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Mehrabipour M, Jasemi NSK, Dvorsky R, Ahmadian MR. A Systematic Compilation of Human SH3 Domains: A Versatile Superfamily in Cellular Signaling. Cells 2023; 12:2054. [PMID: 37626864 PMCID: PMC10453029 DOI: 10.3390/cells12162054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
SRC homology 3 (SH3) domains are fundamental modules that enable the assembly of protein complexes through physical interactions with a pool of proline-rich/noncanonical motifs from partner proteins. They are widely studied modular building blocks across all five kingdoms of life and viruses, mediating various biological processes. The SH3 domains are also implicated in the development of human diseases, such as cancer, leukemia, osteoporosis, Alzheimer's disease, and various infections. A database search of the human proteome reveals the existence of 298 SH3 domains in 221 SH3 domain-containing proteins (SH3DCPs), ranging from 13 to 720 kilodaltons. A phylogenetic analysis of human SH3DCPs based on their multi-domain architecture seems to be the most practical way to classify them functionally, with regard to various physiological pathways. This review further summarizes the achievements made in the classification of SH3 domain functions, their binding specificity, and their significance for various diseases when exploiting SH3 protein modular interactions as drug targets.
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Affiliation(s)
- Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
- Center for Interdisciplinary Biosciences, P. J. Šafárik University, 040 01 Košice, Slovakia
| | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
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2
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Sokolik CG, Qassem N, Chill JH. The Disordered Cellular Multi-Tasker WIP and Its Protein-Protein Interactions: A Structural View. Biomolecules 2020; 10:biom10071084. [PMID: 32708183 PMCID: PMC7407642 DOI: 10.3390/biom10071084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 01/21/2023] Open
Abstract
WASp-interacting protein (WIP), a regulator of actin cytoskeleton assembly and remodeling, is a cellular multi-tasker and a key member of a network of protein-protein interactions, with significant impact on health and disease. Here, we attempt to complement the well-established understanding of WIP function from cell biology studies, summarized in several reviews, with a structural description of WIP interactions, highlighting works that present a molecular view of WIP's protein-protein interactions. This provides a deeper understanding of the mechanisms by which WIP mediates its biological functions. The fully disordered WIP also serves as an intriguing example of how intrinsically disordered proteins (IDPs) exert their function. WIP consists of consecutive small functional domains and motifs that interact with a host of cellular partners, with a striking preponderance of proline-rich motif capable of interactions with several well-recognized binding partners; indeed, over 30% of the WIP primary structure are proline residues. We focus on the binding motifs and binding interfaces of three important WIP segments, the actin-binding N-terminal domain, the central domain that binds SH3 domains of various interaction partners, and the WASp-binding C-terminal domain. Beyond the obvious importance of a more fundamental understanding of the biology of this central cellular player, this approach carries an immediate and highly beneficial effect on drug-design efforts targeting WIP and its binding partners. These factors make the value of such structural studies, challenging as they are, readily apparent.
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3
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Ding W, Tan HY, Zhang JX, Wilczek LA, Hsieh KR, Mulkin JA, Bianco PR. The mechanism of Single strand binding protein-RecG binding: Implications for SSB interactome function. Protein Sci 2020; 29:1211-1227. [PMID: 32196797 PMCID: PMC7184773 DOI: 10.1002/pro.3855] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023]
Abstract
The Escherichia coli single-strand DNA binding protein (SSB) is essential to viability where it functions to regulate SSB interactome function. Here it binds to single-stranded DNA and to target proteins that comprise the interactome. The region of SSB that links these two essential protein functions is the intrinsically disordered linker. Key to linker function is the presence of three, conserved PXXP motifs that mediate binding to oligosaccharide-oligonucleotide binding folds (OB-fold) present in SSB and its interactome partners. Not surprisingly, partner OB-fold deletions eliminate SSB binding. Furthermore, single point mutations in either the PXXP motifs or, in the RecG OB-fold, obliterate SSB binding. The data also demonstrate that, and in contrast to the view currently held in the field, the C-terminal acidic tip of SSB is not required for interactome partner binding. Instead, we propose the tip has two roles. First, and consistent with the proposal of Dixon, to regulate the structure of the C-terminal domain in a biologically active conformation that prevents linkers from binding to SSB OB-folds until this interaction is required. Second, as a secondary binding domain. Finally, as OB-folds are present in SSB and many of its partners, we present the SSB interactome as the first family of OB-fold genome guardians identified in prokaryotes.
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Affiliation(s)
- Wenfei Ding
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| | - Hui Yin Tan
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Present address:
Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndianaUnited States
| | - Jia Xiang Zhang
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| | - Luke A. Wilczek
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
- Present address:
Department of ChemistryBrown UniversityProvidenceRhode IslandUnited States
| | - Karin R. Hsieh
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
| | - Jeffrey A. Mulkin
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
| | - Piero R. Bianco
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
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4
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Stadmiller SS, Aguilar JS, Waudby CA, Pielak GJ. Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis. Biophys J 2020; 118:2537-2548. [PMID: 32348722 DOI: 10.1016/j.bpj.2020.03.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Fluorine incorporation is ideally suited to many NMR techniques, and incorporation of fluorine into proteins and fragment libraries for drug discovery has become increasingly common. Here, we use one-dimensional 19F NMR lineshape analysis to quantify the kinetics and equilibrium thermodynamics for the binding of a fluorine-labeled Src homology 3 (SH3) protein domain to four proline-rich peptides. SH3 domains are one of the largest and most well-characterized families of protein recognition domains and have a multitude of functions in eukaryotic cell signaling. First, we showe that fluorine incorporation into SH3 causes only minor structural changes to both the free and bound states using amide proton temperature coefficients. We then compare the results from lineshape analysis of one-dimensional 19F spectra to those from two-dimensional 1H-15N heteronuclear single quantum coherence spectra. Their agreement demonstrates that one-dimensional 19F lineshape analysis is a robust, low-cost, and fast alternative to traditional heteronuclear single quantum coherence-based experiments. The data show that binding is diffusion limited and indicate that the transition state is highly similar to the free state. We also measured binding as a function of temperature. At equilibrium, binding is enthalpically driven and arises from a highly positive activation enthalpy for association with small entropic contributions. Our results agree with those from studies using different techniques, providing additional evidence for the utility of 19F NMR lineshape analysis, and we anticipate that this analysis will be an effective tool for rapidly characterizing the energetics of protein interactions.
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Affiliation(s)
| | - Jhoan S Aguilar
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Christopher A Waudby
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina.
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5
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Zhao T, Liu Y, Wang Z, He R, Xiang Zhang J, Xu F, Lei M, Deci MB, Nguyen J, Bianco PR. Super-resolution imaging reveals changes in Escherichia coli SSB localization in response to DNA damage. Genes Cells 2019; 24:814-826. [PMID: 31638317 DOI: 10.1111/gtc.12729] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 01/11/2023]
Abstract
The E. coli single-stranded DNA-binding protein (SSB) is essential to viability. It plays key roles in DNA metabolism where it binds to nascent single strands of DNA and to target proteins known as the SSB interactome. There are >2,000 tetramers of SSB per cell with 100-150 associated with the genome at any one time, either at DNA replication forks or at sites of repair. The remaining 1,900 tetramers could constantly diffuse throughout the cytosol or be associated with the inner membrane as observed for other DNA metabolic enzymes. To visualize SSB localization and to ascertain potential spatiotemporal changes in response to DNA damage, SSB-GFP chimeras were visualized using a novel, super-resolution microscope optimized for the study of prokaryotic cells. In the absence of DNA damage, SSB localizes to a small number of foci and the excess protein is associated with the inner membrane where it binds to the major phospholipids. Within five minutes following DNA damage, the vast majority of SSB disengages from the membrane and is found almost exclusively in the cell interior. Here, it is observed in a large number of foci, in discreet structures or, in diffuse form spread over the genome, thereby enabling repair events.
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Affiliation(s)
- Tianyu Zhao
- Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, State Key Laboratory of Transient Optics and Photonics, Xi'an, China
| | - Yan Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zilin Wang
- Center for Single Molecule Biophysics and, Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA
| | - Rongyan He
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jia Xiang Zhang
- Center for Single Molecule Biophysics and, Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ming Lei
- Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, State Key Laboratory of Transient Optics and Photonics, Xi'an, China
| | - Michael B Deci
- Department of Pharmaceutical Sciences, School of Pharmacy, University at Buffalo, Buffalo, NY, USA
| | - Juliane Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University at Buffalo, Buffalo, NY, USA
| | - Piero R Bianco
- Center for Single Molecule Biophysics and, Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA
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6
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Costamagna A, Rossi Sebastiano M, Natalini D, Simoni M, Valabrega G, Defilippi P, Visentin S, Ermondi G, Turco E, Caron G, Cabodi S. Modeling ErbB2-p130Cas interaction to design new potential anticancer agents. Sci Rep 2019; 9:3089. [PMID: 30816273 PMCID: PMC6395809 DOI: 10.1038/s41598-019-39510-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/11/2019] [Indexed: 12/02/2022] Open
Abstract
The ErbB2 receptor tyrosine kinase is overexpressed in approximately 15–20% of breast tumors and associated with aggressive disease and poor clinical outcome. p130Cas represents a nodal scaffold protein regulating cell survival, migration and proliferation in normal and pathological contexts. p130Cas overexpression in ErbB2 human breast cancer correlates with poor prognosis and metastasis formation. Recent data indicate that p130Cas association to ErbB2 protects ErbB2 from degradation, thus enhancing tumorigenesis. Therefore, inhibiting p130Cas/ErbB2 interaction might represent a new therapeutic strategy to target breast cancer. Here we demonstrate by performing Molecular Modeling, Molecular Dynamics, dot blot, ELISA and fluorescence quenching experiments, that p130Cas binds directly to ErbB2. Then, by structure-based virtual screening, we identified two potential inhibitors of p130Cas/ErbB2 interaction. Their experimental validation was performed in vitro and in ErbB2-positive breast cancer cellular models. The results highlight that both compounds interfere with p130Cas/ErbB2 binding and significantly affect cell proliferation and sensitivity to Trastuzumab. Overall, this study identifies p130Cas/ErbB2 complex as a potential breast cancer target revealing new therapeutic perspectives for protein-protein interaction (PPI).
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Affiliation(s)
- Andrea Costamagna
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | | | - Dora Natalini
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Matilde Simoni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | | | - Paola Defilippi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Sonja Visentin
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Emilia Turco
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Sara Cabodi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy.
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7
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Myllykoski M, Eichel MA, Jung RB, Kelm S, Werner HB, Kursula P. High-affinity heterotetramer formation between the large myelin-associated glycoprotein and the dynein light chain DYNLL1. J Neurochem 2018; 147:764-783. [PMID: 30261098 DOI: 10.1111/jnc.14598] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/21/2018] [Accepted: 09/16/2018] [Indexed: 12/13/2022]
Abstract
The close association of myelinated axons and their myelin sheaths involves numerous intercellular molecular interactions. For example, myelin-associated glycoprotein (MAG) mediates myelin-to-axon adhesion and signalling via molecules on the axonal surface. However, knowledge about intracellular binding partners of myelin proteins, including MAG, has remained limited. The two splice isoforms of MAG, S- and L-MAG, display distinct cytoplasmic domains and spatiotemporal expression profiles. We used yeast two-hybrid screening to identify interaction partners of L-MAG and found the dynein light chain DYNLL1 (also termed dynein light chain 8). DYNLL1 homodimers are known to facilitate dimerization of target proteins. L-MAG and DYNLL1 associate with high affinity, as confirmed with recombinant proteins in vitro. Structural analyses of the purified complex indicate that the DYNLL1-binding segment is localized close to the L-MAG C terminus, next to the Fyn kinase Tyr phosphorylation site. The crystal structure of the complex between DYNLL1 and its binding segment on L-MAG shows 2 : 2 binding in a parallel arrangement, indicating a heterotetrameric complex. The homology between L-MAG and previously characterized DYNLL1-ligands is limited, and some details of binding site interactions are unique for L-MAG. The structure of the complex between the entire L-MAG cytoplasmic domain and DYNLL1, as well as that of the extracellular domain of MAG, were modelled based on small-angle X-ray scattering data, allowing structural insights into L-MAG interactions on both membrane surfaces. Our data imply that DYNLL1 dimerizes L-MAG, but not S-MAG, through the formation of a specific 2 : 2 heterotetramer. This arrangement is likely to affect, in an isoform-specific manner, the functions of MAG in adhesion and myelin-to-axon signalling. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* because it provided all relevant information to reproduce the study in the manuscript. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/. Read the Editorial Highlight for this article on page 712.
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Affiliation(s)
- Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Maria A Eichel
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Georg August University School of Science, University of Göttingen, Göttingen, Germany
| | - Ramona B Jung
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Sørge Kelm
- Centre for Biomolecular Interactions Bremen (CBIB), University of Bremen, Bremen, Germany
| | - Hauke B Werner
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Department of Biomedicine, University of Bergen, Bergen, Norway
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8
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Xu YZ, Thuraisingam T, Kanagaratham C, Tao S, Radzioch D. c-Src kinase is involved in the tyrosine phosphorylation and activity of SLC11A1 in differentiating macrophages. PLoS One 2018; 13:e0196230. [PMID: 29723216 PMCID: PMC5933793 DOI: 10.1371/journal.pone.0196230] [Citation(s) in RCA: 6] [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: 10/04/2017] [Accepted: 04/09/2018] [Indexed: 11/18/2022] Open
Abstract
Studies have demonstrated that the solute carrier family 11 member 1 (SLC11A1) is heavily glycosylated and phosphorylated in macrophages. However, the mechanisms of SLC11A1 phosphorylation, and the effects of phosphorylation on SLC11A1 activity remain largely unknown. Here, the tyrosine phosphorylation of SLC11A1 is observed in SLC11A1-expressing U937 cells when differentiated into macrophages by phorbol myristate acetate (PMA). The phosphorylation of SLC11A1 is almost completely blocked by treatment with PP2, a selective inhibitor of Src family kinases. Furthermore, we found that SLC11A1 is a direct substrate for active c-Src kinase and siRNA-mediated knockdown of cellular Src (c-Src) expression results in a significant decrease in tyrosine phosphorylation. We found that PMA induces the interaction of SLC11A1 with c-Src kinase. We demonstrated that SLC11A1 is phosphorylated by Src family kinases at tyrosine 15 and this type of phosphorylation is required for SLC11A1-mediated modulation of NF-κB activation and nitric oxide (NO) production induced by LPS. Our results demonstrate important roles for c-Src tyrosine kinase in phosphorylation and activation of SLC11A1 in macrophages.
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Affiliation(s)
- Yong Zhong Xu
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Thusanth Thuraisingam
- Division of Dermatology, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Cynthia Kanagaratham
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Shao Tao
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Danuta Radzioch
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
- * E-mail:
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9
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Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes. Sci Rep 2018; 8:6196. [PMID: 29670199 PMCID: PMC5906684 DOI: 10.1038/s41598-018-24467-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/04/2018] [Indexed: 11/08/2022] Open
Abstract
SH3-fold-β-barrel domains of the chromo-like superfamily recognize epigenetic marks in eukaryotic proteins. Their provenance has been placed either in archaea, based on apparent structural similarity to chromatin-compacting Sul7d and Cren7 proteins, or in bacteria based on the presence of sequence homologs. Using sequence and structural evidence we establish that the archaeal Cren7/Sul7 proteins emerged from a zinc ribbon (ZnR) ancestor. Further, we show that the ancestral eukaryotic chromo-like domains evolved from bacterial versions, likely acquired from early endosymbioses, which already possessed an aromatic cage for recognition of modified amino-groups. These bacterial versions are part of a radiation of secreted SH3-fold domains, which spawned both chromo-like domains and classical SH3 domains in the context of peptide-recognition in the peptidoglycan or the extracellular matrix. This establishes that Cren7/Sul7 converged to a “SH3”-like state from a ZnR precursor via the loss of metal-chelation and acquisition of stronger hydrophobic interactions; it is unlikely to have participated in the evolution of the chromo-like domains. We show that archaea possess several Cren7/Sul7-related proteins with intact Zn-chelating ligands, which we predict to play previously unstudied roles in chromosome segregation during cell-division comparable to the PRC barrel and CdvA domain proteins.
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10
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Yip KT, Zhong X, Seibel N, Arnolds O, Schöpel M, Stoll R. Human melanoma inhibitory protein binds to the FN12-14 Hep II domain of fibronectin. Biointerphases 2017; 12:02D415. [PMID: 28565914 PMCID: PMC5451317 DOI: 10.1116/1.4984008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/03/2017] [Accepted: 05/10/2017] [Indexed: 11/17/2022] Open
Abstract
The heparin binding site (Hep II) of fibronectin plays a major role in tumor cell metastasis. Its interaction with heparan sulfate proteoglycans occurs in a variety of physiological processes including focal adhesion and migration. The melanoma inhibitory activity (MIA) is an important protein that is functionally involved in melanoma development, progression, and tumor cell invasion. After its secretion by malignant melanoma cells, MIA interacts with fibronectin and thereby actively facilitates focal cell detachment from surrounding structures and strongly promotes tumor cell invasion and the formation of metastases. In this report, the authors have determined the molecular basis of the interaction of MIA with the Hep II domain of fibronectin based on nuclear magnetic resonance spectroscopic binding assays. The authors have identified the type III modules 12 to 14 of fibronectin's Hep II as the major MIA binding sites. These results now provide a new target protein-protein binding interface for the discovery of novel antimetastatic agents against malignant melanoma in the future.
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Affiliation(s)
- King Tuo Yip
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Xueyin Zhong
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Nadia Seibel
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Oliver Arnolds
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Miriam Schöpel
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Raphael Stoll
- Biomolecular NMR, Ruhr University of Bochum, 44780 Bochum, Germany
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11
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Bianco PR, Lyubchenko YL. SSB and the RecG DNA helicase: an intimate association to rescue a stalled replication fork. Protein Sci 2017; 26:638-649. [PMID: 28078722 DOI: 10.1002/pro.3114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 12/26/2016] [Accepted: 12/28/2016] [Indexed: 12/27/2022]
Abstract
In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy. This translocation may be used to clear the fork of obstacles, prior to the initiation of fork regression.
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Affiliation(s)
- Piero R Bianco
- SUNY Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, 321 Cary Hall, 3435 Main St, Buffalo, New York 14214.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York.,Department of Biochemistry, University at Buffalo, Buffalo, New York
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, 68198-6025
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12
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Tan HY, Wilczek LA, Pottinger S, Manosas M, Yu C, Nguyenduc T, Bianco PR. The intrinsically disordered linker of E. coli SSB is critical for the release from single-stranded DNA. Protein Sci 2017; 26:700-717. [PMID: 28078720 DOI: 10.1002/pro.3115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 12/28/2016] [Indexed: 11/08/2022]
Abstract
The Escherichia coli single stranded DNA binding protein (SSB) is crucial for DNA replication, recombination and repair. Within each process, it has two seemingly disparate roles: it stabilizes single-stranded DNA (ssDNA) intermediates generated during DNA processing and, forms complexes with a group of proteins known as the SSB-interactome. Key to both roles is the C-terminal, one-third of the protein, in particular the intrinsically disordered linker (IDL). Previously, they have shown using a series of linker deletion mutants that the IDL links both ssDNA and target protein binding by mediating interactions with the oligosaccharide/oligonucleotide binding fold in the target. In this study, they examine the role of the linker region in SSB function in a variety of DNA metabolic processes in vitro. Using the same linker mutants, the results show that in addition to association reactions (either DNA or protein), the IDL is critical for the release of SSB from DNA. This release can be under conditions of ssDNA competition or active displacement by a DNA helicase or recombinase. Consistent with their previous work these results indicate that SSB linker mutants are defective for SSB-SSB interactions, and when the IDL is removed a terminal SSB-DNA complex results. Formation of this complex inhibits downstream processing of DNA by helicases such as RecG or PriA as well as recombination, mediated by RecA. A model, based on the evidence herein, is presented to explain how the IDL acts in SSB function.
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Affiliation(s)
- Hui Yin Tan
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Luke A Wilczek
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Sasheen Pottinger
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Maria Manosas
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Diagonal 647, 08028, Barcelona, Spain.,CIBER-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Sanidad Carlos III, Madrid, Spain
| | - Cong Yu
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Trong Nguyenduc
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
| | - Piero R Bianco
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York
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13
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Bianco PR, Pottinger S, Tan HY, Nguyenduc T, Rex K, Varshney U. The IDL of E. coli SSB links ssDNA and protein binding by mediating protein-protein interactions. Protein Sci 2017; 26:227-241. [PMID: 28127816 DOI: 10.1002/pro.3072] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/17/2016] [Indexed: 11/10/2022]
Abstract
The E. coli single strand DNA binding protein (SSB) is essential to viability where it functions in two seemingly disparate roles: it binds to single stranded DNA (ssDNA) and to target proteins that comprise the SSB interactome. The link between these roles resides in a previously under-appreciated region of the protein known as the intrinsically disordered linker (IDL). We present a model wherein the IDL is responsible for mediating protein-protein interactions critical to each role. When interactions occur between SSB tetramers, cooperative binding to ssDNA results. When binding occurs between SSB and an interactome partner, storage or loading of that protein onto the DNA takes place. The properties of the IDL that facilitate these interactions include the presence of repeats, a putative polyproline type II helix and, PXXP motifs that may facilitate direct binding to the OB-fold in a manner similar to that observed for SH3 domain binding of PXXP ligands in eukaryotic systems.
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Affiliation(s)
- Piero R Bianco
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Sasheen Pottinger
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Hui Yin Tan
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Trong Nguyenduc
- Department of Microbiology and Immunology, Center for Single Molecule Biophysics, University at Buffalo, Buffalo, New York, 14214
| | - Kervin Rex
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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14
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Bianco PR. The tale of SSB. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 127:111-118. [PMID: 27838363 DOI: 10.1016/j.pbiomolbio.2016.11.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/04/2016] [Indexed: 01/07/2023]
Abstract
The E. coli single stranded DNA binding protein (SSB) is essential to all aspects of DNA metabolism. Here, it has two seemingly disparate but equally important roles: it binds rapidly and cooperatively to single stranded DNA (ssDNA) and it binds to partner proteins that constitute the SSB interactome. These two roles are not disparate but are instead, intimately linked. A model is presented wherein the intrinsically disordered linker (IDL) is directly responsible for mediating protein-protein interactions. It does this by binding, via PXXP motifs, to the OB-fold (aka SH3 domain) of a nearby protein. When the nearby protein is another SSB tetramer, this leads to a highly efficient ssDNA binding reaction that rapidly and cooperatively covers and protects the exposed nucleic acid from degradation. Alternatively, when the nearby protein is a member of the SSB interactome, loading of the enzyme onto the DNA takes places.
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Affiliation(s)
- Piero R Bianco
- Center for Single Molecule Biophysics, Department of Biochemistry, University at Buffalo, Buffalo, NY, 14214, USA; Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.
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15
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Highly homologous proteins exert opposite biological activities by using different interaction interfaces. Sci Rep 2015; 5:11629. [PMID: 26130271 PMCID: PMC4486954 DOI: 10.1038/srep11629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/02/2015] [Indexed: 11/08/2022] Open
Abstract
We present a possible molecular basis for the opposite activity of two homologues proteins that bind similar ligands and show that this is achieved by fine-tuning of the interaction interface. The highly homologous ASPP proteins have opposite roles in regulating apoptosis: ASPP2 induces apoptosis while iASPP inhibits it. The ASPP proteins are regulated by an autoinhibitory interaction between their Ank-SH3 and Pro domains. We performed a detailed biophysical and molecular study of the Pro - Ank-SH3 interaction in iASPP and compared it to the interaction in ASPP2. We found that iASPP Pro is disordered and that the interaction sites are entirely different: iASPP Ank-SH3 binds iASPP Pro via its fourth Ank repeat and RT loop while ASPP2 Ank-SH3 binds ASPP2 Pro via its first Ank repeat and the n-src loop. It is possible that by using different moieties in the same interface, the proteins can have distinct and specific interactions resulting in differential regulation and ultimately different biological activities.
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16
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Register AC, Leonard SE, Maly DJ. SH2-catalytic domain linker heterogeneity influences allosteric coupling across the SFK family. Biochemistry 2014; 53:6910-23. [PMID: 25302671 PMCID: PMC4230323 DOI: 10.1021/bi5008194] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Src-family
kinases (SFKs) make up a family of nine homologous multidomain
tyrosine kinases whose misregulation is responsible for human disease
(cancer, diabetes, inflammation, etc.). Despite overall sequence homology
and identical domain architecture, differences in SH3 and SH2 regulatory
domain accessibility and ability to allosterically autoinhibit the
ATP-binding site have been observed for the prototypical SFKs Src
and Hck. Biochemical and structural studies indicate that the SH2-catalytic
domain (SH2-CD) linker, the intramolecular binding epitope for SFK
SH3 domains, is responsible for allosterically coupling SH3 domain
engagement to autoinhibition of the ATP-binding site through the conformation
of the αC helix. As a relatively unconserved region between
SFK family members, SH2-CD linker sequence variability across the
SFK family is likely a source of nonredundant cellular functions between
individual SFKs via its effect on the availability of SH3 and SH2
domains for intermolecular interactions and post-translational modification.
Using a combination of SFKs engineered with enhanced or weakened regulatory
domain intramolecular interactions and conformation-selective inhibitors
that report αC helix conformation, this study explores how SH2-CD
sequence heterogeneity affects allosteric coupling across the SFK
family by examining Lyn, Fyn1, and Fyn2. Analyses of Fyn1 and Fyn2,
isoforms that are identical but for a 50-residue sequence spanning
the SH2-CD linker, demonstrate that SH2-CD linker sequence differences
can have profound effects on allosteric coupling between otherwise
identical kinases. Most notably, a dampened allosteric connection
between the SH3 domain and αC helix leads to greater autoinhibitory
phosphorylation by Csk, illustrating the complex effects of SH2-CD
linker sequence on cellular function.
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Affiliation(s)
- A C Register
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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17
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Tovo-Rodrigues L, Rohde LA, Menezes AMB, Polanczyk GV, Kieling C, Genro JP, Anselmi L, Hutz MH. DRD4 rare variants in Attention-Deficit/Hyperactivity Disorder (ADHD): further evidence from a birth cohort study. PLoS One 2013; 8:e85164. [PMID: 24391992 PMCID: PMC3877354 DOI: 10.1371/journal.pone.0085164] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/24/2013] [Indexed: 01/02/2023] Open
Abstract
The dopamine receptor D4 (DRD4) is one of the most studied candidate genes for Attention-Deficit/Hyperactivity Disorder (ADHD). An excess of rare variants and non-synonymous mutations in the VNTR region of 7R allele in ADHD subjects was observed in previous studies with clinical samples. We hypothesize that genetic heterogeneity in the VNTR is an important factor in the pathophysiology of ADHD. The subjects included in the present study are members of the 1993 Pelotas Birth Cohort Study (N=5,249). We conducted an association study with the 4,101 subjects who had DNA samples collected. The hyperactivity-inattention scores were assessed through the parent version of the Strengths and Difficulties Questionnaire at 11 and 15 years of age. The contribution of allele’s length and rare variants to high hyperactivity/inattention scores predisposition was evaluated by multivariate logistic regression. No effect of allele length was observed on high scores of hyperactivity-inattention. By contrast, when resequencing/haplotyping was conducted in a subsample, all 7R rare variants as well as non-synonymous 7R rare variants were associated with high hyperactivity/inattention scores (OR=2.561; P=0.024 and OR=3.216; P=0.008 respectively). A trend for association was observed with 4R rare variants. New coding mutations covered 10 novel motifs and many of them are previously unreported deletions leading to different stop codons. Our findings suggest a contribution of DRD4 7R rare variants to high hyperactivity-inattention scores in a population-based sample from a large birth cohort. These findings provide further evidence for an effect of DRD4 7R rare variants and allelic heterogeneity in ADHD genetic susceptibility.
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Affiliation(s)
- Luciana Tovo-Rodrigues
- Genetics Department, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Luis A. Rohde
- Child and Adolescent Psychiatric Division, Hospital de Clinicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), Brazil
| | - Ana M. B. Menezes
- Graduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Guilherme V. Polanczyk
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), Brazil
- Department of Psychiatry, Medical School and Research Support Center on Neurodevelopment and Mental Health, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Christian Kieling
- Child and Adolescent Psychiatric Division, Hospital de Clinicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Julia P. Genro
- Genetics Department, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Luciana Anselmi
- Child and Adolescent Psychiatric Division, Hospital de Clinicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), Brazil
| | - Mara H. Hutz
- Genetics Department, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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18
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Borkar MR, Pissurlenkar RRS, Coutinho EC. HomoSAR: Bridging comparative protein modeling with quantitative structural activity relationship to design new peptides. J Comput Chem 2013; 34:2635-46. [DOI: 10.1002/jcc.23436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/17/2013] [Accepted: 08/21/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Mahesh R. Borkar
- Department of Pharmaceutical Chemistry; Bombay College of Pharmacy; Kalina, Santacruz (East) Mumbai 400098 India
| | - Raghuvir R. S. Pissurlenkar
- Department of Pharmaceutical Chemistry; Bombay College of Pharmacy; Kalina, Santacruz (East) Mumbai 400098 India
| | - Evans C. Coutinho
- Department of Pharmaceutical Chemistry; Bombay College of Pharmacy; Kalina, Santacruz (East) Mumbai 400098 India
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19
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Byrne C, Miclet E, Broutin I, Gallo D, Pelekanou V, Kampa M, Castanas E, Leclercq G, Jacquot Y. Identification of polyproline II regions derived from the proline-rich nuclear receptor coactivators PNRC and PNRC2: new insights for ERα coactivator interactions. Chirality 2013; 25:628-42. [PMID: 23925889 DOI: 10.1002/chir.22188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 04/12/2013] [Indexed: 11/07/2022]
Abstract
Protein-protein interactions are crucial for signal transductions required for cell differentiation and proliferation. Their modulation is therefore key to the development of therapeutic alternatives, particularly in the context of cancer. According to literature data, the polyproline-rich nuclear receptor coactivators PNRC and PNRC2 interact with estrogen receptor (ERα) through their PxxP SH3-binding motifs. In a search to identify the molecular features governing this interaction, we explored using electronic circular dichroism (ECD) spectroscopy and molecular dynamics (MD) calculations, the capacity of a range of putative biologically active peptides derived from these proteins and containing this PxxP motif(s) to form polyproline II (PPII) domains. An additional more exhaustive structural study on a lead PPII peptide was also performed using 2D nuclear magnetic resonance (NMR) spectroscopy. With the exception of one of all the investigated peptides (PNRC-D), binding assays failed to detect any affinity for Grb2 SH3 domains, suggesting that PPII motifs issued from Grb2 antagonists have a binding mode distinct from those derived from Grb2 agonists. Instead, the peptides revealed a competitive binding ability against a synthetic peptide (ERα17p) with a putative PPII-cognate domain located within a coregulator recruitment region of ERα (AF-2 site). Our work, which constitutes the first structure-related interaction study concerning PNRC and PNRC2, supports not only the existence of PxxP-induced PPII sequences in these coregulators, but also confirms the presence of a PPII recognition site in the AF-2 of the steroid receptor ERα, a region important for transcription regulation.
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Affiliation(s)
- C Byrne
- Laboratoire des BioMolécules (LBM), CNRS - UMR 7203, Ecole Normale Supérieure / Université Pierre et Marie Curie 24, rue Lhomond, 75231, Paris Cedex 05, France; Fondation Pierre-Gilles de Gennes pour la Recherche, 29, rue d'Ulm, 75005, Paris, France
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20
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Chaubet G, Coursindel T, Morelli X, Betzi S, Roche P, Guari Y, Lebrun A, Toupet L, Collette Y, Parrot I, Martinez J. Stereoselective synthesis of original spirolactams displaying promising folded structures. Org Biomol Chem 2013; 11:4719-26. [DOI: 10.1039/c3ob40643a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Secondary structure, a missing component of sequence-based minimotif definitions. PLoS One 2012; 7:e49957. [PMID: 23236358 PMCID: PMC3517595 DOI: 10.1371/journal.pone.0049957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 10/15/2012] [Indexed: 12/27/2022] Open
Abstract
Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis of occurrences of minimotifs in structured and disordered regions of proteins, and review of the literature support a new model for minimotif definitions that includes sequence, structure, and function.
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22
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Abstract
Tight junctions (TJs) are intercellular contacts that seal the space between the individual cells of an epithelial sheet or stratifying epithelia, such as the epidermis, so that they can collectively separate tissue compartments. Intercellular junctions, such as adherens and TJs, play a crucial role in the formation and maintenance of epithelial and endothelial barriers. A variety of components including claudins, occludin, tricellulin, zonula occluden proteins and junctional adhesion molecules have been identified in complex localization patterns in mammalian epidermis. In several skin diseases that are characterized by impaired skin barrier function, altered proliferation/differentiation of the epidermis and/or infiltration of inflammatory cells, altered expression patterns of TJ proteins have been observed. This review is aimed at providing an insight into the molecular composition, tools for identification and understanding the role of TJs in skin diseases and barrier function regulation.
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23
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Gushchina LV, Gabdulkhakov AG, Nikonov SV, Filimonov VV. High-resolution crystal structure of spectrin SH3 domain fused with a proline-rich peptide. J Biomol Struct Dyn 2012; 29:485-95. [PMID: 22066535 DOI: 10.1080/07391102.2011.10507400] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A new chimeric protein, named WT-CIIA, was designed by connecting the proline-rich decapeptide PPPVPPYSAG to the C-terminus of the alpha-spectrin SH3 domain through a natural twelve-residue linker to obtain a single-chain model that would imitate intramolecular SH3-ligand interaction. The crystal structure of this fusion protein was determined at 1.7 Å resolution. The asymmetric unit of the crystal contained two SH3 globules contacting with one PPPVPPY fragment located between them. The domains are related by the two-fold non-crystallographic axis and the ligand lies in two opposite orientations with respect to the conservative binding sites of SH3 domains.
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Affiliation(s)
- Liubov V Gushchina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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24
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SH3 domains: modules of protein-protein interactions. Biophys Rev 2012; 5:29-39. [PMID: 28510178 DOI: 10.1007/s12551-012-0081-z] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/29/2012] [Indexed: 01/01/2023] Open
Abstract
Src homology 3 (SH3) domains are involved in the regulation of important cellular pathways, such as cell proliferation, migration and cytoskeletal modifications. Recognition of polyproline and a number of noncanonical sequences by SH3 domains has been extensively studied by crystallography, nuclear magnetic resonance and other methods. High-affinity peptides that bind SH3 domains are used in drug development as candidates for anticancer treatment. This review summarizes the latest achievements in deciphering structural determinants of SH3 function.
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25
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Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains. FEBS Lett 2012; 586:2619-30. [DOI: 10.1016/j.febslet.2012.04.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/27/2012] [Accepted: 04/30/2012] [Indexed: 01/16/2023]
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26
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Tovo-Rodrigues L, Rohde LA, Roman T, Schmitz M, Polanczyk G, Zeni C, Marques FZC, Contini V, Grevet EH, Belmonte-de-Abreu P, Bau CHD, Hutz MH. Is there a role for rare variants in DRD4 gene in the susceptibility for ADHD? Searching for an effect of allelic heterogeneity. Mol Psychiatry 2012; 17:520-6. [PMID: 21403674 DOI: 10.1038/mp.2011.12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Although several studies have demonstrated an association between the 7-repeat (7R) allele in the 48-bp variable number of tandem repeats (VNTRs) in the exon 3 at dopamine receptor D4 (DRD4) gene and attention-deficit/hyperactivity disorder (ADHD), others failed to replicate this finding. In this study, a total of 786 individuals with ADHD were genotyped for DRD4 exon 3 VNTR. All 7R homozygous subjects were selected for VNTR re-sequencing. Subjects homozygous for the 4R allele were selected paired by age, ancestry and disorder subtypes in order to have a sample as homogeneous as possible with 7R/7R individuals. Using these criteria, 103 individuals (66 with ADHD and 37 control individuals) were further investigated. An excess of rare variants were observed in the 7R alleles of ADHD patient when compared with controls (P=0.031). This difference was not observed in 4R allele. Furthermore, nucleotide changes that predict synonymous and non-synonymous substitutions were more common in the 7R sample (P=0.008 for total substitutions and P=0.043 for non-synonymous substitutions). In silico prediction of structural/functional alterations caused by these variants have also been observed. Our findings suggest that not only repeat length but also DNA sequence should be assessed to better understand the role of DRD4 exon 3 VNTR in ADHD genetic susceptibility.
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Affiliation(s)
- L Tovo-Rodrigues
- Departament of Genetics, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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27
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Transient protein-protein interaction of the SH3-peptide complex via closely located multiple binding sites. PLoS One 2012; 7:e32804. [PMID: 22457720 PMCID: PMC3310816 DOI: 10.1371/journal.pone.0032804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 02/05/2012] [Indexed: 01/20/2023] Open
Abstract
Protein-protein interactions play an essential role in cellular processes. Certain proteins form stable complexes with their partner proteins, whereas others function by forming transient complexes. The conventional protein-protein interaction model describes an interaction between two proteins under the assumption that a protein binds to its partner protein through a single binding site. In this study, we improved the conventional interaction model by developing a Multiple-Site (MS) model in which a protein binds to its partner protein through closely located multiple binding sites on a surface of the partner protein by transiently docking at each binding site with individual binding free energies. To test this model, we used the protein-protein interaction mediated by Src homology 3 (SH3) domains. SH3 domains recognize their partners via a weak, transient interaction and are therefore promiscuous in nature. Because the MS model requires large amounts of data compared with the conventional interaction model, we used experimental data from the positionally addressable syntheses of peptides on cellulose membranes (SPOT-synthesis) technique. From the analysis of the experimental data, individual binding free energies for each binding site of peptides were extracted. A comparison of the individual binding free energies from the analysis with those from atomistic force fields gave a correlation coefficient of 0.66. Furthermore, application of the MS model to 10 SH3 domains lowers the prediction error by up to 9% compared with the conventional interaction model. This improvement in prediction originates from a more realistic description of complex formation than the conventional interaction model. The results suggested that, in many cases, SH3 domains increased the protein complex population through multiple binding sites of their partner proteins. Our study indicates that the consideration of general complex formation is important for the accurate description of protein complex formation, and especially for those of weak or transient protein complexes.
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28
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Interfacial water molecules in SH3 interactions: a revised paradigm for polyproline recognition. Biochem J 2012; 442:443-51. [DOI: 10.1042/bj20111089] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In spite of its biomedical relevance, polyproline recognition is still not fully understood. The disagreement between the current description of SH3 (Src homology 3) complexes and their thermodynamic behaviour calls for a revision of the SH3-binding paradigm. Recently, Abl-SH3 was demonstrated to recognize its ligands by a dual binding mechanism involving a robust network of water-mediated hydrogen bonds that complements the canonical hydrophobic interactions. The systematic analysis of the SH3 structural database in the present study reveals that this dual binding mode is universal to SH3 domains. Tightly bound buried-interfacial water molecules were found in all SH3 complexes studied mediating the interaction between the peptide ligand and the domain. Moreover, structural waters were also identified in a high percentage of the free SH3 domains. A detailed analysis of the pattern of water-mediated interactions enabled the identification of conserved hydration sites in the polyproline-recognition region and the establishment of relationships between hydration profiles and the sequence of both ligands and SH3 domains. Water-mediated interactions were also systematically observed in WW (protein–protein interaction domain containing two conserved tryptophan residues), UEV (ubiquitin-conjugating enzyme E2 variant) and EVH-1 [Ena/VASP (vasodilator-stimulated phosphoprotein) homology 1] structures. The results of the present study clearly indicate that the current description of proline-rich sequence recognition by protein–protein interaction modules is incomplete and insufficient for a correct understanding of these systems. A new binding paradigm is required that includes interfacial water molecules as relevant elements in polyproline recognition.
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29
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Balakrishnan S, Scheuermann MJ, Zondlo NJ. Arginine mimetics using α-guanidino acids: introduction of functional groups and stereochemistry adjacent to recognition guanidiniums in peptides. Chembiochem 2012; 13:259-70. [PMID: 22213184 PMCID: PMC3712784 DOI: 10.1002/cbic.201100638] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Indexed: 01/19/2023]
Abstract
Arginine residues are broadly employed for specific biomolecular recognition, including in protein-protein, protein-DNA, and protein-RNA interactions. Arginine recognition commonly exploits the potential for bidentate electrostatic and hydrogen-bonding interactions. However, in arginine residues, the guanidinium functional group is located at the terminus of a flexible hydrocarbon side chain, which lacks the functionality to contribute to specific arginine-mediated recognition and may entropically disfavor binding. In order to enhance the potential for specificity and affinity in arginine-mediated molecular recognition, we have developed an approach to the synthesis of peptides that incorporates an α-guanidino acid as a novel arginine mimetic. α-Guanidino acids, derived from α-amino acids, with guanidinylation of the amino group, were incorporated stereospecifically into peptides on solid phase via coupling of an Fmoc amino acid to diaminopropionic acid (Dap), Fmoc deprotection, guanidinylation of the amine on solid phase, and deprotection, generating a peptide containing an α-functionalized arginine mimetic. This approach was examined by incorporating arginine mimetics into ligands for the Src, Grb, and Crk SH3 domains at the site of the key recognition arginine. Protein binding was examined for peptides containing guanidino acids derived from Gly, L-Val, L-Phe, L-Trp, D-Val, D-Phe, and D-Trp. We demonstrate that paralogue specificity and target site affinity may be modulated with the use of α-guanidino acid-derived arginine mimetics, generating peptides that exhibit enhanced Src specificity by selection against Grb and peptides that reverse the specificity of the native peptide ligand, with enhancements in Src target specificity of up to 15-fold (1.6 kcal mol(-1)).
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Affiliation(s)
- Shalini Balakrishnan
- Department of Chemistry and Biochemistry University of Delaware Newark, Delaware 19716 (USA)
| | - Michael J. Scheuermann
- Department of Chemistry and Biochemistry University of Delaware Newark, Delaware 19716 (USA)
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry University of Delaware Newark, Delaware 19716 (USA)
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González-Mariscal L, Quirós M, Díaz-Coránguez M. ZO proteins and redox-dependent processes. Antioxid Redox Signal 2011; 15:1235-53. [PMID: 21294657 DOI: 10.1089/ars.2011.3913] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
SIGNIFICANCE ZO-1, ZO-2, and ZO-3 are scaffold proteins of the tight junction (TJ) that belong to the MAGUK protein family characterized for exhibiting PDZ, SH3, and GuK domains. ZO proteins are present only in multicellular organisms, being the placozoa the first to have them. ZO proteins associate among themselves and with other integral and adaptor proteins of the TJ, of the ZA and of gap junctions, as with numerous signaling proteins and the actin cytoskeleton. ZO proteins are also present at the nucleus of proliferating cells. RECENT ADVANCES Oxidative stress disassembles the TJs of endothelial and epithelial cells. CRITICAL ISSUES Oxidative stress alters ZO proteins expression and localization, in conditions like hypoxia, bacterial and viral infections, vitamin deficiencies, age-related diseases, diabetes and inflammation, alcohol and tobacco consumption. FUTURE DIRECTIONS Molecules present in the signaling pathways triggered by oxidative stress can be targets for therapeutic intervention.
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Affiliation(s)
- Lorenza González-Mariscal
- Department of Physiology, Biophysics and Neuroscience, Center for Research and Advanced Studies (Cinvestav), Mexico DF, México.
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32
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Gorelik M, Stanger K, Davidson AR. A Conserved residue in the yeast Bem1p SH3 domain maintains the high level of binding specificity required for function. J Biol Chem 2011; 286:19470-7. [PMID: 21489982 DOI: 10.1074/jbc.m111.229294] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The yeast Bem1p SH3b and Nbp2p SH3 domains are unusual because they bind to peptides containing the same consensus sequence, yet they perform different functions and display low sequence similarity. In this work, by analyzing the interactions of these domains with six biologically relevant peptides containing the consensus sequence, they are shown to possess finely tuned and distinct binding specificities. We also identify a residue in the Bem1p SH3b domain that inhibits binding, yet is highly conserved for the purpose of preventing nonspecific interactions. Substitution of this residue results in a marked reduction of in vivo function that is caused by titration of the domain away from its proper targets through nonspecific interactions with other proteins. This work provides a clear illustration of the importance of intrinsic binding specificity for the function of protein-protein interaction modules, and the key role of "negative" interactions in determining the specificity of a domain.
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Affiliation(s)
- Maryna Gorelik
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Kutyshenko VP, Gushchina LV, Khristoforov VS, Prokhorov DA, Timchenko MA, Kudrevatykh YA, Fedyukina DV, Filimonov VV. NMR structure and dynamics of the chimeric protein SH3-F2. Mol Biol 2010. [DOI: 10.1134/s0026893310060129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Xue B, Dunker AK, Uversky VN. Retro-MoRFs: identifying protein binding sites by normal and reverse alignment and intrinsic disorder prediction. Int J Mol Sci 2010; 11:3725-47. [PMID: 21152297 PMCID: PMC2996789 DOI: 10.3390/ijms11103725] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 09/10/2010] [Accepted: 09/15/2010] [Indexed: 11/16/2022] Open
Abstract
Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying MoRF-based protein-protein interactions. The method of reverse sequence alignment is also rationalized here as a novel approach for finding additional interaction regions, leading to the concept of a retro-MoRF, which has the reversed sequence of an identified MoRF. The set of retro-MoRF binding partners likely overlap the partner-sets of the originally identified MoRFs. The high abundance of MoRF-containing intrinsically disordered proteins in nature suggests the possibility that the number of retro-MoRFs could likewise be very high. This hypothesis provides new grounds for exploring the mysteries of protein-protein interaction networks at the genome level.
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Affiliation(s)
- Bin Xue
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; E-Mails: (B.X.); (A.K.D.)
- Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; E-Mails: (B.X.); (A.K.D.)
- Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Vladimir N. Uversky
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; E-Mails: (B.X.); (A.K.D.)
- Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- * Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-317-278-6448; Fax: +1-317-278-9217
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Cai J, Ou R, Xu YS, Yang L, Lin Z, Shu M. Modeling and predicting interactions between the human amphiphysin SH3 domains and their peptide ligands based on amino acid information. J Pept Sci 2010; 16:627-32. [DOI: 10.1002/psc.1274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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36
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Li C, Pazgier M, Li J, Li C, Liu M, Zou G, Li Z, Chen J, Tarasov SG, Lu WY, Lu W. Limitations of peptide retro-inverso isomerization in molecular mimicry. J Biol Chem 2010; 285:19572-81. [PMID: 20382735 PMCID: PMC2885236 DOI: 10.1074/jbc.m110.116814] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 04/09/2010] [Indexed: 12/13/2022] Open
Abstract
A retro-inverso peptide is made up of d-amino acids in a reversed sequence and, when extended, assumes a side chain topology similar to that of its parent molecule but with inverted amide peptide bonds. Despite their limited success as antigenic mimicry, retro-inverso isomers generally fail to emulate the protein-binding activities of their parent peptides of an alpha-helical nature. In studying the interaction between the tumor suppressor protein p53 and its negative regulator MDM2, Sakurai et al. (Sakurai, K., Chung, H. S., and Kahne, D. (2004) J. Am. Chem. Soc. 126, 16288-16289) made a surprising finding that the retro-inverso isomer of p53(15-29) retained the same binding activity as the wild type peptide as determined by inhibition enzyme-linked immunosorbent assay. The authors attributed the unusual outcome to the ability of the D-peptide to adopt a right-handed helical conformation upon MDM2 binding. Using a battery of biochemical and biophysical tools, we found that retro-inverso isomerization diminished p53 (15-29) binding to MDM2 or MDMX by 3.2-3.3 kcal/mol. Similar results were replicated with the C-terminal domain of HIV-1 capsid protein (3.0 kcal/mol) and the Src homology 3 domain of Abl tyrosine kinase (3.4 kcal/mol). CD and NMR spectroscopic as well as x-ray crystallographic studies showed that D-peptide ligands of MDM2 invariably adopted left-handed helical conformations in both free and bound states. Our findings reinforce that the retro-inverso strategy works poorly in molecular mimicry of biologically active helical peptides, due to inherent differences at the secondary and tertiary structure levels between an l-peptide and its retro-inverso isomer despite their similar side chain topologies at the primary structure level.
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Affiliation(s)
- Chong Li
- From the School of Pharmacy, Fudan University, Shanghai 201203, China
- the Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Marzena Pazgier
- the Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Jing Li
- the Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Changqing Li
- the Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Min Liu
- the Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Guozhang Zou
- the Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Zhenyu Li
- the Molecular Oncology Program, H. Lee Moffitt Cancer Center, Tampa, Florida 33612, and
| | - Jiandong Chen
- the Molecular Oncology Program, H. Lee Moffitt Cancer Center, Tampa, Florida 33612, and
| | - Sergey G. Tarasov
- the Structural Biophysics Laboratory, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Wei-Yue Lu
- From the School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Wuyuan Lu
- the Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
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Prymula K, Sałapa K, Roterman I. "Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids. J Mol Model 2010; 16:1269-82. [PMID: 20084418 DOI: 10.1007/s00894-009-0639-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Accepted: 12/07/2009] [Indexed: 12/25/2022]
Abstract
The proteins composed of short polypeptides (about 70 amino acid residues) representing the following functional groups (according to PDB notation): growth hormones, serine protease inhibitors, antifreeze proteins, chaperones and proteins of unknown function, were selected for structural and functional analysis. Classification based on the distribution of hydrophobicity in terms of deficiency/excess as the measure of structural and functional specificity is presented. The experimentally observed distribution of hydrophobicity in the protein body is compared to the idealized one expressed by a three-dimensional Gauss function. The differences between these two distributions reveal the specificity of structural/functional characteristics of the protein. The residues of hydrophobicity deficiency versus the idealized distribution are assumed to indicate cavities with the potential to bind ligands, while the residues of hydrophobicity excess are interpreted as potentially participating in protein-protein complexation. The distribution of hydrophobicity irregularity seems to be specific for particular structures and functions of proteins. A comparative analysis of such profiles is carried out to identify the potential biological activity of proteins of unknown function.
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Affiliation(s)
- Katarzyna Prymula
- Department of Bioinformatics, Telemedicine Jagiellonian University - Collegium Medicum, Lazarza 16, 31-530, Krakow, Poland
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38
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Terentiev AA, Moldogazieva NT, Shaitan KV. Dynamic proteomics in modeling of the living cell. Protein-protein interactions. BIOCHEMISTRY (MOSCOW) 2010; 74:1586-607. [DOI: 10.1134/s0006297909130112] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Structural differences between the SH3-HOOK-GuK domains of SAP90/PSD-95 and SAP97. Protein Expr Purif 2009; 68:201-7. [DOI: 10.1016/j.pep.2009.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 07/14/2009] [Accepted: 07/20/2009] [Indexed: 11/24/2022]
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40
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Palencia A, Camara-Artigas A, Pisabarro MT, Martinez JC, Luque I. Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl. J Biol Chem 2009; 285:2823-33. [PMID: 19906645 DOI: 10.1074/jbc.m109.048033] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design.
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Affiliation(s)
- Andres Palencia
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
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41
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Gushchina LV, Gabdulkhakov AG, Filimonov VV. Design and structural thermodynamic studies of the chimeric protein derived from spectrin SH3 domain. Mol Biol 2009. [DOI: 10.1134/s0026893309030121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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42
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Grosdidier S, Fernández-Recio J. Docking and scoring: applications to drug discovery in the interactomics era. Expert Opin Drug Discov 2009; 4:673-86. [DOI: 10.1517/17460440903002067] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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43
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Kapitán J, Gallo D, Goasdoué N, Nicaise M, Desmadril M, Hecht L, Leclercq G, Barron LD, Jacquot Y. Identification of a human estrogen receptor α-derived antiestrogenic peptide that adopts a polyproline II conformation. J Pept Sci 2009; 15:455-64. [DOI: 10.1002/psc.1136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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44
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Bell AJ, Guerra C, Phung V, Nair S, Seetharam R, Satir P. GEF1 is a ciliary Sec7 GEF of Tetrahymena thermophila. CELL MOTILITY AND THE CYTOSKELETON 2009; 66:483-99. [PMID: 19267341 DOI: 10.1002/cm.20348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Ciliary guanine nucleotide exchange factors (GEFs) potentially activate G proteins in intraflagellar transport (IFT) cargo release. Several classes of GEFs have been localized to cilia or basal bodies and shown to be functionally important in the prevention of ciliopathies, but ciliary Arl-type Sec 7 related GEFs have not been well characterized. Nair et al. [ 1999] identified a Paramecium ciliary Sec7 GEF, PSec7. In Tetrahymena, Gef1p (GEF1), tentatively identified by PSec7 antibody, possesses ciliary and nuclear targeting sequences and like PSec7 localizes to cilia and macronuclei. Upregulation of GEF1 RNA followed deciliation and subsequent ciliary regrowth. Corresponding to similar Psec7 domains, GEF1domains contain IQ-like motifs and putative PH domains, in addition to GBF/BIG canonical motifs. Genomic analysis identified two additional Tetrahymena GBF/BIG Sec7 family GEFs (GEF2, GEF3), which do not possess ciliary targeting sequences. GEF1 and GEF2 were HA modified to determine cellular localization. Cells transformed to produce appropriately truncated GEF1-HA showed localization to somatic and oral cilia, but not to macronuclei. Subtle defects in ciliary stability and function were detected. GEF2-HA localized near basal bodies but not to cilia. These results indicate that GEF1 is the resident Tetrahymena ciliary protein orthologous to PSec7. Cell Motil. Cytoskeleton 2009. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Aaron J Bell
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA.
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45
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Intertwined dimeric structure for the SH3 domain of the c-Src tyrosine kinase induced by polyethylene glycol binding. FEBS Lett 2009; 583:749-53. [PMID: 19185573 DOI: 10.1016/j.febslet.2009.01.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 11/21/2022]
Abstract
Here we report the first crystal structure of the SH3 domain of the cellular Src tyrosine kinase (c-Src-SH3) domain on its own. In the crystal two molecules of c-Src-SH3 exchange their -RT loops generating an intertwined dimer, in which the two SH3 units, preserving the binding site configuration, are oriented to allow simultaneous binding of two ligand molecules. The dimerization of c-Src-SH3 is induced, both in the crystal and in solution, by the binding of a PEG molecule at the dimer interface, indicating that this type of conformations are energetically close to the native structure. These results have important implications respect to in vivo oligomerization and amyloid aggregation.
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46
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Zhou P, Tian F, Chen X, Shang Z. Modeling and prediction of binding affinities between the human amphiphysin SH3 domain and its peptide ligands using genetic algorithm-Gaussian processes. Biopolymers 2008; 90:792-802. [DOI: 10.1002/bip.21091] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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47
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Liang G, Chen G, Niu W, Li Z. Factor Analysis Scales of Generalized Amino Acid Information as Applied in Predicting Interactions between the Human Amphiphysin-1 SH3 Domains and Their Peptide Ligands. Chem Biol Drug Des 2008; 71:345-51. [DOI: 10.1111/j.1747-0285.2008.00641.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Dokainish H, Gavicherla B, Shen Y, Ireton K. The carboxyl-terminal SH3 domain of the mammalian adaptor CrkII promotes internalization of Listeria monocytogenes through activation of host phosphoinositide 3-kinase. Cell Microbiol 2008; 9:2497-516. [PMID: 17848169 DOI: 10.1111/j.1462-5822.2007.00976.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The intracellular bacterial pathogen Listeria monocytogenes causes food-borne illnesses leading to gastroenteritis, meningitis or abortion. Listeria induces its internalization into some mammalian cells through binding of the bacterial surface protein InlB to its host receptor, the Met Receptor Tyrosine Kinase. InlB-induced activation of Met stimulates host signal transduction pathways that culminate in cell surface changes driving pathogen engulfment. One mammalian protein with the potential to couple Met to downstream signalling is the adaptor CrkII. CrkII contains an unusual carboxyl-terminal SH3 domain (SH3C) that promotes entry of Listeria. However, binding partners or downstream effectors of SH3C remain unknown. Here, we use RNA interference and overexpression studies to demonstrate that SH3C affects bacterial uptake, at least in part, through stimulation of host phosphatidylinositide (PI) 3-kinase. Experiments with latex beads coated with InlB protein indicated that one potential role of SH3C and PI 3 kinase is to promote changes in the F-actin cytoskeleton necessary for particle engulfment. Taken together, our results indicate that the CrkII SH3C domain engages a cellular ligand that regulates PI 3 kinase activity and host cell surface rearrangements.
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Affiliation(s)
- Hatem Dokainish
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
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49
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Guo L, Feng Y, Zhang Z, Yao H, Luo Y, Wang J, Huang L. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea. Nucleic Acids Res 2008; 36:1129-37. [PMID: 18096617 PMCID: PMC2275093 DOI: 10.1093/nar/gkm1128] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 12/03/2007] [Accepted: 12/04/2007] [Indexed: 11/13/2022] Open
Abstract
Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo. The solution structure and DNA-binding surface of Cren7 from the hyperthermophilic crenarchaeon Sulfolobus solfataricus were determined by NMR. The protein adopts an SH3-like fold. It interacts with duplex DNA through a beta-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure. These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization.
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Affiliation(s)
- Li Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Yingang Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Hongwei Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Yuanming Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Jinfeng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
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50
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Robinson RA, Lu X, Jones EY, Siebold C. Biochemical and Structural Studies of ASPP Proteins Reveal Differential Binding to p53, p63, and p73. Structure 2008; 16:259-68. [DOI: 10.1016/j.str.2007.11.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 11/08/2007] [Accepted: 11/09/2007] [Indexed: 01/03/2023]
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