1
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Levillayer L, Brighelli C, Demeret C, Sakuntabhai A, Bureau JF. Role of two modules controlling the interaction between SKAP1 and SRC kinases comparison with SKAP2 architecture and consequences for evolution. PLoS One 2024; 19:e0296230. [PMID: 38483858 PMCID: PMC10939263 DOI: 10.1371/journal.pone.0296230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
SRC kinase associated phosphoprotein 1 (SKAP1), an adaptor for protein assembly, plays an important role in the immune system such as stabilizing immune synapses. Understanding how these functions are controlled at the level of the protein-protein interactions is necessary to describe these processes and to develop therapeutics. Here, we dissected the SKAP1 modular organization to recognize SRC kinases and compared it to that of its paralog SRC kinase associated phosphoprotein 2 (SKAP2). Different conserved motifs common to either both proteins or specific to SKAP2 were found using this comparison. Two modules harboring different binding properties between SKAP1 and SKAP2 were identified: one composed of two conserved motifs located in the second interdomain interacting at least with the SH2 domain of SRC kinases and a second one composed of the DIM domain modulated by the SH3 domain and the activation of SRC kinases. This work suggests a convergent evolution of the binding properties of some SRC kinases interacting specifically with either SKAP1 or SKAP2.
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Affiliation(s)
- Laurine Levillayer
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Camille Brighelli
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Caroline Demeret
- Institut Pasteur, Université de Paris-Cité, Laboratoire Interactomique, ARN et Immunité ‐ Interactomics, RNA and Immunity, Paris, France
| | - Anavaj Sakuntabhai
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Jean-François Bureau
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
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2
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Yehorova D, Crean RM, Kasson PM, Kamerlin SCL. Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families. Protein Sci 2024; 33:e4911. [PMID: 38358258 PMCID: PMC10868456 DOI: 10.1002/pro.4911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction networks across evolutionarily related groups of proteins. KIN is available for download under a GNU General Public License, version 2, from https://www.github.com/kamerlinlab/KIN. KIN can operate on experimentally determined structures, predicted structures, or molecular dynamics trajectories, providing insight into both conserved and missing interactions across evolutionarily related proteins. This provides useful insight both into protein evolution, as well as a tool that can be exploited for protein engineering efforts. As a showcase system, we demonstrate applications of this tool to understanding the evolutionary-relevant conserved interaction networks across the class A β-lactamases.
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Affiliation(s)
- Dariia Yehorova
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rory M Crean
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Peter M Kasson
- Department of Molecular Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Shina C L Kamerlin
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
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3
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Sidhanta SPD, Sowdhamini R, Srinivasan N. Comparative analysis of permanent and transient domain-domain interactions in multi-domain proteins. Proteins 2023. [PMID: 37828826 DOI: 10.1002/prot.26581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 10/14/2023]
Abstract
Protein domains are structural, functional, and evolutionary units. These domains bring out the diversity of functionality by means of interactions with other co-existing domains and provide stability. Hence, it is important to study intra-protein inter-domain interactions from the perspective of types of interactions. Domains within a chain could interact over short timeframes or permanently, rather like protein-protein interactions (PPIs). However, no systematic study has been carried out between two classes, namely permanent and transient domain-domain interactions. In this work, we studied 263 two-domain proteins, belonging to either of these classes and their interfaces on the basis of several factors, such as interface area and details of interactions (number, strength, and types of interactions). We also characterized them based on residue conservation at the interface, correlation of residue motions across domains, its involvement in repeat formation, and their involvement in particular molecular processes. Finally, we could analyze the interactions arising from domains in two-domain monomeric proteins, and we observed significant differences between these two classes of domain interactions and a few similarities. This study will help to obtain a better understanding of structure-function and folding principles of multi-domain proteins.
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Affiliation(s)
| | - Ramanathan Sowdhamini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Computational Approaches to Protein Science, National Centre for Biological Sciences, Bangalore, India
- Computational Biology, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
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4
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Saibu OA, Hammed SO, Oladipo OO, Odunitan TT, Ajayi TM, Adejuyigbe AJ, Apanisile BT, Oyeneyin OE, Oluwafemi AT, Ayoola T, Olaoba OT, Alausa AO, Omoboyowa DA. Protein-protein interaction and interference of carcinogenesis by supramolecular modifications. Bioorg Med Chem 2023; 81:117211. [PMID: 36809721 DOI: 10.1016/j.bmc.2023.117211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023]
Abstract
Protein-protein interactions (PPIs) are essential in normal biological processes, but they can become disrupted or imbalanced in cancer. Various technological advancements have led to an increase in the number of PPI inhibitors, which target hubs in cancer cell's protein networks. However, it remains difficult to develop PPI inhibitors with desired potency and specificity. Supramolecular chemistry has only lately become recognized as a promising method to modify protein activities. In this review, we highlight recent advances in the use of supramolecular modification approaches in cancer therapy. We make special note of efforts to apply supramolecular modifications, such as molecular tweezers, to targeting the nuclear export signal (NES), which can be used to attenuate signaling processes in carcinogenesis. Finally, we discuss the strengths and weaknesses of using supramolecular approaches to targeting PPIs.
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Affiliation(s)
- Oluwatosin A Saibu
- Department of Environmental Toxicology, Universitat Duisburg-Essen, NorthRhine-Westphalia, Germany
| | - Sodiq O Hammed
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oladapo O Oladipo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria.
| | - Tope T Odunitan
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Temitope M Ajayi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Aderonke J Adejuyigbe
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife T Apanisile
- Department of Nutrition and Dietetics, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oluwatoba E Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Adenrele T Oluwafemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Tolulope Ayoola
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olamide T Olaoba
- Department of Molecular Pathogenesis and Therapeutics, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Abdullahi O Alausa
- Department of Molecular Biology and Biotechnology, ITMO University, St Petersburg, Russia
| | - Damilola A Omoboyowa
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
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5
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Lyu Y, He R, Hu J, Wang C, Gong X. Prediction of the tetramer protein complex interaction based on CNN and SVM. Front Genet 2023; 14:1076904. [PMID: 36777731 PMCID: PMC9909274 DOI: 10.3389/fgene.2023.1076904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Protein-protein interactions play an important role in life activities. The study of protein-protein interactions helps to better understand the mechanism of protein complex interaction, which is crucial for drug design, protein function annotation and three-dimensional structure prediction of protein complexes. In this paper, we study the tetramer protein complex interaction. The research has two parts: The first part is to predict the interaction between chains of the tetramer protein complex. In this part, we proposed a feature map to represent a sample generated by two chains of the tetramer protein complex, and constructed a Convolutional Neural Network (CNN) model to predict the interaction between chains of the tetramer protein complex. The AUC value of testing set is 0.6263, which indicates that our model can be used to predict the interaction between chains of the tetramer protein complex. The second part is to predict the tetramer protein complex interface residue pairs. In this part, we proposed a Support Vector Machine (SVM) ensemble method based on under-sampling and ensemble method to predict the tetramer protein complex interface residue pairs. In the top 10 predictions, when at least one protein-protein interaction interface is correctly predicted, the accuracy of our method is 82.14%. The result shows that our method is effective for the prediction of the tetramer protein complex interface residue pairs.
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Affiliation(s)
- Yanfen Lyu
- Department of Mathematics and PhysicsScience and Engineering, Hebei University of Engineering, Handan, China
| | - Ruonan He
- School of Information, Renmin University of China, Beijing, China
| | - Jingjing Hu
- Department of Mathematics and PhysicsScience and Engineering, Hebei University of Engineering, Handan, China
| | - Chunxia Wang
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China,*Correspondence: Chunxia Wang, ; Xinqi Gong,
| | - Xinqi Gong
- Mathematical Intelligence Application Lab, Institute for Mathematical Sciences, School of Math, Renmin University of China, Beijing, China,Beijing Academy of Artificial Intelligence, Beijing, China,*Correspondence: Chunxia Wang, ; Xinqi Gong,
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6
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Lee B, Wang T. A Modular Scaffold for Controlling Transcriptional Activation via Homomeric Protein-Protein Interactions. ACS Synth Biol 2022; 11:3198-3206. [PMID: 36215660 DOI: 10.1021/acssynbio.2c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein-protein interactions (PPIs) have been extensively utilized in synthetic biology to construct artificial gene networks. However, synthetic regulation of gene expression by PPIs in E. coli has largely relied upon repressors, and existing PPI-controlled transcriptional activators have generally been employed with heterodimeric interactions. Here we report a highly modular, PPI-dependent transcriptional activator, cCadC, that was designed to be compatible with homomeric interactions. We describe the process of engineering cCadC from a transmembrane protein into a soluble cytosolic regulator. We then show that gene transcription by cCadC can be controlled by homomeric PPIs and furthermore discriminates between dimeric and higher-order interactions. Finally, we demonstrate that cCadC activity can be placed under small molecule regulation using chemically induced dimerization or ligand dependent stabilization. This work should greatly expand the scope of PPIs that can be employed in artificial gene circuits in E. coli and complements the existing repertoire of tools for transcriptional regulation in synthetic biology.
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Affiliation(s)
- ByungUk Lee
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Tina Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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7
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Chakrabarti P, Chakravarty D. Intrinsically disordered proteins/regions and insight into their biomolecular interactions. Biophys Chem 2022; 283:106769. [DOI: 10.1016/j.bpc.2022.106769] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
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8
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Jhaveri A, Maisuria D, Varga M, Mohammadyani D, Johnson ME. Thermodynamics and Free Energy Landscape of BAR-Domain Dimerization from Molecular Simulations. J Phys Chem B 2021; 125:3739-3751. [PMID: 33826319 DOI: 10.1021/acs.jpcb.0c10992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteins with BAR domains function to bind to and remodel biological membranes, where the dimerization of BAR domains is a key step in this function. These domains can dimerize in solution or after localizing to the membrane surface. Here, we characterize the binding thermodynamics of homodimerization between the LSP1 BAR domain proteins in solution, using molecular dynamics (MD) simulations. By combining the MARTINI coarse-grained protein models with enhanced sampling through metadynamics, we construct a two-dimensional free energy surface quantifying the bound versus unbound ensembles as a function of two distance variables. With this methodology, our simulations can simultaneously characterize the structures and relative stabilities of a range of sampled dimers, portraying a heterogeneous and extraordinarily stable bound ensemble, where the proper crystal structure dimer is the most stable in a 100 mM NaCl solution. Nonspecific dimers that are sampled involve contacts that are consistent with experimental structures of higher-order oligomers formed by the LSP1 BAR domain. Because the BAR dimers and oligomers can assemble on membranes, we characterize the relative alignment of the known membrane binding patches, finding that only the specific dimer is aligned to form strong interactions with the membrane. Hence, we would predict a strong selection of the specific dimer in binding to or assembling when on the membrane. Establishing the pairwise stabilities of homodimer contacts is difficult experimentally when the proteins form stable oligomers, but through the method used here, we can isolate these contacts, providing a foundation to study the same interactions on the membrane.
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Affiliation(s)
- Adip Jhaveri
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, United States
| | - Dhruw Maisuria
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, United States
| | - Matthew Varga
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, United States
| | - Dariush Mohammadyani
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, United States
| | - Margaret E Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, United States
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9
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Tandon H, de Brevern AG, Srinivasan N. Transient association between proteins elicits alteration of dynamics at sites far away from interfaces. Structure 2020; 29:371-384.e3. [PMID: 33306961 DOI: 10.1016/j.str.2020.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
Proteins are known to undergo structural changes upon binding to partner proteins. However, the prevalence, extent, location, and function of change in protein dynamics due to transient protein-protein interactions is not well documented. Here, we have analyzed a dataset of 58 protein-protein complexes of known three-dimensional structure and structures of their corresponding unbound forms to evaluate dynamics changes induced by binding. Fifty-five percent of cases showed significant dynamics change away from the interfaces. This change is not always accompanied by an observed structural change. Binding of protein partner is found to alter inter-residue communication within the tertiary structure in about 90% of cases. Also, residue motions accessible to proteins in unbound form were not always maintained in the bound form. Further analyses revealed functional roles for the distant site where dynamics change was observed. Overall, the results presented here strongly suggest that alteration of protein dynamics due to binding of a partner protein commonly occurs.
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Affiliation(s)
- Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, 75739 Paris, France; Univ Paris, UMR_S 1134, 75739 Paris, France; Institut National de la Transfusion Sanguine (INTS), 75739 Paris, France; Laboratoire d'Excellence GR-Ex, 75739 Paris, France
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10
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Lyu Y, Huang H, Gong X. A Novel Index of Contact Frequency from Noise Protein-Protein Interaction Data Help for Accurate Interface Residue Pair Prediction. Interdiscip Sci 2020; 12:204-216. [PMID: 32185690 DOI: 10.1007/s12539-020-00364-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/23/2020] [Accepted: 02/24/2020] [Indexed: 11/24/2022]
Abstract
Protein-protein interactions are important for most biological processes and have been studied for decades. However, the detailed formation mechanism of protein-protein interaction interface is still ambiguous, which makes it difficult to accurately predict the protein-protein interaction interface residue pairs. Here, we extract the interface residue-residue contacts from the decoys in the ZDOCK protein-protein complex decoy set with RMSD mostly larger than 3 Å. To accurately compute the interface residue-residue contacts, we define a new constant called interface residue pairs frequency, which counts the atom contact numbers between two interface residues. We normalize interface residue pairs frequency to pick out the top residue-residue pairs from all the possible pairs preferential to be on correct protein-protein interaction interface. When tested on 37 protein dimers from the decoy set where most decoys are incorrect, our method successfully predicts 30 protein dimers with a success rate of up to 81.1%. Higher accuracy than some other state-of-the-art methods confirmed the performance of our method.
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Affiliation(s)
- Yanfen Lyu
- Mathematical Intelligence Application Lab, Institute for Mathematical Sciences, School of Math, Renmin University of China, Beijing, 100872, China
| | - He Huang
- Mathematical Intelligence Application Lab, Institute for Mathematical Sciences, School of Math, Renmin University of China, Beijing, 100872, China
| | - Xinqi Gong
- Mathematical Intelligence Application Lab, Institute for Mathematical Sciences, School of Math, Renmin University of China, Beijing, 100872, China.
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11
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Bludau I, Aebersold R. Proteomic and interactomic insights into the molecular basis of cell functional diversity. Nat Rev Mol Cell Biol 2020; 21:327-340. [PMID: 32235894 DOI: 10.1038/s41580-020-0231-2] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
The ability of living systems to adapt to changing conditions originates from their capacity to change their molecular constitution. This is achieved by multiple mechanisms that modulate the quantitative composition and the diversity of the molecular inventory. Molecular diversification is particularly pronounced on the proteome level, at which multiple proteoforms derived from the same gene can in turn combinatorially form different protein complexes, thus expanding the repertoire of functional modules in the cell. The study of molecular and modular diversity and their involvement in responses to changing conditions has only recently become possible through the development of new 'omics'-based screening technologies. This Review explores our current knowledge of the mechanisms regulating functional diversification along the axis of gene expression, with a focus on the proteome and interactome. We explore the interdependence between different molecular levels and how this contributes to functional diversity. Finally, we highlight several recent techniques for studying molecular diversity, with specific focus on mass spectrometry-based analysis of the proteome and its organization into functional modules, and examine future directions for this rapidly growing field.
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Affiliation(s)
- Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. .,Faculty of Science, University of Zurich, Zurich, Switzerland.
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12
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Wu Z, Liao Q, Liu B. A comprehensive review and evaluation of computational methods for identifying protein complexes from protein–protein interaction networks. Brief Bioinform 2019; 21:1531-1548. [DOI: 10.1093/bib/bbz085] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 02/04/2023] Open
Abstract
Abstract
Protein complexes are the fundamental units for many cellular processes. Identifying protein complexes accurately is critical for understanding the functions and organizations of cells. With the increment of genome-scale protein–protein interaction (PPI) data for different species, various computational methods focus on identifying protein complexes from PPI networks. In this article, we give a comprehensive and updated review on the state-of-the-art computational methods in the field of protein complex identification, especially focusing on the newly developed approaches. The computational methods are organized into three categories, including cluster-quality-based methods, node-affinity-based methods and ensemble clustering methods. Furthermore, the advantages and disadvantages of different methods are discussed, and then, the performance of 17 state-of-the-art methods is evaluated on two widely used benchmark data sets. Finally, the bottleneck problems and their potential solutions in this important field are discussed.
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Affiliation(s)
- Zhourun Wu
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong, China
| | - Qing Liao
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
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13
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Alakus TB, Turkoglu I. Prediction of Protein-Protein Interactions with LSTM Deep Learning Model. 2019 3RD INTERNATIONAL SYMPOSIUM ON MULTIDISCIPLINARY STUDIES AND INNOVATIVE TECHNOLOGIES (ISMSIT) 2019. [DOI: 10.1109/ismsit.2019.8932876] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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14
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Zhang J, Zhong C, Huang Y, Lin HX, Wang M. A method for identifying protein complexes with the features of joint co-localization and joint co-expression in static PPI networks. Comput Biol Med 2019; 111:103333. [PMID: 31376777 DOI: 10.1016/j.compbiomed.2019.103333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/01/2019] [Accepted: 06/17/2019] [Indexed: 02/09/2023]
Abstract
Identifying protein complexes in static protein-protein interaction (PPI) networks is essential for understanding the underlying mechanism of biological processes. Proteins in a complex are co-localized at the same place and co-expressed at the same time. We propose a novel method to identify protein complexes with the features of joint co-localization and joint co-expression in static PPI networks. To achieve this goal, we define a joint localization vector to construct a joint co-localization criterion of a protein group, and define a joint gene expression to construct a joint co-expression criterion of a gene group. Moreover, the functional similarity of proteins in a complex is an important characteristic. Thus, we use the CC-based, MF-based, and BP-based protein similarities to devise functional similarity criterion to determine whether a protein is functionally similar to a protein cluster. Based on the core-attachment structure and following to seed expanding strategy, we use four types of biological data including PPI data with reliability score, protein localization data, gene expression data, and gene ontology annotations, to identify protein complexes. The experimental results on yeast data show that comparing with existing methods our proposed method can efficiently and exactly identify more protein complexes, especially more protein complexes of sizes from 2 to 6. Furthermore, the enrichment analysis demonstrates that the protein complexes identified by our method have significant biological meaning.
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Affiliation(s)
- Jinxiong Zhang
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China; School of Computer, Electronics and Information, Guangxi University, Nanning, China.
| | - Cheng Zhong
- School of Computer, Electronics and Information, Guangxi University, Nanning, China.
| | - Yiran Huang
- School of Computer, Electronics and Information, Guangxi University, Nanning, China.
| | - Hai Xiang Lin
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands.
| | - Mian Wang
- College of Life Science and Technology, Guangxi University, Nanning, China.
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15
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McBride Z, Chen D, Lee Y, Aryal UK, Xie J, Szymanski DB. A Label-free Mass Spectrometry Method to Predict Endogenous Protein Complex Composition. Mol Cell Proteomics 2019; 18:1588-1606. [PMID: 31186290 PMCID: PMC6683005 DOI: 10.1074/mcp.ra119.001400] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/05/2019] [Indexed: 12/15/2022] Open
Abstract
Information on the composition of protein complexes can accelerate mechanistic analyses of cellular systems. Protein complex composition identifies genes that function together and provides clues about regulation within and between cellular pathways. Cytosolic protein complexes control metabolic flux, signal transduction, protein abundance, and the activities of cytoskeletal and endomembrane systems. It has been estimated that one third of all cytosolic proteins in leaves exist in an oligomeric state, yet the composition of nearly all remain unknown. Subunits of stable protein complexes copurify, and combinations of mass-spectrometry-based protein correlation profiling and bioinformatic analyses have been used to predict protein complex subunits. Because of uncertainty regarding the power or availability of bioinformatic data to inform protein complex predictions across diverse species, it would be highly advantageous to predict composition based on elution profile data alone. Here we describe a mass spectrometry-based protein correlation profiling approach to predict the composition of hundreds of protein complexes based on biochemical data. Extracts were obtained from an intact organ and separated in parallel by size and charge under nondenaturing conditions. More than 1000 proteins with reproducible elution profiles across all replicates were subjected to clustering analyses. The resulting dendrograms were used to predict the composition of known and novel protein complexes, including many that are likely to assemble through self-interaction. An array of validation experiments demonstrated that this new method can drive protein complex discovery, guide hypothesis testing, and enable systems-level analyses of protein complex dynamics in any organism with a sequenced genome.
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Affiliation(s)
- Zachary McBride
- ‡Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana
| | - Donglai Chen
- §Department of Statistics, Purdue University, West Lafayette, Indiana
| | - Youngwoo Lee
- ‡Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana
| | - Uma K Aryal
- ¶Purdue Proteomics Facility, Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette, Indiana
| | - Jun Xie
- §Department of Statistics, Purdue University, West Lafayette, Indiana
| | - Daniel B Szymanski
- ‡Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana; ‖Department of Biological Sciences,Purdue University, West Lafayette, Indiana.
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16
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Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies. Oncotarget 2018; 7:75810-75826. [PMID: 27713118 PMCID: PMC5342780 DOI: 10.18632/oncotarget.12416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/15/2016] [Indexed: 12/14/2022] Open
Abstract
RAS proteins are the founding members of the RAS superfamily of GTPases. They are involved in key signaling pathways regulating essential cellular functions such as cell growth and differentiation. As a result, their deregulation by inactivating mutations often results in aberrant cell proliferation and cancer. With the exception of the relatively well-known KRAS, HRAS and NRAS proteins, little is known about how the interactions of the other RAS human paralogs affect cancer evolution and response to treatment. In this study we performed a comprehensive analysis of the relationship between the phylogeny of RAS proteins and their location in the protein interaction network. This analysis was integrated with the structural analysis of conserved positions in available 3D structures of RAS complexes. Our results show that many RAS proteins with divergent sequences are found close together in the human interactome. We found specific conserved amino acid positions in this group that map to the binding sites of RAS with many of their signaling effectors, suggesting that these pairs could share interacting partners. These results underscore the potential relevance of cross-talking in the RAS signaling network, which should be taken into account when considering the inhibitory activity of drugs targeting specific RAS oncoproteins. This study broadens our understanding of the human RAS signaling network and stresses the importance of considering its potential cross-talk in future therapies.
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17
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Dey S, Levy ED. Inferring and Using Protein Quaternary Structure Information from Crystallographic Data. Methods Mol Biol 2018; 1764:357-375. [PMID: 29605927 DOI: 10.1007/978-1-4939-7759-8_23] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A precise knowledge of the quaternary structure of proteins is essential to illuminate both their function and their evolution. The major part of our knowledge on quaternary structure is inferred from X-ray crystallography data, but this inference process is hard and error-prone. The difficulty lies in discriminating fortuitous protein contacts, which make up the lattice of protein crystals, from biological protein contacts that exist in the native cellular environment. Here, we review methods devised to discriminate between both types of contacts and describe resources for downloading protein quaternary structure information and identifying high-confidence quaternary structures. The use of high-confidence datasets of quaternary structures will be critical for the analysis of structural, functional, and evolutionary properties of proteins.
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Affiliation(s)
- Sucharita Dey
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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18
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Madhumitha D, Dhathathreyan A. Interaction of Myoglobin colloids with BSA in solution: Insights into complex formation and elastic compliance. Int J Biol Macromol 2017; 105:1259-1268. [DOI: 10.1016/j.ijbiomac.2017.07.157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/19/2017] [Accepted: 07/26/2017] [Indexed: 11/15/2022]
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19
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Biswas R, Bagchi A. Structural Characterization of the Trimerization of TRAF6 Protein Through Molecular Dynamics Simulations. Interdiscip Sci 2017; 11:428-436. [PMID: 28895065 DOI: 10.1007/s12539-017-0259-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/31/2017] [Accepted: 08/30/2017] [Indexed: 11/26/2022]
Abstract
The tumour necrosis factor (TNF) receptor-associated factor (TRAF) family of proteins having E3 ligase activity are the key molecules involved in cellular immune response pathways. TRAF6 is a unique member of the TRAF superfamily differing from other members of the family, owing to its specific interactions with molecules outside the TNF receptor superfamily. The C-terminal domain of TRAF proteins contains the catalytic residues and are known to be involved in self-oligomerization forming a mushroom-shaped trimeric structure, which is the functional form of the protein. However, the monomeric crystal structure of TRAF6 C-terminal domain has been already determined, but the trimeric structure of the same is still not available. We here applied computational structural modelling and molecular dynamics simulations studies to get insights into the molecular interactions involved in determining the trimeric structure of the TRAF6 C-terminal domain. The non-availability of the trimeric structure of the TRAF6 C-terminal domain prevented the elucidation of the molecular mechanism of many different biological processes. Our results suggest that the trimer complex is transient in nature. The amino acid residues Lys340 and Glu345 in the coiled coil domain in the C-terminus of TRAF6 play a critical role in trimer structure formation. This structural modelling study may therefore be utilized to obtain the experimentally validated trimeric structure of this important protein.
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Affiliation(s)
- Ria Biswas
- Department of Biochemistry and Biophysics, University of Kalyani, Nadia, Kalyani, 741235, India
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Nadia, Kalyani, 741235, India.
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20
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Holland DO, Shapiro BH, Xue P, Johnson ME. Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks. Sci Rep 2017; 7:5631. [PMID: 28717235 PMCID: PMC5514078 DOI: 10.1038/s41598-017-05686-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/01/2017] [Indexed: 01/30/2023] Open
Abstract
Protein-protein interactions networks (PPINs) are known to share a highly conserved structure across all organisms. What is poorly understood, however, is the structure of the child interface interaction networks (IINs), which map the binding sites proteins use for each interaction. In this study we analyze four independently constructed IINs from yeast and humans and find a conserved structure of these networks with a unique topology distinct from the parent PPIN. Using an IIN sampling algorithm and a fitness function trained on the manually curated PPINs, we show that IIN topology can be mostly explained as a balance between limits on interface diversity and a need for physico-chemical binding complementarity. This complementarity must be optimized both for functional interactions and against mis-interactions, and this selectivity is encoded in the IIN motifs. To test whether the parent PPIN shapes IINs, we compared optimal IINs in biological PPINs versus random PPINs. We found that the hubs in biological networks allow for selective binding with minimal interfaces, suggesting that binding specificity is an additional pressure for a scale-free-like PPIN. We confirm through phylogenetic analysis that hub interfaces are strongly conserved and rewiring of interactions between proteins involved in endocytosis preserves interface binding selectivity.
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Affiliation(s)
- David O Holland
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Benjamin H Shapiro
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pei Xue
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Margaret E Johnson
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.
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21
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Osmanović D, Rabin Y. Effect of non-specific interactions on formation and stability of specific complexes. J Chem Phys 2017; 144:205104. [PMID: 27250332 DOI: 10.1063/1.4952981] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We introduce a simple model to describe the interplay between specific and non-specific interactions. We study the influence of various physical factors on the static and dynamic properties of the specific interactions of our model and show that contrary to intuitive expectations, non-specific interactions can assist in the formation of specific complexes and increase their stability. We then discuss the relevance of these results for biological systems.
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Affiliation(s)
- Dino Osmanović
- Department of Physics, and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yitzhak Rabin
- Department of Physics, and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
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22
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Horenstein AL, Chillemi A, Quarona V, Zito A, Mariani V, Faini AC, Morandi F, Schiavoni I, Ausiello CM, Malavasi F. Antibody mimicry, receptors and clinical applications. Hum Antibodies 2017; 25:75-85. [PMID: 28035914 DOI: 10.3233/hab-160305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This review focuses on the concept of antibodies acting as receptor agonists and antagonists, and on the potential relevance of this notion in applied medicine. Antibodies are composed of three functional units: two antigen-binding fragments (Fabs) that confer antigen specificity and one constant fragment (Fc) linking antibodies to immune effector functions. The proof-of-concept that large amounts of highly specific and homogeneous antibodies could be produced was provided in 1975 by César Milstein and Georges Köhler. These monoclonal antibody (mAb) reagents started a revolution in medical research, diagnostics, and clinical applications. Alongside diagnostic applications, mAbs were successfully used in vivo: (i) to bind (neutralize/antagonize) antigens expressed on the surface of tumor cells; (ii) to activate immune effector mechanisms; (iii) to crosslink plasma membrane receptors and hence activate therapeutic signaling pathways; and lastly, (iv) the technique was expanded to produce bispecific mAbs, which can bind two different antigens while retaining the ability to activate immune effector functions. The abilities of mAbs to bind, transduce signals, and exert immunostimulatory agonistic capacities are the central issues of this review. The starting point is that some mAbs operate as molecular agonists, substituting for the natural ligand of the receptor. Our analysis is restricted to mAbs that act as receptor agonist/antagonists by either mimicking ligand binding, or through allosteric modulation mediated by binding sites that are topographically distinct from the orthosteric binding site. Functional considerations based on the agonistic stimulation of human CD38 by specific mAbs as surrogate ligands are described as examples of the features of such molecules.
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Affiliation(s)
- Alberto L Horenstein
- Laboratory of Immunogenetics, Department of Medical Sciences, University of Torino, Torino 10126, Italy
- CeRMS, University of Torino, Torino 10126, Italy
| | - Antonella Chillemi
- Laboratory of Immunogenetics, Department of Medical Sciences, University of Torino, Torino 10126, Italy
- CeRMS, University of Torino, Torino 10126, Italy
| | - Valeria Quarona
- Laboratory of Immunogenetics, Department of Medical Sciences, University of Torino, Torino 10126, Italy
- CeRMS, University of Torino, Torino 10126, Italy
| | - Andrea Zito
- Laboratory of Immunogenetics, Department of Medical Sciences, University of Torino, Torino 10126, Italy
- CeRMS, University of Torino, Torino 10126, Italy
| | - Valentina Mariani
- Laboratory of Immunogenetics, Department of Medical Sciences, University of Torino, Torino 10126, Italy
- CeRMS, University of Torino, Torino 10126, Italy
| | - Angelo C Faini
- Laboratory of Immunogenetics, Department of Medical Sciences, University of Torino, Torino 10126, Italy
- CeRMS, University of Torino, Torino 10126, Italy
| | - Fabio Morandi
- Laboratory of Oncology, Istituto Giannina Gaslini, Genova 16148, Italy
| | - Ilaria Schiavoni
- Department of Infectious, Parasitic, and Immune-Mediated Diseases, Istituto Superiore di Sanità, Roma 00161, Italy
| | - Clara Maria Ausiello
- Department of Infectious, Parasitic, and Immune-Mediated Diseases, Istituto Superiore di Sanità, Roma 00161, Italy
| | - Fabio Malavasi
- Laboratory of Immunogenetics, Department of Medical Sciences, University of Torino, Torino 10126, Italy
- CeRMS, University of Torino, Torino 10126, Italy
- Transplantation Immunology, Città della Salute e della Scienza, Torino 10126, Italy
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23
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Dai W, Wu A, Ma L, Li YX, Jiang T, Li YY. A novel index of protein-protein interface propensity improves interface residue recognition. BMC SYSTEMS BIOLOGY 2016; 10:112. [PMID: 28155660 PMCID: PMC5259823 DOI: 10.1186/s12918-016-0351-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Background Protein-protein interface holds important information of protein-protein interactions which play key roles in most biological processes. In the past few years, a lot of efforts have been made to improve interface residue recognition by characterizing protein-protein interfaces and extracting relevant features. However, most previous studies were carried out in a qualitative level, and there are also some inconsistencies between them. Results In the present work, to improve interface residue recognition, we built a novel quantitative residue protein-protein interface propensity index (QIPI) and gained a comprehensive picture of protein-protein interface through analyzing protein-protein interfaces on our comprehensive protein-protein interfaces dataset (Astral2.05-40-4506). Furthermore, in order to assess the effect of QIPI in improving the protein-protein interface prediction, we developed an interface residue recognition method SPR (Single domain based Patch Recognition) based on the QIPI. The evaluation results proved that our novel QIPI is able to improve the interface residue recognition. Conclusions Through a comprehensive quantitative analysis of protein-protein interface, we constructed a novel quantitative protein-protein interface propensity index (QIPI), which could be easily applied to improve the interface residue recognition and helpful in understanding the protein-protein interface. Availability QIPI and SPR are available to non-commercial users at our website: http://www.scbit.org/QIPI/. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0351-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wentao Dai
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 2012035, People's Republic of China.,Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Liangxiao Ma
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 2012035, People's Republic of China
| | - Yi-Xue Li
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 2012035, People's Republic of China.,Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.,Shanghai Engineering Research Center of Pharmaceutical Translation, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China
| | - Taijiao Jiang
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China. .,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 2012035, People's Republic of China. .,Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,Shanghai Engineering Research Center of Pharmaceutical Translation, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.
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24
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Zhang Y, Lin H, Yang Z, Wang J, Liu Y, Sang S. A method for predicting protein complex in dynamic PPI networks. BMC Bioinformatics 2016; 17 Suppl 7:229. [PMID: 27454775 PMCID: PMC4965712 DOI: 10.1186/s12859-016-1101-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Accurate determination of protein complexes has become a key task of system biology for revealing cellular organization and function. Up to now, the protein complex prediction methods are mostly focused on static protein protein interaction (PPI) networks. However, cellular systems are highly dynamic and responsive to cues from the environment. The shift from static PPI networks to dynamic PPI networks is essential to accurately predict protein complex. RESULTS The gene expression data contains crucial dynamic information of proteins and PPIs, along with high-throughput experimental PPI data, are valuable for protein complex prediction. Firstly, we exploit gene expression data to calculate the active time point and the active probability of each protein and PPI. The dynamic active information is integrated into high-throughput PPI data to construct dynamic PPI networks. Secondly, a novel method for predicting protein complexes from the dynamic PPI networks is proposed based on core-attachment structural feature. Our method can effectively exploit not only the dynamic active information but also the topology structure information based on the dynamic PPI networks. CONCLUSIONS We construct four dynamic PPI networks, and accurately predict many well-characterized protein complexes. The experimental results show that (i) the dynamic active information significantly improves the performance of protein complex prediction; (ii) our method can effectively make good use of both the dynamic active information and the topology structure information of dynamic PPI networks to achieve state-of-the-art protein complex prediction capabilities.
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Affiliation(s)
- Yijia Zhang
- College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China.
| | - Hongfei Lin
- College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China
| | - Zhihao Yang
- College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China
| | - Jian Wang
- College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China
| | - Yiwei Liu
- College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China
| | - Shengtian Sang
- College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China
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25
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An extended loop in CE7 carbohydrate esterase family is dispensable for oligomerization but required for activity and thermostability. J Struct Biol 2016; 194:434-45. [DOI: 10.1016/j.jsb.2016.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/07/2016] [Accepted: 04/13/2016] [Indexed: 11/20/2022]
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26
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Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution. Sci Rep 2016; 6:26737. [PMID: 27220911 PMCID: PMC4879665 DOI: 10.1038/srep26737] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/06/2016] [Indexed: 11/08/2022] Open
Abstract
Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions.
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27
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Hanna EM, Zaki N, Amin A. Detecting Protein Complexes in Protein Interaction Networks Modeled as Gene Expression Biclusters. PLoS One 2015; 10:e0144163. [PMID: 26641660 PMCID: PMC4671556 DOI: 10.1371/journal.pone.0144163] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/13/2015] [Indexed: 12/13/2022] Open
Abstract
Developing suitable methods for the detection of protein complexes in protein interaction networks continues to be an intriguing area of research. The importance of this objective originates from the fact that protein complexes are key players in most cellular processes. The more complexes we identify, the better we can understand normal as well as abnormal molecular events. Up till now, various computational methods were designed for this purpose. However, despite their notable performance, questions arise regarding potential ways to improve them, in addition to ameliorative guidelines to introduce novel approaches. A close interpretation leads to the assent that the way in which protein interaction networks are initially viewed should be adjusted. These networks are dynamic in reality and it is necessary to consider this fact to enhance the detection of protein complexes. In this paper, we present "DyCluster", a framework to model the dynamic aspect of protein interaction networks by incorporating gene expression data, through biclustering techniques, prior to applying complex-detection algorithms. The experimental results show that DyCluster leads to higher numbers of correctly-detected complexes with better evaluation scores. The high accuracy achieved by DyCluster in detecting protein complexes is a valid argument in favor of the proposed method. DyCluster is also able to detect biologically meaningful protein groups. The code and datasets used in the study are downloadable from https://github.com/emhanna/DyCluster.
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Affiliation(s)
| | - Nazar Zaki
- Intelligent Systems, College of Info. Tech., UAEU, Al Ain 17551, UAE
| | - Amr Amin
- Department of Biology, College of Science, UAEU, Al Ain 15551, UAE
- Faculty of Science, Cairo University, Cairo, Egypt
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28
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Wodak SJ, Malevanets A, MacKinnon SS. The Landscape of Intertwined Associations in Homooligomeric Proteins. Biophys J 2015; 109:1087-100. [PMID: 26340815 DOI: 10.1016/j.bpj.2015.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/06/2015] [Accepted: 08/03/2015] [Indexed: 01/22/2023] Open
Abstract
We present an overview of the full repertoire of intertwined associations in homooligomeric proteins. This overview summarizes recent findings on the different categories of intertwined associations in known protein structures, their assembly modes, the properties of their interfaces, and their structural plasticity. Furthermore, the current body of knowledge on the so-called three-dimensional domain-swapped systems is reexamined in the context of the wider landscape of intertwined homooligomers, with a particular focus on the mechanistic aspects that underpin intertwined self-association processes in proteins. Insights gained from this integrated overview into the physical and biological roles of intertwining are highlighted.
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Affiliation(s)
- Shoshana J Wodak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; VIB Structural Biology Research Center, Brussels, Belgium.
| | | | - Stephen S MacKinnon
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Cyclica, Inc., Toronto, Ontario, Canada
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29
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Arisi I, D'Onofrio M, Brandi R, Cattaneo A, Bertolazzi P, Cumbo F, Felici G, Guerra C. Time dynamics of protein complexes in the AD11 transgenic mouse model for Alzheimer's disease like pathology. BMC Neurosci 2015; 16:28. [PMID: 25925689 PMCID: PMC4436769 DOI: 10.1186/s12868-015-0155-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/11/2015] [Indexed: 11/20/2022] Open
Abstract
Background Many approaches exist to integrate protein-protein interaction data with other sources of information, most notably with gene co-expression data, to obtain information on network dynamics. It is of interest to look at groups of interacting gene products that form a protein complex. We were interested in applying new tools to the characterization of pathogenesis and dynamic events of an Alzheimer’s-like neurodegenerative model, the AD11 mice, expressing an anti-NGF monoclonal antibody. The goal was to quantify the impact of neurodegeneration on protein complexes, by measuring the correlation between gene expression data by different metrics. Results Data were extracted from the gene expression profile of AD11 brain, obtained by Agilent microarray, at 1, 3, 6, 15 months of age. For genes coding proteins in complexes, the correlation matrix of pairwise expression was computed. The dynamics between correlation matrices at different time points was evaluated: paired T-test between average correlation levels and a normalized Euclidean distance with z-score. We unveiled a differential wiring of interactions in a set of complexes, whose network structure discriminates between transgenic and control mice. Furthermore, we analyzed the dynamics of gene expression values, by looking at changes in gene-to-gene correlation over time and identified those complexes that exhibit a different timedependent behaviour between transgenic and controls. The most significant changes in correlation dynamics are concentrated in the early stage of disease, with higher correlation in AD11 mice compared to controls. Many complexes go through dynamic changes over time, showing the role of the dysfunctional immunoproteasome, as early neurodegenerative disease event. Furthermore, this analysis shows key events in the neurodegeneration process of the AD11 model, by identifying significant differences in co-expression values of other complexes, such as parvulin complex, with a role in protein misfolding and proteostasis, and of complexes involved in transcriptional mechanisms. Conclusions We have proposed a novel approach to analyze the network structure of protein complexes, by two different measures to evaluate the dynamics of gene-gene correlation matrices from gene expression profiles. The methodology was able to investigate the re-organization of interactions within protein complexes in the AD11 model of neurodegeneration.
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Affiliation(s)
- Ivan Arisi
- Genomics Facility, European Brain Research Institute (EBRI) Rita Levi-Montalcini, Via del Fosso di Fiorano, 64, 00143, Rome, Italy.
| | - Mara D'Onofrio
- Genomics Facility, European Brain Research Institute (EBRI) Rita Levi-Montalcini, Via del Fosso di Fiorano, 64, 00143, Rome, Italy.
| | - Rossella Brandi
- Genomics Facility, European Brain Research Institute (EBRI) Rita Levi-Montalcini, Via del Fosso di Fiorano, 64, 00143, Rome, Italy.
| | - Antonino Cattaneo
- Neurotrophic Factors and Neurodegenerative Diseases Unit, EBRI, Rome, Italy. .,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Paola Bertolazzi
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI-CNR), Rome, Italy.
| | - Fabio Cumbo
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI-CNR), Rome, Italy.
| | - Giovanni Felici
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI-CNR), Rome, Italy.
| | - Concettina Guerra
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI-CNR), Rome, Italy. .,College of Computing, Georgia Institute of Technology, Atlanta, GA, USA.
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30
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Module organization and variance in protein-protein interaction networks. Sci Rep 2015; 5:9386. [PMID: 25797237 PMCID: PMC4369690 DOI: 10.1038/srep09386] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 03/03/2015] [Indexed: 12/13/2022] Open
Abstract
A module is a group of closely related proteins that act in concert to perform specific biological functions through protein–protein interactions (PPIs) that occur in time and space. However, the underlying module organization and variance remain unclear. In this study, we collected module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores and interface evolution scores to describe the module elements, including core and ring components. Functions of core components were highly correlated with those of essential genes. In comparison with ring components, core proteins/PPIs were conserved across multiple species. Subsequently, protein/module variance of PPI networks confirmed that core components form dynamic network hubs and play key roles in various biological functions. Based on the analyses of gene essentiality, module variance, and gene co-expression, we summarize the observations of module organization and variance as follows: 1) a module consists of core and ring components; 2) core components perform major biological functions and collaborate with ring components to execute certain functions in some cases; 3) core components are more conserved and essential during organizational changes in different biological states or conditions.
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Extracting high confidence protein interactions from affinity purification data: at the crossroads. J Proteomics 2015; 118:63-80. [PMID: 25782749 DOI: 10.1016/j.jprot.2015.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 02/27/2015] [Accepted: 03/09/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED Deriving protein-protein interactions from data generated by affinity-purification and mass spectrometry (AP-MS) techniques requires application of scoring methods to measure the reliability of detected putative interactions. Choosing the appropriate scoring method has become a major challenge. Here we apply six popular scoring methods to the same AP-MS dataset and compare their performance. The comparison was carried out for six distinct datasets from human, fly and yeast, which focus on different biological processes and differ in their coverage of the proteome. Results show that the performance of a given scoring method may vary substantially depending on the dataset. Disturbingly, we find that the high confidence (HC) PPI networks built by applying the six scoring methods to the same raw AP-MS dataset display very poor overlap, with only 1.7-4.1% of the HC interactions present in all the networks built, respectively, from the proteome-wide human, fly or yeast datasets. Various properties of the shared versus unique interactions in each network, including biases in protein abundance, suggest that current scoring methods are able to eliminate only the most obvious contaminants, but still fail to reliably single out specific interactions from the large body of spurious associations detected in the AP-MS experiments. BIOLOGICAL SIGNIFICANCE The fast progress in AP-MS techniques has prompted the development of a multitude of scoring methods, which are relied upon to remove contaminants and non-specific binders. Choosing the appropriate scoring scheme for a given AP-MS dataset has become a major challenge. The comparative analysis of 6 of the most popular scoring methods, presented here, reveals that overall these methods do not perform as expected. Evidence is provided that this is due to 3 closely related issues: the high 'noise' levels of the raw AP-MS data, the limited capacity of current scoring methods to deal with such high noise levels, and the biases introduced using Gold Standard datasets to benchmark the scoring functions and threshold the networks. For the field to move forward, all three issues will have to be addressed. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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Abstract
The challenging task of studying and modeling complex dynamics of biological systems in order to describe various human diseases has gathered great interest in recent years. Major biological processes are mediated through protein interactions, hence there is a need to understand the chaotic network that forms these processes in pursuance of understanding human diseases. The applications of protein interaction networks to disease datasets allow the identification of genes and proteins associated with diseases, the study of network properties, identification of subnetworks, and network-based disease gene classification. Although various protein interaction network analysis strategies have been employed, grand challenges are still existing. Global understanding of protein interaction networks via integration of high-throughput functional genomics data from different levels will allow researchers to examine the disease pathways and identify strategies to control them. As a result, it seems likely that more personalized, more accurate and more rapid disease gene diagnostic techniques will be devised in the future, as well as novel strategies that are more personalized. This mini-review summarizes the current practice of protein interaction networks in medical research as well as challenges to be overcome.
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Affiliation(s)
- Tuba Sevimoglu
- Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
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Sudha G, Nussinov R, Srinivasan N. An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:141-50. [PMID: 25077409 DOI: 10.1016/j.pbiomolbio.2014.07.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/13/2014] [Indexed: 12/20/2022]
Abstract
Rich data bearing on the structural and evolutionary principles of protein-protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial 'driver' mutations in oncogenesis. They also provide the foundation toward the design of protein-protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein-protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein-protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview.
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Affiliation(s)
- Govindarajan Sudha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| | - Ruth Nussinov
- Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, MD 21702, USA; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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Andreani J, Guerois R. Evolution of protein interactions: From interactomes to interfaces. Arch Biochem Biophys 2014; 554:65-75. [DOI: 10.1016/j.abb.2014.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/28/2014] [Accepted: 05/12/2014] [Indexed: 12/16/2022]
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Different subunits belonging to the same protein complex often exhibit discordant expression levels and evolutionary properties. Curr Opin Struct Biol 2014; 26:113-20. [DOI: 10.1016/j.sbi.2014.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/27/2014] [Accepted: 06/04/2014] [Indexed: 11/21/2022]
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36
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Choi YS, Yoon S, Kim KL, Yoo J, Song P, Kim M, Shin YE, Yang WJ, Noh JE, Cho HS, Kim S, Chung J, Ryu SH. Computational design of binding proteins to EGFR domain II. PLoS One 2014; 9:e92513. [PMID: 24710267 PMCID: PMC3977815 DOI: 10.1371/journal.pone.0092513] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 02/24/2014] [Indexed: 12/03/2022] Open
Abstract
We developed a process to produce novel interactions between two previously unrelated proteins. This process selects protein scaffolds and designs protein interfaces that bind to a surface patch of interest on a target protein. Scaffolds with shapes complementary to the target surface patch were screened using an exhaustive computational search of the human proteome and optimized by directed evolution using phage display. This method was applied to successfully design scaffolds that bind to epidermal growth factor receptor (EGFR) domain II, the interface of EGFR dimerization, with high reactivity toward the target surface patch of EGFR domain II. One potential application of these tailor-made protein interactions is the development of therapeutic agents against specific protein targets.
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Affiliation(s)
- Yoon Sup Choi
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- KT Institute of Convergence Technology, Seocho-gu, Seoul, Korea
| | - Soomin Yoon
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Kyung-Lock Kim
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jiho Yoo
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Parkyong Song
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Minsoo Kim
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Scripps Korea Antibody Institute, Chuncheon, Republic of Korea
| | - Young-Eun Shin
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Won Jun Yang
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Jung-eun Noh
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Hyun-soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Sanguk Kim
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Division of IT Convergence Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- * E-mail: (SK); (JC); (SHR)
| | - Junho Chung
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University School of Medicine, Seoul, Republic of Korea
- * E-mail: (SK); (JC); (SHR)
| | - Sung Ho Ryu
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- * E-mail: (SK); (JC); (SHR)
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Nguyen NT, Zhang X, Wu C, Lange RA, Chilton RJ, Lindsey ML, Jin YF. Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map. PLoS Comput Biol 2014; 10:e1003472. [PMID: 24651374 PMCID: PMC3961365 DOI: 10.1371/journal.pcbi.1003472] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 01/02/2014] [Indexed: 01/04/2023] Open
Abstract
Vast research efforts have been devoted to providing clinical diagnostic markers of myocardial infarction (MI), leading to over one million abstracts associated with “MI” and “Cardiovascular Diseases” in PubMed. Accumulation of the research results imposed a challenge to integrate and interpret these results. To address this problem and better understand how the left ventricle (LV) remodels post-MI at both the molecular and cellular levels, we propose here an integrative framework that couples computational methods and experimental data. We selected an initial set of MI-related proteins from published human studies and constructed an MI-specific protein-protein-interaction network (MIPIN). Structural and functional analysis of the MIPIN showed that the post-MI LV exhibited increased representation of proteins involved in transcriptional activity, inflammatory response, and extracellular matrix (ECM) remodeling. Known plasma or serum expression changes of the MIPIN proteins in patients with MI were acquired by data mining of the PubMed and UniProt knowledgebase, and served as a training set to predict unlabeled MIPIN protein changes post-MI. The predictions were validated with published results in PubMed, suggesting prognosticative capability of the MIPIN. Further, we established the first knowledge map related to the post-MI response, providing a major step towards enhancing our understanding of molecular interactions specific to MI and linking the molecular interaction, cellular responses, and biological processes to quantify LV remodeling. Heart attack, known medically as myocardial infarction, often occurs as a result of partial shortage of blood supply to a portion of the heart, leading to the death of heart muscle cells. Following myocardial infarction, complications might arise, including arrhythmia, myocardial rupture, left ventricular dysfunction, and heart failure. Although myocardial infarction can be quickly diagnosed using a various number of tests, including blood tests and electrocardiography, there have been no available prognostic tests to predict the long-term outcome in response to myocardial infarction. Here, we present a framework to analyze how the left ventricle responds to myocardial infarction by combining protein interactome and experimental results retrieved from published human studies. The framework organized current understanding of molecular interactions specific to myocardial infarction, cellular responses, and biological processes to quantify left ventricular remodeling process. Specifically, our knowledge map showed that transcriptional activity, inflammatory response, and extracellular matrix remodeling are the main functional themes post myocardial infarction. In addition, text analytics of relevant abstracts revealed differentiated protein expressions in plasma or serum expressions from patients with myocardial infarction. Using this data, we predicted expression levels of other proteins following myocardial infarction.
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Affiliation(s)
- Nguyen T. Nguyen
- Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America
- San Antonio Cardiovascular Proteomics Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Xiaolin Zhang
- Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Cathy Wu
- Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, Delaware, United States of America
| | - Richard A. Lange
- San Antonio Cardiovascular Proteomics Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Robert J. Chilton
- San Antonio Cardiovascular Proteomics Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Merry L. Lindsey
- San Antonio Cardiovascular Proteomics Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- Mississippi Center for Heart Research, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- Research Service, G.V. (Sonny) Montgomery Veterans Affairs Medical Center, Jackson, Mississippi, United States of America
| | - Yu-Fang Jin
- Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America
- San Antonio Cardiovascular Proteomics Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- * E-mail:
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38
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Chen B, Fan W, Liu J, Wu FX. Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks. Brief Bioinform 2014; 15:177-194. [PMID: 23780996 DOI: 10.1093/bib/bbt039] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2024] Open
Abstract
Cellular processes are typically carried out by protein complexes and functional modules. Identifying them plays an important role for our attempt to reveal principles of cellular organizations and functions. In this article, we review computational algorithms for identifying protein complexes and/or functional modules from protein-protein interaction (PPI) networks. We first describe issues and pitfalls when interpreting PPI networks. Then based on types of data used and main ideas involved, we briefly describe protein complex and/or functional module identification algorithms in four categories: (i) those based on topological structures of unweighted PPI networks; (ii) those based on characters of weighted PPI networks; (iii) those based on multiple data integrations; and (iv) those based on dynamic PPI networks. The PPI networks are modelled increasingly precise when integrating more types of data, and the study of protein complexes would benefit by shifting from static to dynamic PPI networks.
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Affiliation(s)
- Bolin Chen
- School of Computer, Wuhan University, Wuhan 430072, China. Tel.: +86-27-6877-5711; Fax: +86-27-6877-5711; ; Fang-Xiang Wu, College of Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK S7N 5A9, Canada. Tel.: +1-306-966-5280; Fax: +1-306-966-5427; E-mail:
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39
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Coelho ED, Arrais JP, Matos S, Pereira C, Rosa N, Correia MJ, Barros M, Oliveira JL. Computational prediction of the human-microbial oral interactome. BMC SYSTEMS BIOLOGY 2014; 8:24. [PMID: 24576332 PMCID: PMC3975954 DOI: 10.1186/1752-0509-8-24] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 02/17/2014] [Indexed: 11/12/2022]
Abstract
BACKGROUND The oral cavity is a complex ecosystem where human chemical compounds coexist with a particular microbiota. However, shifts in the normal composition of this microbiota may result in the onset of oral ailments, such as periodontitis and dental caries. In addition, it is known that the microbial colonization of the oral cavity is mediated by protein-protein interactions (PPIs) between the host and microorganisms. Nevertheless, this kind of PPIs is still largely undisclosed. To elucidate these interactions, we have created a computational prediction method that allows us to obtain a first model of the Human-Microbial oral interactome. RESULTS We collected high-quality experimental PPIs from five major human databases. The obtained PPIs were used to create our positive dataset and, indirectly, our negative dataset. The positive and negative datasets were merged and used for training and validation of a naïve Bayes classifier. For the final prediction model, we used an ensemble methodology combining five distinct PPI prediction techniques, namely: literature mining, primary protein sequences, orthologous profiles, biological process similarity, and domain interactions. Performance evaluation of our method revealed an area under the ROC-curve (AUC) value greater than 0.926, supporting our primary hypothesis, as no single set of features reached an AUC greater than 0.877. After subjecting our dataset to the prediction model, the classified result was filtered for very high confidence PPIs (probability ≥ 1-10-7), leading to a set of 46,579 PPIs to be further explored. CONCLUSIONS We believe this dataset holds not only important pathways involved in the onset of infectious oral diseases, but also potential drug-targets and biomarkers. The dataset used for training and validation, the predictions obtained and the network final network are available at http://bioinformatics.ua.pt/software/oralint.
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Affiliation(s)
- Edgar D Coelho
- Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal
| | - Joel P Arrais
- Department of Informatics Engineering (DEI), University of Coimbra, Coimbra, Portugal
- Centre for Informatics and Systems of the University at Coimbra (CISUC), University of Coimbra, Coimbra, Portugal
| | - Sérgio Matos
- Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal
| | - Carlos Pereira
- Centre for Informatics and Systems of the University at Coimbra (CISUC), University of Coimbra, Coimbra, Portugal
- Department of Informatics Engineering and Systems, Polytechnic Institute of Coimbra, Engineering Institute of Coimbra (IPC-ISEC), Coimbra, Portugal
| | - Nuno Rosa
- Department of Health Sciences, Institute of Health Sciences, The Catholic University of Portugal, Viseu, Portugal
| | - Maria José Correia
- Department of Health Sciences, Institute of Health Sciences, The Catholic University of Portugal, Viseu, Portugal
| | - Marlene Barros
- Department of Health Sciences, Institute of Health Sciences, The Catholic University of Portugal, Viseu, Portugal
- Centre for Neurosciences and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - José Luís Oliveira
- Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal
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Buijsman W, Sheinman M. Efficient fold-change detection based on protein-protein interactions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:022712. [PMID: 25353514 DOI: 10.1103/physreve.89.022712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 06/04/2023]
Abstract
Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the past few years, fold-change detecting mechanisms, based on transcriptional networks, have been proposed. Here we present a fold-change detecting mechanism, based on protein-protein interactions, consisting of two interacting proteins. This mechanism does not consume chemical energy and is not subject to transcriptional and translational noise, in contrast to previously proposed mechanisms. We show by analytical and numerical calculations that the mechanism is robust and can have a fast, precise, and efficient response for parameters that are relevant to eukaryotic cells.
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Affiliation(s)
- W Buijsman
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands
| | - M Sheinman
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands and Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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Rid R, Strasser W, Siegl D, Frech C, Kommenda M, Kern T, Hintner H, Bauer JW, Önder K. PRIMOS: an integrated database of reassessed protein-protein interactions providing web-based access to in silico validation of experimentally derived data. Assay Drug Dev Technol 2014; 11:333-46. [PMID: 23772554 DOI: 10.1089/adt.2013.506] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Steady improvements in proteomics present a bioinformatic challenge to retrieve, store, and process the accumulating and often redundant amount of information. In particular, a large-scale comparison and analysis of protein-protein interaction (PPI) data requires tools for data interpretation as well as validation. At this juncture, the Protein Interaction and Molecule Search (PRIMOS) platform represents a novel web portal that unifies six primary PPI databases (BIND, Biomolecular Interaction Network Database; DIP, Database of Interacting Proteins; HPRD, Human Protein Reference Database; IntAct; MINT, Molecular Interaction Database; and MIPS, Munich Information Center for Protein Sequences) into a single consistent repository, which currently includes more than 196,700 redundancy-removed PPIs. PRIMOS supports three advanced search strategies centering on disease-relevant PPIs, on inter- and intra-organismal crosstalk relations (e.g., pathogen-host interactions), and on highly connected protein nodes analysis ("hub" identification). The main novelties distinguishing PRIMOS from other secondary PPI databases are the reassessment of known PPIs, and the capacity to validate personal experimental data by our peer-reviewed, homology-based validation. This article focuses on definite PRIMOS use cases (presentation of embedded biological concepts, example applications) to demonstrate its broad functionality and practical value. PRIMOS is publicly available at http://primos.fh-hagenberg.at.
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Affiliation(s)
- Raphaela Rid
- Division of Molecular Dermatology, Department of Dermatology, Paracelsus Medical University Salzburg, Salzburg, Austria
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Dias DM, Van Molle I, Baud MGJ, Galdeano C, Geraldes CFGC, Ciulli A. Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions? ACS Med Chem Lett 2014; 5:23-28. [PMID: 24436777 PMCID: PMC3891296 DOI: 10.1021/ml400296c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/02/2013] [Indexed: 01/18/2023] Open
Abstract
Modulation of protein-protein interactions (PPIs) with small molecules has been hampered by a lack of lucid methods capable of reliably identifying high-quality hits. In fragment screening, the low ligand efficiencies associated with PPI target sites pose significant challenges to fragment binding detection. Here, we investigate the requirements for ligand-based NMR techniques to detect rule-of-three compliant fragments that form part of known high-affinity inhibitors of the PPI between the von Hippel-Lindau protein and the alpha subunit of hypoxia-inducible factor 1 (pVHL:HIF-1α). Careful triaging allowed rescuing weak but specific binding of fragments that would otherwise escape detection at this PPI. Further structural information provided by saturation transfer difference (STD) group epitope mapping, protein-based NMR, competitive isothermal titration calorimetry (ITC), and X-ray crystallography confirmed the binding mode of the rescued fragments. Our findings have important implications for PPI druggability assessment by fragment screening as they reveal an accessible threshold for fragment detection and validation.
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Affiliation(s)
- David M. Dias
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
- Department of Life Sciences, Faculty of
Science and Technology, Centre for Neurosciences and Cell Biology
and Chemistry Centre, University of Coimbra, Coimbra, Portugal
| | - Inge Van Molle
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | | | - Carles Galdeano
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Carlos F. G. C. Geraldes
- Department of Life Sciences, Faculty of
Science and Technology, Centre for Neurosciences and Cell Biology
and Chemistry Centre, University of Coimbra, Coimbra, Portugal
| | - Alessio Ciulli
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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Wodak SJ, Vlasblom J, Turinsky AL, Pu S. Protein–protein interaction networks: the puzzling riches. Curr Opin Struct Biol 2013; 23:941-53. [DOI: 10.1016/j.sbi.2013.08.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 07/14/2013] [Accepted: 08/08/2013] [Indexed: 12/13/2022]
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Ortega DR, Mo G, Lee K, Zhou H, Baudry J, Dahlquist FW, Zhulin IB. Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein. PLoS Comput Biol 2013; 9:e1003337. [PMID: 24244143 PMCID: PMC3828127 DOI: 10.1371/journal.pcbi.1003337] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/27/2013] [Indexed: 11/25/2022] Open
Abstract
Bacterial chemotaxis is one of the best studied signal transduction pathways. CheW is a scaffold protein that mediates the association of the chemoreceptors and the CheA kinase in a ternary signaling complex. The effects of replacing conserved Arg62 of CheW with other residues suggested that the scaffold protein plays a more complex role than simply binding its partner proteins. Although R62A CheW had essentially the same affinity for chemoreceptors and CheA, cells expressing the mutant protein are impaired in chemotaxis. Using a combination of molecular dynamics simulations (MD), NMR spectroscopy, and circular dichroism (CD), we addressed the role of Arg62. Here we show that Arg62 forms a salt bridge with another highly conserved residue, Glu38. Although this interaction is unimportant for overall protein stability, it is essential to maintain the correct alignment of the chemoreceptor and kinase binding sites of CheW. Computational and experimental data suggest that the role of the salt bridge in maintaining the alignment of the two partner binding sites is fundamental to the function of the signaling complex but not to its assembly. We conclude that a key feature of CheW is to maintain the specific geometry between the two interaction sites required for its function as a scaffold. Signal transduction is a universal biological process and a common target of drug design. The chemotaxis machinery in Escherichia coli is a model signal transduction system, and the CheW protein is one of its core components. CheW is thought to work as a scaffold protein that mediates the formation of the signaling complex with the CheA histidine kinase and the chemoreceptors. A mutation targeting a highly conserved residue, Arg62, impairs chemotaxis while maintaining normal binding affinity for both partners, suggesting that CheW might play a more complex role than previously proposed. Using a series of molecular dynamics simulations, we found that the residue Arg62 can form a stable salt bridge with another highly conserved residue, Glu38. We determined that this bridge does not contribute to the overall stability of the protein. However, the bridge stabilizes the local backbone structure of CheW and stabilizes the relative position of the binding sites for the chemoreceptor and kinase. The geometry of these interactions appears to be vital for the function of the signaling complex. We validated and complemented our computational findings using NMR spectroscopy and circular dichroism analysis.
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Affiliation(s)
- Davi R. Ortega
- Joint Institute for Computational Sciences, University of Tennessee - Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Physics, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Guoya Mo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
| | - Kwangwoon Lee
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
| | - Hongjun Zhou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
| | - Jerome Baudry
- Department of Biochemistry and Cell and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- Center for Molecular Biophysics, University of Tennessee - Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Frederick W. Dahlquist
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, United States of America
| | - Igor B. Zhulin
- Joint Institute for Computational Sciences, University of Tennessee - Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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45
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Rodrigues JPGLM, Melquiond ASJ, Karaca E, Trellet M, van Dijk M, van Zundert GCP, Schmitz C, de Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AMJJ. Defining the limits of homology modeling in information-driven protein docking. Proteins 2013; 81:2119-28. [PMID: 23913867 DOI: 10.1002/prot.24382] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/16/2013] [Accepted: 07/25/2013] [Indexed: 12/28/2022]
Abstract
Information-driven docking is currently one of the most successful approaches to obtain structural models of protein interactions as demonstrated in the latest round of CAPRI. While various experimental and computational techniques can be used to retrieve information about the binding mode, the availability of three-dimensional structures of the interacting partners remains a limiting factor. Fortunately, the wealth of structural information gathered by large-scale initiatives allows for homology-based modeling of a significant fraction of the protein universe. Defining the limits of information-driven docking based on such homology models is therefore highly relevant. Here we show, using previous CAPRI targets, that out of a variety of measures, the global sequence identity between template and target is a simple but reliable predictor of the achievable quality of the docking models. This indicates that a well-defined overall fold is critical for the interaction. Furthermore, the quality of the data at our disposal to characterize the interaction plays a determinant role in the success of the docking. Given reliable interface information we can obtain acceptable predictions even at low global sequence identity. These results, which define the boundaries between trustworthy and unreliable predictions, should guide both experts and nonexperts in defining the limits of what is achievable by docking. This is highly relevant considering that the fraction of the interactome amenable for docking is only bound to grow as the number of experimentally solved structures increases.
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Affiliation(s)
- J P G L M Rodrigues
- Faculty of Science/Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH, The Netherlands
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Bhagawati M, You C, Piehler J. Quantitative real-time imaging of protein-protein interactions by LSPR detection with micropatterned gold nanoparticles. Anal Chem 2013; 85:9564-71. [PMID: 24016060 DOI: 10.1021/ac401673e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Localized surface plasmon resonance (LSPR) offers powerful means for sensitive label-free detection of protein-protein interactions in a highly multiplexed format. We have here established self-assembly and surface modification of plasmonic nanostructures on solid support suitable for quantitative protein-protein interaction analysis by spectroscopic and microscopic LSPR detection. These architectures were obtained by layer-by-layer assembly via electrostatic attraction. Gold nanoparticles (AuNP) were adsorbed on a biocompatible amine-terminated poly(ethylene glycol) (PEG) polymer brush and further functionalized by poly-l-lysine graft PEG (PLL-PEG) copolymers. Stable yet reversible protein immobilization was achieved via tris(nitrilotriacetic acid) groups incorporated into the PLL-PEG coating. Thus, site-specific immobilization of His-tagged proteins via complexed Ni(II) ions was achieved. Functional protein immobilization on the surface was confirmed by real-time detection of LSPR scattering by reflectance spectroscopy. Association and dissociation rate constants obtained for a reversible protein-protein interaction were in good agreement with the data obtained by other surface-sensitive detection techniques. For spatially resolved detection, AuNP were assembled into micropatterns by means of photolithographic uncaging of surface amines. LSPR imaging of reversible protein-protein interactions was possible in a conventional wide field microscope, yielding detection limits of ∼30 protein molecules within a diffraction-limited surface area.
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Affiliation(s)
- Maniraj Bhagawati
- Department of Biology, University of Osnabrück , Barbarastrasse 11, 49076 Osnabrück, Germany
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47
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Abstract
Cells face a constant challenge as they produce new proteins. The newly synthesized polypeptides must be folded properly to avoid aggregation. If proteins do misfold, they must be cleared to maintain a functional and healthy proteome. Recent work is revealing the complex mechanisms that work cotranslationally to ensure protein quality control during biogenesis at the ribosome. Indeed, the ribosome is emerging as a central hub in coordinating these processes, particularly in sensing the nature of the nascent protein chain, recruiting protein folding and translocation components, and integrating mRNA and nascent chain quality control. The tiered and complementary nature of these decision-making processes confers robustness and fidelity to protein homeostasis during protein synthesis.
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Affiliation(s)
- Sebastian Pechmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
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48
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MacKinnon SS, Malevanets A, Wodak S. Intertwined Associations in Structures of Homooligomeric Proteins. Structure 2013; 21:638-49. [DOI: 10.1016/j.str.2013.01.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 12/24/2012] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
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49
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Abstract
The rapid technological developments following the Human Genome Project have made possible the availability of personalized genomes. As the focus now shifts from characterizing genomes to making personalized disease associations, in combination with the availability of other omics technologies, the next big push will be not only to obtain a personalized genome, but to quantitatively follow other omics. This will include transcriptomes, proteomes, metabolomes, antibodyomes, and new emerging technologies, enabling the profiling of thousands of molecular components in individuals. Furthermore, omics profiling performed longitudinally can probe the temporal patterns associated with both molecular changes and associated physiological health and disease states. Such data necessitates the development of computational methodology to not only handle and descriptively assess such data, but also construct quantitative biological models. Here we describe the availability of personal genomes and developing omics technologies that can be brought together for personalized implementations and how these novel integrated approaches may effectively provide a precise personalized medicine that focuses on not only characterization and treatment but ultimately the prevention of disease.
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50
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Barh D, Gupta K, Jain N, Khatri G, León-Sicairos N, Canizalez-Roman A, Tiwari S, Verma A, Rahangdale S, Shah Hassan S, Rodrigues dos Santos A, Ali A, Carlos Guimarães L, Thiago Jucá Ramos R, Devarapalli P, Barve N, Bakhtiar M, Kumavath R, Ghosh P, Miyoshi A, Silva A, Kumar A, Narayan Misra A, Blum K, Baumbach J, Azevedo V. Conserved host–pathogen PPIs Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target inC. pseudotuberculosis,C. diphtheriae,M. tuberculosis,C. ulcerans,Y. pestis, andE. colitargeted byPiper betelcompounds. Integr Biol (Camb) 2013; 5:495-509. [DOI: 10.1039/c2ib20206a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India. Fax: +91-944 955 0032; Tel: +91-944 955 0032
- Department of Biosciences and Biotechnology, School of Biotechnology, Fakir Mohan University, Jnan Bigyan Vihar, Balasore, Orissa, India
| | - Krishnakant Gupta
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India. Fax: +91-944 955 0032; Tel: +91-944 955 0032
- School of Biotechnology, Devi Ahilya University, Khandwa Road Campus, Indore, MP, India
| | - Neha Jain
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India. Fax: +91-944 955 0032; Tel: +91-944 955 0032
| | - Gourav Khatri
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India. Fax: +91-944 955 0032; Tel: +91-944 955 0032
- School of Biotechnology, Devi Ahilya University, Khandwa Road Campus, Indore, MP, India
| | - Nidia León-Sicairos
- Unidad de investigacion, Facultad de Medicina, Universidad Autónoma de Sinaloa. Cedros y Sauces, Fraccionamiento Fresnos, Culiacán Sinaloa 80246, México
| | - Adrian Canizalez-Roman
- Unidad de investigacion, Facultad de Medicina, Universidad Autónoma de Sinaloa. Cedros y Sauces, Fraccionamiento Fresnos, Culiacán Sinaloa 80246, México
| | - Sandeep Tiwari
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India. Fax: +91-944 955 0032; Tel: +91-944 955 0032
| | - Ankit Verma
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India. Fax: +91-944 955 0032; Tel: +91-944 955 0032
- School of Biotechnology, Devi Ahilya University, Khandwa Road Campus, Indore, MP, India
| | - Sachin Rahangdale
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India. Fax: +91-944 955 0032; Tel: +91-944 955 0032
- School of Biotechnology, Devi Ahilya University, Khandwa Road Campus, Indore, MP, India
| | - Syed Shah Hassan
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Amjad Ali
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luis Carlos Guimarães
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Pratap Devarapalli
- Department of Genomic Science, School of Biological Sciences, Riverside Transit Campus, Central University of Kerala, Kasaragod, India
| | - Neha Barve
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India. Fax: +91-944 955 0032; Tel: +91-944 955 0032
- School of Biotechnology, Devi Ahilya University, Khandwa Road Campus, Indore, MP, India
| | - Marriam Bakhtiar
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Riverside Transit Campus, Central University of Kerala, Kasaragod, India
| | - Preetam Ghosh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India. Fax: +91-944 955 0032; Tel: +91-944 955 0032
- Department of Computer Science and Center for the Study of Biological Complexity, Virginia Commonwealth University, 401 West Main Street, Room E4234, P.O. Box 843019, Richmond, Virginia 23284-3019, USA
| | - Anderson Miyoshi
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Anil Kumar
- School of Biotechnology, Devi Ahilya University, Khandwa Road Campus, Indore, MP, India
| | - Amarendra Narayan Misra
- Department of Biosciences and Biotechnology, School of Biotechnology, Fakir Mohan University, Jnan Bigyan Vihar, Balasore, Orissa, India
- Center for Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand State, India
| | - Kenneth Blum
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India. Fax: +91-944 955 0032; Tel: +91-944 955 0032
- University of Florida, College of Medicine, Gainesville, Florida, USA
- Global Integrated Services Unit University of Vermont Center for Clinical & Translational Science, College of Medicine, Burlington, VT, USA
- Dominion Diagnostics LLC, North Kingstown, Rhode Island, USA
| | - Jan Baumbach
- Computational Biology Group Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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