys Chem B 2013; 117:535-52. [PMID: 23240736 DOI: 10.1021/jp310753z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibody-antigen recognition plays a key role in the immune response against pathogens. Here, we have investigated various aspects of this problem by analyzing a large and diverse set of antibodies and their respective complexes with protein antigens through atomistic simulations. Common features of antibody response to the presence of antigens are elucidated by the analysis of the proteins' internal dynamics and coordination in different ligand states, combined with the analysis of the interaction networks implicated in the stabilization of functional structures. The use of a common structural reference reveals preferential changes in the dynamic coordination and intramolecular interaction networks induced by antigen binding and shared by all antibodies. Such changes propagate from the binding region through the whole immunoglobulin domains. Overall, complexed antibodies show more diffuse networks of nonbonded interactions and a general higher internal dynamic coordination, which preferentially involve the immunoglobulin (Ig) domains of the heavy chain. The combined results provide atomistic insights into the correlations between the modulation of conformational dynamics, structural stability, and allosteric signal transduction. In particular, the results suggest that specific networks of residues, shared among all the analyzed proteins, define the molecular pathways by which antibody structures respond to antigen binding. Our studies may have implications in practical use, such as the rational design of antibodies with specifically modulated antigen-binding affinities.
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Affiliation(s)
- Dario Corrada
- Istituto di Chimica del Riconoscimento Molecolare - Consiglio Nazionale delle Ricerche (CNR-ICRM), via Mario Bianco 9, 20131 Milano, Italy
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340
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Levy ED, Teichmann S. Structural, evolutionary, and assembly principles of protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:25-51. [PMID: 23663964 DOI: 10.1016/b978-0-12-386931-9.00002-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
In the protein universe, 30-50% of proteins self-assemble to form symmetrical complexes consisting of multiple copies of themselves, called homomers. The prevalence of homomers motivates us to review many of their properties. In Section 1, we describe the methods and challenges associated with quaternary structure inference-these methods are indeed at the basis of any analysis on homomers. In Section 2, we describe the morphological properties of homomers, as well as the database 3DComplex, which provides a taxonomy for both homomeric and heteromeric protein complexes. In Section 3, we review interface properties of homomeric complexes. In Section 4, we then present recent findings on the evolution of homomer interfaces, which we link in Section 5 to the evolution of homomers as entire entities. In Section 6, we discuss mechanisms involved in their assembly and how these mechanisms can be linked to evolution.
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Affiliation(s)
- Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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341
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Bouhallab S, Croguennec T. Spontaneous Assembly and Induced Aggregation of Food Proteins. ADVANCES IN POLYMER SCIENCE 2013. [DOI: 10.1007/12_2012_201] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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342
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Dasgupta B, Nakamura H, Kinjo AR. Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin. Protein Sci 2012; 22:168-78. [PMID: 23169174 DOI: 10.1002/pro.2195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/15/2012] [Accepted: 11/09/2012] [Indexed: 11/07/2022]
Abstract
Date hub proteins are a type of proteins that show multispecificity in a time-dependent manner. To understand dynamic aspects of such multispecificity we studied Ubiquitin as a typical example of a date hub protein. Here we analyzed 9 biologically relevant Ubiquitin-protein (ligand) heterodimer structures by using normal mode analysis based on an elastic network model. Our result showed that the self-coupled motion of Ubiquitin in the complex, rather than its ligand-coupled motion, is similar to the motion of Ubiquitin in the unbound condition. The ligand-coupled motions are correlated to the conformational change between the unbound and bound conditions of Ubiquitin. Moreover, ligand-coupled motions favor the formation of the bound states, due to its in-phase movements of the contacting atoms at the interface. The self-coupled motions at the interface indicated loss of conformational entropy due to binding. Therefore, such motions disfavor the formation of the bound state. We observed that the ligand-coupled motions are embedded in the motions of unbound Ubiquitin. In conclusion, multispecificity of Ubiquitin can be characterized by an intricate balance of the ligand- and self-coupled motions, both of which are embedded in the motions of the unbound form.
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Affiliation(s)
- Bhaskar Dasgupta
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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343
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Structural and functional analysis of multi-interface domains. PLoS One 2012; 7:e50821. [PMID: 23272073 PMCID: PMC3522720 DOI: 10.1371/journal.pone.0050821] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 10/29/2012] [Indexed: 02/03/2023] Open
Abstract
A multi-interface domain is a domain that can shape multiple and distinctive binding sites to contact with many other domains, forming a hub in domain-domain interaction networks. The functions played by the multiple interfaces are usually different, but there is no strict bijection between the functions and interfaces as some subsets of the interfaces play the same function. This work applies graph theory and algorithms to discover fingerprints for the multiple interfaces of a domain and to establish associations between the interfaces and functions, based on a huge set of multi-interface proteins from PDB. We found that about 40% of proteins have the multi-interface property, however the involved multi-interface domains account for only a tiny fraction (1.8%) of the total number of domains. The interfaces of these domains are distinguishable in terms of their fingerprints, indicating the functional specificity of the multiple interfaces in a domain. Furthermore, we observed that both cooperative and distinctive structural patterns, which will be useful for protein engineering, exist in the multiple interfaces of a domain.
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344
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Kastritis PL, Bonvin AMJJ. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2012; 10:20120835. [PMID: 23235262 PMCID: PMC3565702 DOI: 10.1098/rsif.2012.0835] [Citation(s) in RCA: 276] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition.
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Affiliation(s)
- Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Faculty of Science, Chemistry, Utrecht University, , Padualaan 8, Utrecht, The Netherlands
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345
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Białońska A, Bronisz R, Kusz J, Weselski M, Zubko M. How Nonequivalency of the Flexibility of the Ligand Bridges Leads to Anisotropy of Perturbation Transmission in a 3D Spin‐Crossover Coordination Network. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200645] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Agata Białońska
- Faculty of Chemistry, University of Wrocław, F. Joliot‐Curie 14, 50‐383, Wrocław, Poland
| | - Robert Bronisz
- Faculty of Chemistry, University of Wrocław, F. Joliot‐Curie 14, 50‐383, Wrocław, Poland
| | - Joachim Kusz
- Institute of Physics, University of Silesia, 40007 Katowice, Poland
| | - Marek Weselski
- Faculty of Chemistry, University of Wrocław, F. Joliot‐Curie 14, 50‐383, Wrocław, Poland
| | - Maciej Zubko
- Institute of Physics, University of Silesia, 40007 Katowice, Poland
- Current address: Institute of Materials Science, University of Silesia, 40007 Katowice, Poland
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346
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Trana EN, Nocek JM, Knutson AK, Hoffman BM. Evolving the [myoglobin, cytochrome b(5)] complex from dynamic toward simple docking: charging the electron transfer reactive patch. Biochemistry 2012; 51:8542-53. [PMID: 23067206 DOI: 10.1021/bi301134f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We describe photoinitiated electron transfer (ET) from a suite of Zn-substituted myoglobin (Mb) variants to cytochrome b(5) (b(5)). An electrostatic interface redesign strategy has led to the introduction of positive charges into the vicinity of the heme edge through D/E → K charge-reversal mutation combinations at "hot spot" residues (D44, D60, and E85), augmented by the elimination of negative charges from Mb or b(5) by neutralization of heme propionates. These variations create an unprecedentedly large range in the product of the ET partners' total charges (-5 < -q(Mb)q(b(5)) < 40). The binding affinity (K(a)) increases 1000-fold as -q(Mb)q(b(5)) increases through this range and exhibits a surprisingly simple, exponential dependence on -q(Mb)q(b(5)). This is explained in terms of electrostatic interactions between a "charged reactive patch" (crp) on each partner's surface, defined as a compact region around the heme edge that (i) contains the total protein charge of each variant and (ii) encompasses a major fraction of the "reactive region" (Rr) comprising surface atoms with large matrix elements for electron tunneling to the heme. As -q(Mb)q(b(5)) increases, the complex undergoes a transition from fast to slow-exchange dynamics on the triplet ET time scale, with a correlated progression in the rate constants for intracomplex (k(et)) and bimolecular (k(2)) ET. This progression is analyzed by integrating the crp and Rr descriptions of ET into the textbook steady-state treatment of reversible binding between partners that undergo intracomplex ET and found to encompass the full range of behaviors predicted by the model. The generality of this approach is demonstrated by its application to the extensive body of data for the ET complex between the photosynthetic reaction center and cytochrome c(2). Deviations from this model also are discussed.
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Affiliation(s)
- Ethan N Trana
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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347
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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348
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Engin HB, Keskin O, Nussinov R, Gursoy A. A strategy based on protein-protein interface motifs may help in identifying drug off-targets. J Chem Inf Model 2012; 52:2273-86. [PMID: 22817115 PMCID: PMC3979525 DOI: 10.1021/ci300072q] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Networks are increasingly used to study the impact of drugs at the systems level. From the algorithmic standpoint, a drug can "attack" nodes or edges of a protein-protein interaction network. In this work, we propose a new network strategy, "The Interface Attack", based on protein-protein interfaces. Similar interface architectures can occur between unrelated proteins. Consequently, in principle, a drug that binds to one has a certain probability of binding to others. The interface attack strategy simultaneously removes from the network all interactions that consist of similar interface motifs. This strategy is inspired by network pharmacology and allows inferring potential off-targets. We introduce a network model that we call "Protein Interface and Interaction Network (P2IN)", which is the integration of protein-protein interface structures and protein interaction networks. This interface-based network organization clarifies which protein pairs have structurally similar interfaces and which proteins may compete to bind the same surface region. We built the P2IN with the p53 signaling network and performed network robustness analysis. We show that (1) "hitting" frequent interfaces (a set of edges distributed around the network) might be as destructive as eleminating high degree proteins (hub nodes), (2) frequent interfaces are not always topologically critical elements in the network, and (3) interface attack may reveal functional changes in the system better than the attack of single proteins. In the off-target detection case study, we found that drugs blocking the interface between CDK6 and CDKN2D may also affect the interaction between CDK4 and CDKN2D.
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Affiliation(s)
- H. Billur Engin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
- Sackler Inst. Of Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
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349
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Hamp T, Rost B. Alternative protein-protein interfaces are frequent exceptions. PLoS Comput Biol 2012; 8:e1002623. [PMID: 22876170 PMCID: PMC3410849 DOI: 10.1371/journal.pcbi.1002623] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 06/11/2012] [Indexed: 11/18/2022] Open
Abstract
The intricate molecular details of protein-protein interactions (PPIs) are crucial for function. Therefore, measuring the same interacting protein pair again, we expect the same result. This work measured the similarity in the molecular details of interaction for the same and for homologous protein pairs between different experiments. All scores analyzed suggested that different experiments often find exceptions in the interfaces of similar PPIs: up to 22% of all comparisons revealed some differences even for sequence-identical pairs of proteins. The corresponding number for pairs of close homologs reached 68%. Conversely, the interfaces differed entirely for 12-29% of all comparisons. All these estimates were calculated after redundancy reduction. The magnitude of interface differences ranged from subtle to the extreme, as illustrated by a few examples. An extreme case was a change of the interacting domains between two observations of the same biological interaction. One reason for different interfaces was the number of copies of an interaction in the same complex: the probability of observing alternative binding modes increases with the number of copies. Even after removing the special cases with alternative hetero-interfaces to the same homomer, a substantial variability remained. Our results strongly support the surprising notion that there are many alternative solutions to make the intricate molecular details of PPIs crucial for function.
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Affiliation(s)
- Tobias Hamp
- TUM, Bioinformatik - I12, Informatik, Garching, Germany
| | - Burkhard Rost
- TUM, Bioinformatik - I12, Informatik, Garching, Germany
- Institute of Advanced Study (IAS), TUM, Garching, Germany
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- * E-mail:
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350
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Features of protein-protein interactions that translate into potent inhibitors: topology, surface area and affinity. Expert Rev Mol Med 2012; 14:e16. [PMID: 22831787 DOI: 10.1017/erm.2012.10] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-protein interactions (PPIs) control the assembly of multi-protein complexes and, thus, these contacts have enormous potential as drug targets. However, the field has produced a mix of both exciting success stories and frustrating challenges. Here, we review known examples and explore how the physical features of a PPI, such as its affinity, hotspots, off-rates, buried surface area and topology, might influence the chances of success in finding inhibitors. This analysis suggests that concise, tight binding PPIs are most amenable to inhibition. However, it is also clear that emerging technical methods are expanding the repertoire of 'druggable' protein contacts and increasing the odds against difficult targets. In particular, natural product-like compound libraries, high throughput screens specifically designed for PPIs and approaches that favour discovery of allosteric inhibitors appear to be attractive routes. The first group of PPI inhibitors has entered clinical trials, further motivating the need to understand the challenges and opportunities in pursuing these types of targets.
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