1
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Timalsina B, Lee S, Kaang BK. Advances in the labelling and selective manipulation of synapses. Nat Rev Neurosci 2024; 25:668-687. [PMID: 39174832 DOI: 10.1038/s41583-024-00851-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Synapses are highly specialized neuronal structures that are essential for neurotransmission, and they are dynamically regulated throughout the lifetime. Although accumulating evidence indicates that these structures are crucial for information processing and storage in the brain, their precise roles beyond neurotransmission are yet to be fully appreciated. Genetically encoded fluorescent tools have deepened our understanding of synaptic structure and function, but developing an ideal methodology to selectively visualize, label and manipulate synapses remains challenging. Here, we provide an overview of currently available synapse labelling techniques and describe their extension to enable synapse manipulation. We categorize these approaches on the basis of their conceptual bases and target molecules, compare their advantages and limitations and propose potential modifications to improve their effectiveness. These methods have broad utility, particularly for investigating mechanisms of synaptic function and synaptopathy.
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Affiliation(s)
- Binod Timalsina
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Sangkyu Lee
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Bong-Kiun Kaang
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea.
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2
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Ramli AH, Swain P, Mohd Fahmi MSA, Abas F, Leong SW, Tejo BA, Shaari K, Ali AH, Agustar HK, Awang R, Ng YL, Lau YL, Md Razali MA, Mastuki SN, Mohmad Misnan N, Mohd Faudzi SM, Kim CH. Preliminary insight on diarylpentanoids as potential antimalarials: In silico, in vitro pLDH and in vivo zebrafish toxicity assessment. Heliyon 2024; 10:e27462. [PMID: 38495201 PMCID: PMC10943399 DOI: 10.1016/j.heliyon.2024.e27462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
Malaria remains a major public health problem worldwide, including in Southeast Asia. Chemotherapeutic agents such as chloroquine (CQ) are effective, but problems with drug resistance and toxicity have necessitated a continuous search for new effective antimalarial agents. Here we report on a virtual screening of ∼300 diarylpentanoids and derivatives, in search of potential Plasmodium falciparum lactate dehydrogenase (PfLDH) inhibitors with acceptable drug-like properties. Several molecules with binding affinities comparable to CQ were chosen for in vitro validation of antimalarial efficacy. Among them, MS33A, MS33C and MS34C are the most promising against CQ-sensitive (3D7) with EC50 values of 1.6, 2.5 and 3.1 μM, respectively. Meanwhile, MS87 (EC50 of 1.85 μM) shown the most active against the CQ-resistant Gombak A strain, and MS33A and MS33C the most effective P. knowlesi inhibitors (EC50 of 3.6 and 5.1 μM, respectively). The in vitro cytotoxicity of selected diarylpentanoids (MS33A, MS33C, MS34C and MS87) was tested on Vero mammalian cells to evaluate parasite selectivity (SI), showing moderate to low cytotoxicity (CC50 > 82 μM). In addition, MS87 exhibited a high SI and the lowest resistance index (RI), suggesting that MS87 may exert effective parasite inhibition with low resistance potential in the CQ-resistant P. falciparum strain. Furthermore, the in vivo toxicity of the molecules on early embryonic development, the cardiovascular system, heart rate, motor activity and apoptosis were assessed in a zebrafish animal model. The overall results indicate the preliminary potential of diarylpentanoids, which need further investigation for their development as new antimalarial agents.
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Affiliation(s)
- Amirah Hani Ramli
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Puspanjali Swain
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea
| | - Muhammad Syafiq Akmal Mohd Fahmi
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Faridah Abas
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
- Department of Food Science, Faculty of Food Science & Technology, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Sze Wei Leong
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Bimo Ario Tejo
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Khozirah Shaari
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Amatul Hamizah Ali
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Hani Kartini Agustar
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Rusdam Awang
- UPM - MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yee Ling Ng
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Siti Nurulhuda Mastuki
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Norazlan Mohmad Misnan
- Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, 40170, Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Siti Munirah Mohd Faudzi
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea
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3
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Zhao S, Shen L, Wang Q, Lu W. Dynamics simulation, energetics calculation and experimental analysis of the intermolecular interaction between human neonatal ABL SH3 domain and its N-substituted peptoid ligands. J Biomol Struct Dyn 2023:1-8. [PMID: 37909467 DOI: 10.1080/07391102.2023.2272344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/08/2023] [Indexed: 11/03/2023]
Abstract
Non-receptor tyrosine kinase of neonatal ABL (nABL) is distributed in the nucleus and cytoplasm of proliferating cells in embryo and neonate, and has been implicated in the pathogenesis of neonatal leukemia and other hematological diseases. The kinase contains a regulatory Src homology 3 (SH3) domain that can specifically recognize proline-rich peptide segments on its partner protein surface. In this study, we systematically investigated the N-substitution effect on the binding of an empirically designed proline-rich peptide p9 to nABL SH3 domain by integrating dynamics simulations, energetics calculations and fluorescence affinity assays. The p9 is an almost all proline-composed decapeptide, with only a sole tyrosine at its residue 4, which has been found to bind nABL SH3 domain at a micromolar level in a class I mode. Here, the non-key residues of p9 peptide were independently replaced by various N-substituted amino acids to create a systematic N-substitution profile, from which we can identify those favorable, neutral and unfavorable substitutions at each peptide residue. On this basis a combinatorial peptoid library was rationally designed by systematically combining the favorable N-substituted amino acids at non-key residues of p9 peptide, thus resulting in a number of its peptoid counterparts. The binding affinity of top peptoid hits was observed to be comparable with or improved moderately relative to p9 peptide, with Kd ranging between 3.1 and 76 μM. Structural analysis revealed that the peptoids can be divided into exposed, polar and hydrophobic regions from N- to C-termini, in which the polar and hydrophobic regions confer specificity and stability to the domain-peptoid interaction, respectively. In addition, a designed peptoid was also observed to exhibit 5.3-fold SH3-selectivity for nABL over cSRC, suggesting that the N-substitution can be used to improve not only binding affinity but also recognition specificity of SH3 binders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shijian Zhao
- Department of Gynaecology and Obstetrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, China
| | - Lili Shen
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, China
| | - Qiuqin Wang
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiao Lu
- Department of Gynaecology and Obstetrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, China
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4
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Fu H, Chen H, Blazhynska M, Goulard Coderc de Lacam E, Szczepaniak F, Pavlova A, Shao X, Gumbart JC, Dehez F, Roux B, Cai W, Chipot C. Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations. Nat Protoc 2022; 17:1114-1141. [PMID: 35277695 PMCID: PMC10082674 DOI: 10.1038/s41596-021-00676-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/07/2021] [Indexed: 11/09/2022]
Abstract
Designing a reliable computational methodology to calculate protein:ligand standard binding free energies is extremely challenging. The large change in configurational enthalpy and entropy that accompanies the association of ligand and protein is notoriously difficult to capture in naive brute-force simulations. Addressing this issue, the present protocol rests upon a rigorous statistical mechanical framework for the determination of protein:ligand binding affinities together with the comprehensive Binding Free-Energy Estimator 2 (BFEE2) application software. With the knowledge of the bound state, available from experiments or docking, application of the BFEE2 protocol with a reliable force field supplies in a matter of days standard binding free energies within chemical accuracy, for a broad range of protein:ligand complexes. Limiting undesirable human intervention, BFEE2 assists the end user in preparing all the necessary input files and performing the post-treatment of the simulations towards the final estimate of the binding affinity.
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Affiliation(s)
- Haohao Fu
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, China
| | - Haochuan Chen
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, China
| | - Marharyta Blazhynska
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Emma Goulard Coderc de Lacam
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Florence Szczepaniak
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Xueguang Shao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, China
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - François Dehez
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,Department of Chemistry, University of Chicago, Chicago, IL, USA.,Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL, USA
| | - Wensheng Cai
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin, China.
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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5
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Martinez JC, Castillo F, Ruiz-Sanz J, Murciano-Calles J, Camara-Artigas A, Luque I. Understanding binding affinity and specificity of modular protein domains: A focus in ligand design for the polyproline-binding families. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:161-188. [PMID: 35534107 DOI: 10.1016/bs.apcsb.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Within the modular protein domains there are five families that recognize proline-rich sequences: SH3, WW, EVH1, GYF and UEV domains. This chapter reviews the main strategies developed for the design of ligands for these families, including peptides, peptidomimetics and drugs. We also describe some studies aimed to understand the molecular reasons responsible for the intrinsic affinity and specificity of these domains.
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Affiliation(s)
- Jose C Martinez
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
| | - Francisco Castillo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Javier Ruiz-Sanz
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Javier Murciano-Calles
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Ana Camara-Artigas
- Departamento de Química Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario ceiA3 y CIAMBITAL, Almeria, Spain
| | - Irene Luque
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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6
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Chen F, Wang Q, Mu Y, Sun S, Yuan X, Shang P, Ji B. Systematic profiling and identification of the peptide-mediated interactions between human Yes-associated protein and its partners in esophageal cancer. J Mol Recognit 2021; 35:e2947. [PMID: 34964176 DOI: 10.1002/jmr.2947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/26/2021] [Accepted: 12/10/2021] [Indexed: 11/07/2022]
Abstract
Human Yes-associated protein (YAP) is involved in the Hippo signaling pathway and serves as a coactivator to modulate gene expression, which contains a transactivation domain (TD) responsible for binding to the downstream TEA domain family (TEAD) of transcription factors and two WW1/2 domains that recognize the proline-rich motifs (PRMs) present in a variety of upstream protein partners through peptide-mediated interactions (PMIs). The downstream YAP TD-TEAD interactions are closely associated with gastric cancer, and a number of therapeutic agents have been developed to target the interactions. In contrast, the upstream YAP WW1/2-partner interactions are thought to be involved in esophageal cancer but still remain largely unexplored. Here, we attempted to elucidate the complicated PMIs between the YAP WW1/2 domains and various PRMs of YAP-interacting proteins. A total of 106 peptide segments carrying the class I WW-binding motif [P/L]Px[Y/P] were extracted from 22 partner candidates, which are potential recognition sites of YAP WW1/2 domains. Structural and energetic analyses of the intermolecular interactions between the domains and peptides created a systematic domain-peptide binding profile, from which a number of biologically functional PMIs were identified and then substantiated in vitro using fluorescence spectroscopy assays. It is revealed that: (a) The sequence requirement for the partner recognition site binding to YAP WW1/2 domains is a decapeptide segment that contains a core PRM motif as well as two three-residue extensions from each side of the motif; the core motif and extended sections are responsible for the binding stability and recognition specificity of domain-peptide interaction, respectively. (b) There is an exquisite difference in the recognition specificity of the two domains; the LPxP and PPxP appear to more prefer WW1 than WW2, whereas the WW2 can bind more effectively to LPxY and PPxY than WW1. (c) WW2 generally exhibits a higher affinity to the panel of recognition site candidates than WW1. In addition, a number of partner peptides were found as promising recognition sites of the two domains and/or to have a good selectivity between the two domains. For example, the DVL1 peptide was determined to have moderate affinity to WW2 and strong selectivity for WW2 over WW1. Hydrogen bonds play a central role in selectivity.
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Affiliation(s)
- Fei Chen
- Department of Gastroenterology, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Qifei Wang
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Yushu Mu
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Shibin Sun
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Xulong Yuan
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Pan Shang
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Bo Ji
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
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Montecchini O, Braidotti S, Franca R, Zudeh G, Boni C, Sorio C, Toffoletti E, Rabusin M, Tommasini A, Decorti G, Stocco G. A Novel ELISA-Based Peptide Biosensor Assay for Screening ABL1 Activity in vitro: A Challenge for Precision Therapy in BCR-ABL1 and BCR-ABL1 Like Leukemias. Front Pharmacol 2021; 12:749361. [PMID: 34867354 PMCID: PMC8640483 DOI: 10.3389/fphar.2021.749361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
The pathogenic role of the overactivated ABL1 tyrosine kinase (TK) pathway is well recognized in some forms of BCR-ABL1 like acute lymphoblastic leukemia (ALL); TK inhibitors represent a useful therapeutic choice in these patients who respond poorly to conventional chemotherapy. Here we report a novel peptide biosensor (PABL)-ELISA assay to investigate ABL1 activity in four immortalized leukemic cell lines with different genetic background. The PABL sequence comprises an ABL1 tyrosine (Y) phosphorylation site and a targeting sequence that increases the specificity for ABL1; additional peptides (Y-site-mutated (PABL-F) and fully-phosphorylated (PPHOSPHO-ABL) biosensors) were included in the assay. After incubation with whole cell lysates, average PABL phosphorylation was significantly increased (basal vs. PABL phosphorylation: 6.84 ± 1.46% vs. 32.44 ± 3.25%, p-value < 0.0001, two-way ANOVA, Bonferroni post-test, percentages relative to PPHOSPHO-ABL in each cell line). Cell lines expressing ABL1-chimeric proteins (K562, ALL-SIL) presented the higher TK activity on PABL; a lower signal was instead observed for NALM6 and REH (p < 0.001 and p < 0.05 vs. K562, respectively). Phosphorylation was ABL1-mediated, as demonstrated by the specific inhibition of imatinib (p < 0.001 for K562, NALM6, ALL-SIL and p < 0.01 for REH) in contrast to ruxolitinib (JAK2-inhibitor), and occurred on the ABL1 Y-site, as demonstrated by PABL-F whose phosphorylation was comparable to basal levels. In order to validate this novel PABL-ELISA assay on leukemic cells isolated from patient’s bone marrow aspirates, preliminary analysis on blasts derived from an adult affected by chronic myeloid leukaemia (BCR-ABL1 positive) and a child affected by ALL (BCR-ABL1 negative) were performed. Phosphorylation of PABL was specifically inhibited after the incubation of BCR-ABL1 positive cell lysates with imatinib, but not with ruxolitinib. While requiring further optimization and validation in leukemic blasts to be of clinical interest, the PABL-based ELISA assay provides a novel in vitro tool for screening both the aberrant ABL1 activity in BCR-ABL1 like ALL leukemic cells and their potential response to TK inhibitors.
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Affiliation(s)
- Oksana Montecchini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Stefania Braidotti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Raffaella Franca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Giulia Zudeh
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Christian Boni
- Department of Medicine, University of Verona, Verona, Italy
| | - Claudio Sorio
- Department of Medicine, University of Verona, Verona, Italy
| | - Eleonora Toffoletti
- Division of Hematology and Bone Marrow Transplantation, Azienda Ospedaliero-Universitaria, Udine, Italy
| | - Marco Rabusin
- Institute for Maternal and Child Health (I.R.C.C.S) Burlo Garofolo, Trieste, Italy
| | - Alberto Tommasini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health (I.R.C.C.S) Burlo Garofolo, Trieste, Italy
| | - Giuliana Decorti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health (I.R.C.C.S) Burlo Garofolo, Trieste, Italy
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
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8
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Merő B, Koprivanacz K, Cserkaszky A, Radnai L, Vas V, Kudlik G, Gógl G, Sok P, Póti ÁL, Szeder B, Nyitray L, Reményi A, Geiszt M, Buday L. Characterization of the Intramolecular Interactions and Regulatory Mechanisms of the Scaffold Protein Tks4. Int J Mol Sci 2021; 22:ijms22158103. [PMID: 34360869 PMCID: PMC8348221 DOI: 10.3390/ijms22158103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 01/01/2023] Open
Abstract
The scaffold protein Tks4 is a member of the p47phox-related organizer superfamily. It plays a key role in cell motility by being essential for the formation of podosomes and invadopodia. In addition, Tks4 is involved in the epidermal growth factor (EGF) signaling pathway, in which EGF induces the translocation of Tks4 from the cytoplasm to the plasma membrane. The evolutionarily-related protein p47phox and Tks4 share many similarities in their N-terminal region: a phosphoinositide-binding PX domain is followed by two SH3 domains (so called “tandem SH3”) and a proline-rich region (PRR). In p47phox, the PRR is followed by a relatively short, disordered C-terminal tail region containing multiple phosphorylation sites. These play a key role in the regulation of the protein. In Tks4, the PRR is followed by a third and a fourth SH3 domain connected by a long (~420 residues) unstructured region. In p47phox, the tandem SH3 domain binds the PRR while the first SH3 domain interacts with the PX domain, thereby preventing its binding to the membrane. Based on the conserved structural features of p47phox and Tks4 and the fact that an intramolecular interaction between the third SH3 and the PX domains of Tks4 has already been reported, we hypothesized that Tks4 is similarly regulated by autoinhibition. In this study, we showed, via fluorescence-based titrations, MST, ITC, and SAXS measurements, that the tandem SH3 domain of Tks4 binds the PRR and that the PX domain interacts with the third SH3 domain. We also investigated a phosphomimicking Thr-to-Glu point mutation in the PRR as a possible regulator of intramolecular interactions. Phosphatidylinositol-3-phosphate (PtdIns(3)P) was identified as the main binding partner of the PX domain via lipid-binding assays. In truncated Tks4 fragments, the presence of the tandem SH3, together with the PRR, reduced PtdIns(3)P binding, while the presence of the third SH3 domain led to complete inhibition.
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Affiliation(s)
- Balázs Merő
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - Kitti Koprivanacz
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - Anna Cserkaszky
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - László Radnai
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - Virag Vas
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - Gyöngyi Kudlik
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - Gergő Gógl
- Department of Biochemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (G.G.); (L.N.)
| | - Péter Sok
- Research Centre for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary; (P.S.); (Á.L.P.); (A.R.)
| | - Ádám L. Póti
- Research Centre for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary; (P.S.); (Á.L.P.); (A.R.)
| | - Bálint Szeder
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (G.G.); (L.N.)
| | - Attila Reményi
- Research Centre for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary; (P.S.); (Á.L.P.); (A.R.)
| | - Miklós Geiszt
- Department of Physiology, Semmelweis University, 1094 Budapest, Hungary;
| | - László Buday
- Department of Biochemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (G.G.); (L.N.)
- Department of Molecular Biology, Semmelweis University Medical School, 1094 Budapest, Hungary
- Correspondence:
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9
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Fraser A, Prokhorov NS, Jiao F, Pettitt BM, Scheuring S, Leiman PG. Quantitative description of a contractile macromolecular machine. SCIENCE ADVANCES 2021; 7:7/24/eabf9601. [PMID: 34117062 PMCID: PMC8195476 DOI: 10.1126/sciadv.abf9601] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/23/2021] [Indexed: 05/14/2023]
Abstract
Contractile injection systems (CISs) [type VI secretion system (T6SS), phage tails, and tailocins] use a contractile sheath-rigid tube machinery to breach cell walls and lipid membranes. The structures of the pre- and postcontraction states of several CISs are known, but the mechanism of contraction remains poorly understood. Combining structural information of the end states of the 12-megadalton R-type pyocin sheath-tube complex with thermodynamic and force spectroscopy analyses and an original modeling procedure, we describe the mechanism of pyocin contraction. We show that this nanomachine has an activation energy of 160 kilocalories/mole (kcal/mol), and it releases 2160 kcal/mol of heat and develops a force greater than 500 piconewtons. Our combined approach provides a quantitative and experimental description of the membrane penetration process by a CIS.
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Affiliation(s)
- Alec Fraser
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (SCSB), The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Nikolai S Prokhorov
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (SCSB), The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Fang Jiao
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (SCSB), The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (SCSB), The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.
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10
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Zhao G, Zhang L, Che L, Li H, Liu Y, Fang J. Revisiting bone morphogenetic protein-2 knuckle epitope and redesigning the epitope-derived peptides. J Pept Sci 2021; 27:e3309. [PMID: 33619824 DOI: 10.1002/psc.3309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 02/04/2023]
Abstract
The bone morphogenetic protein-2 (BMP2) plays a crucial role in bone formation, growth and regeneration, which adopts a conformational wrist epitope and a linear knuckle epitope to interact with its type-I (BRI) and type-II (BRII) receptors, respectively. In this study, we systematically examine the BRII-recognition site of BMP2 at structural, energetic and dynamic levels and accurately locate hotspots of the recognition at BMP2-BRII complex interface. It is revealed that the traditional knuckle epitope (BMP2 residue range 73-92) do fully match the identified hotspots; the BMP2-recognition site includes the C-terminal region of traditional knuckle epitope as well as its flanked β-strands. In addition, the protein context of full-length BMP2 is also responsible for the recognition by addressing conformational constraint on the native epitope segment. Therefore, we herein redefine the knuckle epitope to BMP2 residue range 84-102, which has a similar sequence length but is slid along the protein sequence by ~10 residues as compared to traditional knuckle epitope. The redefined one is also a linear epitope that is natively a double-stranded β-sheet with two asymmetric arms as compared to the natively single β-strand of the traditional version, although their sequences are partially overlapped to each other. It is revealed that the redefined epitope-derived peptide LN84-102 exhibits an improved affinity by >3-fold relative to the traditional epitope-derived peptide KL73-92 . Even so, the LN84-102 peptide still cannot fully represent the BMP2 recognition event by BRII that has been reported to have a nanomolar affinity. We further introduce a disulfide bond across the two arms of double-stranded β-sheet to constrain the free LN84-102 peptide conformation, which mimics the conformational constraint addressed by protein context. Consequently, several cyclic peptides are redesigned, in which the LN84-102 (cyc89-101) is determined to exhibit a sub-micromolar affinity; this value is ~5-fold higher than its linear counterpart. Structural analysis also reveals that the cyclic peptide can interact with BRII in a similar binding mode with the redefined knuckle epitope region in full-length BMP2 protein.
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Affiliation(s)
- Guangzong Zhao
- Department of Orthopedics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, China
| | - Longqiang Zhang
- Department of Orthopedics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, China
| | - Lifan Che
- Department of Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, China
| | - Huazhuang Li
- Department of Orthopedics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, China
| | - Yao Liu
- Department of Gynecology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, China
| | - Jun Fang
- Department of Orthopedics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, China
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11
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Ruiz-Blanco YB, Sanchez-Garcia E. CL-FEP: An End-State Free Energy Perturbation Approach. J Chem Theory Comput 2020; 16:1396-1410. [DOI: 10.1021/acs.jctc.9b00725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasser B. Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
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12
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Fu H, Shao X, Cai W, Chipot C. Taming Rugged Free Energy Landscapes Using an Average Force. Acc Chem Res 2019; 52:3254-3264. [PMID: 31680510 DOI: 10.1021/acs.accounts.9b00473] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The observation of complex structural transitions in biological and abiological molecular objects within time scales amenable to molecular dynamics (MD) simulations is often hampered by significant free energy barriers associated with entangled movements. Importance-sampling algorithms, a powerful class of numerical schemes for the investigation of rare events, have been widely used to extend simulations beyond the time scale common to MD. However, probing processes spanning milliseconds through microsecond molecular simulations still constitutes in practice a daunting challenge because of the difficulty of taming the ruggedness of multidimensional free energy surfaces by means of naive transition coordinates. To address this limitation, in recent years we have elaborated importance-sampling methods relying on an adaptive biasing force (ABF). In this Account, we review recent developments of algorithms aimed at mapping rugged free energy landscapes that correspond to complex processes of physical, chemical, and biological relevance. Through these developments, we have broadened the spectrum of applications of the popular ABF algorithm while improving its computational efficiency, notably for multidimensional free energy calculations. One major algorithmic advance, coined meta-eABF, merges the key features of metadynamics and an extended Lagrangian variant of ABF (eABF) by simultaneously shaving the barriers and flooding the valleys of the free energy landscape, and it possesses a convergence rate up to 5-fold greater than those of other importance-sampling algorithms. Through faster convergence and enhanced ergodic properties, meta-eABF represents a significant step forward in the simulation of millisecond-time-scale events. Here we introduce extensions of the algorithm, notably its well-tempered and replica-exchange variants, which further boost the sampling efficiency while gaining in numerical stability, thus allowing quantum-mechanical/molecular-mechanical free energy calculations to be performed at a lower cost. As a paradigm to bridge microsecond simulations to millisecond events by means of free energy calculations, we have applied the ABF family of algorithms to decompose complex movements in molecular objects of biological and abiological nature. We show here how water lubricates the shuttling of an amide-based rotaxane by altering the mechanism that underlies the concerted translation and isomerization of the macrocycle. Introducing novel collective variables in a computational workflow for the rigorous determination of standard binding free energies, we predict with utmost accuracy the thermodynamics of protein-ligand reversible association. Because of their simplicity, versatility, and robust mathematical foundations, the algorithms of the ABF family represent an appealing option for the theoretical investigation of a broad range of problems relevant to physics, chemistry, and biology.
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Affiliation(s)
- Haohao Fu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xueguang Shao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
- State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Wensheng Cai
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana−Champaign, UMR 7019, Université de Lorraine, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France
- Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
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13
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Marciel MP, Hoffmann PR. Molecular Mechanisms by Which Selenoprotein K Regulates Immunity and Cancer. Biol Trace Elem Res 2019; 192:60-68. [PMID: 31187393 PMCID: PMC6801056 DOI: 10.1007/s12011-019-01774-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
Abstract
Many of the 25 members of the selenoprotein family function as enzymes that utilize their selenocysteine (Sec) residues to catalyze redox-based reactions. However, some selenoproteins likely do not exert enzymatic activity by themselves and selenoprotein K (SELENOK) is one such selenoprotein family member that uses its Sec residue in an alternative manner. SELENOK is an endoplasmic reticulum (ER) transmembrane protein that has been shown to be important for ER stress and for calcium-dependent signaling. Molecular mechanisms for the latter have recently been elucidated using knockout mice and genetically manipulated cell lines. These studies have shown that SELENOK interacts with an enzyme in the ER membrane, DHHC6 (letters represent the amino acids aspartic acid, histidine, histidine, and cysteine in the catalytic domain), and the SELENOK/DHHC6 complex catalyzes the transfer of acyl groups such as palmitate to cysteine residues in target proteins, i.e., palmitoylation. One protein palmitoylated by SELENOK/DHHC6 is the calcium channel protein, the inositol 1,4,5-trisphosphate receptor (IP3R), which is acylated as a means for stabilizing the tetrameric calcium channel in the ER membrane. Factors that lower SELENOK levels or function impair IP3R-driven calcium flux. This role for SELENOK is important for the activation and proliferation of immune cells, and recently, a critical role for SELENOK in promoting calcium flux for the progression of melanoma has been demonstrated. This review provides a summary of these findings and their implications in terms of designing new therapeutic interventions that target SELENOK for treating cancers like melanoma.
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Affiliation(s)
- Michael P Marciel
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Peter R Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA.
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14
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Liu H, Xu L, Huang H, Zhao P, Yang R, Zhou Q, Liu G. Systematic profiling of clinical missence mutation effects on the intermolecular interaction between human growth hormone and its receptor in isolated growth hormone deficiency. J Mol Graph Model 2019; 92:1-7. [PMID: 31279174 DOI: 10.1016/j.jmgm.2019.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 11/17/2022]
Abstract
Isolated growth hormone deficiency (IGHD) is the most common pituitary hormone deficiency and can result from congenital or acquired causes. Among the known factors, genetic mutations in human growth hormone (hGH) remain the most frequent cause of IGHD, which influence the binding of hGH to its cognate receptor (hGHbp). Although previous studies have systematically investigated the residue importance at hGH-hGHbp complex interface, the molecular role of IGHD-associated residue mutations in the complex function still remains largely unexplored. Here, a total of 21 known hGH naturally-occurring missence mutations that have been clinically observed to be involved in IGHD disorder are collected and confirmed by original literature; they effects on the conformation, energetics and dynamics of hGH-hGHbp recognition and interaction are dissected at molecular level by using atomistic dynamics simulations, binding energy calculations and fluorescence spectroscopy assays. A systematic profile of hGH-hGHbp binding response to these clinical missence mutations is created, based on which it is revealed that (i) most mutations have appreciably unfavorable effect on the binding, which potentially destabilize the complex interaction, while only very few are predicted as moderate stabilizers for the complex system, and (ii) these disease-related mutations can locate either at complex interface or in hGH protein interior far away from the interface; both can influence the complex binding through either direct interaction or indirect allostericity. Two mutations, E100K (non-interface) and G146R (interface), are identified to address potent destabilization effect on hGH-hGHbp complex system; they can reduce the complex binding affinity by 8-fold (Kd changes from 0.76 to 5.9 nM) and 46-fold (Kd changes from 0.76 to 34.7 nM), respectively.
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Affiliation(s)
- Hui Liu
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Hailong Huang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Peiran Zhao
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Rongrong Yang
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Qing Zhou
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Guanghua Liu
- Department of Pediatrics, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China.
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15
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Choi JH, Sim SE, Kim JI, Choi DI, Oh J, Ye S, Lee J, Kim T, Ko HG, Lim CS, Kaang BK. Interregional synaptic maps among engram cells underlie memory formation. Science 2018; 360:430-435. [PMID: 29700265 DOI: 10.1126/science.aas9204] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/22/2018] [Indexed: 12/14/2022]
Abstract
Memory resides in engram cells distributed across the brain. However, the site-specific substrate within these engram cells remains theoretical, even though it is generally accepted that synaptic plasticity encodes memories. We developed the dual-eGRASP (green fluorescent protein reconstitution across synaptic partners) technique to examine synapses between engram cells to identify the specific neuronal site for memory storage. We found an increased number and size of spines on CA1 engram cells receiving input from CA3 engram cells. In contextual fear conditioning, this enhanced connectivity between engram cells encoded memory strength. CA3 engram to CA1 engram projections strongly occluded long-term potentiation. These results indicate that enhanced structural and functional connectivity between engram cells across two directly connected brain regions forms the synaptic correlate for memory formation.
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Affiliation(s)
- Jun-Hyeok Choi
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Su-Eon Sim
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Ji-Il Kim
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Dong Il Choi
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Jihae Oh
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Sanghyun Ye
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Jaehyun Lee
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - TaeHyun Kim
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Hyoung-Gon Ko
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Chae-Seok Lim
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Bong-Kiun Kaang
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea.
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16
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Fu H, Cai W, Hénin J, Roux B, Chipot C. New Coarse Variables for the Accurate Determination of Standard Binding Free Energies. J Chem Theory Comput 2017; 13:5173-5178. [DOI: 10.1021/acs.jctc.7b00791] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haohao Fu
- Research
Center for Analytical Sciences, College of Chemistry, Tianjin Key
Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China
| | - Wensheng Cai
- Research
Center for Analytical Sciences, College of Chemistry, Tianjin Key
Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
| | - Jérôme Hénin
- Laboratoire
de Biochimie Théorique, CNRS and Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, 75005 Paris, France
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, Gordon Center for Integrative
Science, University of Chicago, Chicago, Illinois 60637, United States
- Leadership
Computing Facility, Argonne National Laboratory, 9700 Cass Avenue, Building 240, Argonne, Illinois 60439, United States
| | - Christophe Chipot
- Laboratoire
International Associé Centre National de la Recherche Scientifique
et University of Illinois at Urbana−Champaign, Unité
Mixte de Recherche No. 7565, Université de Lorraine, B.P. 70239, 54506 Cedex Vandœuvre-lès-Nancy, France
- Theoretical
and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
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17
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Structure-based design of competitive ligands to target Spon2 in gastric cancer: An integration of molecular modeling and in vitro assay. Bioorg Chem 2017; 74:115-121. [PMID: 28772159 DOI: 10.1016/j.bioorg.2017.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/16/2017] [Accepted: 07/17/2017] [Indexed: 11/21/2022]
Abstract
Spon2 is a proto-oncogene matrix protein that plays an essential role in the tumorigenesis and metastasis of gastric cancer. The protein has recently been found to function as a guanine nucleotide exchange factor through the activation of RhoGTPase. Here, computational modeling and bioinformatics analysis were employed to investigate the molecular mechanism and biological implication underlying Spon2 autoinhibition. It is revealed that the binding of PxxP motif to SH domain can stabilize the intramolecular interaction between the N-terminal helix and DH domain of Spon2, thus shifting the protein into an autoinhibitory state. Here, we proposed releasing Spon2 autoinhibition by targeting SH domain with competitive peptide ligands. To verify this notion, the PxxP sequence was adopted as the start to derive an array of efficient SH binders by using a structure-based rational design strategy, which were then substantiated with fluorescence spectroscopy analysis and guanine nucleotide exchange test. Consequently, the obtained peptide ligands were determined to have a moderate or high affinity for SH domain; they can also enhance Spon2 exchange activity by 1.2-6.1 folds, exhibiting a significant correlation with their SH-binding affinity (Pearson's coefficient=0.92). In addition, neutral substitution of conserved residues in a high-affinity peptide ligand can largely reduce its Spon2-activating potency, confirming that the designed peptide activates Spon2 by competitively disrupting SH-PxxP interaction.
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18
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Wong ML, Murphy J, Harrington E, Gower CM, Jain RK, Schirle M, Thomas JR. Examining the influence of specificity ligands and ATP-competitive ligands on the overall effectiveness of bivalent kinase inhibitors. Proteome Sci 2017; 15:17. [PMID: 28725163 PMCID: PMC5513037 DOI: 10.1186/s12953-017-0125-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/03/2017] [Indexed: 01/02/2023] Open
Abstract
Background Identifying selective kinase inhibitors remains a major challenge. The design of bivalent inhibitors provides a rational strategy for accessing potent and selective inhibitors. While bivalent kinase inhibitors have been successfully designed, no comprehensive assessment of affinity and selectivity for a series of bivalent inhibitors has been performed. Here, we present an evaluation of the structure activity relationship for bivalent kinase inhibitors targeting ABL1. Methods Various SNAPtag constructs bearing different specificity ligands were expressed in vitro. Bivalent inhibitor formation was accomplished by synthesizing individual ATP-competitive kinase inhibitors containing a SNAPtag targeting moiety, enabling the spontaneous self-assembly of the bivalent inhibitor. Assembled bivalent inhibitors were incubated with K562 lysates, and then subjected to affinity enrichment using various ATP-competitive inhibitors immobilized to sepharose beads. Resulting eluents were analyzed using Tandem Mass Tag (TMT) labeling and two-dimensional liquid chromatography-tandem mass spectrometry (2D–LC-MS/MS). Relative binding affinity of the bivalent inhibitor was determined by calculating the concentration at which 50% of a given kinase remained bound to the affinity matrix. Results The profiling of three parental ATP-competitive inhibitors and nine SNAPtag conjugates led to the identification of 349 kinase proteins. In all cases, the bivalent inhibitors exhibited enhanced binding affinity and selectivity for ABL1 when compared to the parental compound conjugated to SNAPtag alone. While the rank order of binding affinity could be predicted by considering the binding affinities of the individual specificity ligands, the resulting affinity of the assembled bivalent inhibitor was not predictable. The results from this study suggest that as the potency of the ATP-competitive ligand increases, the contribution of the specificity ligand towards the overall binding affinity of the bivalent inhibitor decreases. However, the affinity of the specificity components in its interaction with the target is essential for achieving selectivity. Conclusion Through comprehensive chemical proteomic profiling, this work provides the first insight into the influence of ATP-competitive and specificity ligands binding to their intended target on a proteome-wide scale. The resulting data suggest a subtle interplay between the ATP-competitive and specificity ligands that cannot be accounted for by considering the specificity or affinity of the individual components alone. Electronic supplementary material The online version of this article (doi:10.1186/s12953-017-0125-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margaret L Wong
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Jason Murphy
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Edmund Harrington
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Carrie M Gower
- Departments of Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Rishi K Jain
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Jason R Thomas
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
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19
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Yan T, Shi X, Fu J. Identification of peptide-mediated interactions between human PTTG and SH3 domains in pALL gene expression profile. J Mol Graph Model 2017; 76:11-16. [PMID: 28667917 DOI: 10.1016/j.jmgm.2017.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 11/17/2022]
Abstract
Human pituitary tumor-transforming gene (PTTG) plays an essential role in the development and progression of pediatric acute lymphoblastic leukemia (pALL). PTTG has two SH3-binding peptide motifs that can be recognized by a variety of SH3-containing proteins in the pALL through peptide-mediated interactions. In this study, the gene expression profile of pALL was examined in detail by integrating computational modeling and experimental assay, aiming to identify those potential partner proteins of human PTTG. The binding potency of domain candidates to peptide motifs was ranked using knowledge-based scoring and fluorescence titration. A number of SH3 domains found in a variety of pALL proteins were identified as potent binders with moderate or high affinity for PTTG. It is revealed that the PTTG peptide motifs show different affinity profiles for various candidate proteins, indicating that the PTTG selectivity is optimized across pALL gene expression space. The PTTG peptides were then mutated rationally to target the SH3 domains of identified partner proteins by competing with the native peptide motifs.
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Affiliation(s)
- Tingting Yan
- Department of Pediatrics, The Second People's Hospital of Huai'an, Huai'an 223002, PR China.
| | - Xiangxiang Shi
- Department of Pediatrics, The Second People's Hospital of Huai'an, Huai'an 223002, PR China
| | - Jing Fu
- ICU, The Second People's Hospital of Huai'an, Huai'an 223002, PR China
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20
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Liu J, Wang D, Li Y, Yao H, Zhang N, Zhang X, Zhong F, Huang Y. Integrated In Silico-In Vitro Identification and Characterization of the SH3-Mediated Interaction between Human PTTG and its Cognate Partners in Medulloblastoma. Cell Biochem Biophys 2017. [PMID: 28646413 DOI: 10.1007/s12013-017-0810-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The human pituitary tumor-transforming gene is an oncogenic protein which serves as a central hub in the cellular signaling network of medulloblastoma. The protein contains two vicinal PxxP motifs at its C terminus that are potential binding sites of peptide-recognition SH3 domains. Here, a synthetic protocol that integrated in silico analysis and in vitro assay was described to identify the SH3-binding partners of pituitary tumor-transforming gene in the gene expression profile of medulloblastoma. In the procedure, a variety of structurally diverse, non-redundant SH3 domains with high gene expression in medulloblastoma were compiled, and their three-dimensional structures were either manually retrieved from the protein data bank database or computationally modeled through bioinformatics technique. The binding capability of these domains towards the two PxxP-containing peptides m1p: 161LGPPSPVK168 and m2p: 168KMPSPPWE175 of pituitary tumor-transforming gene were ranked by structure-based scoring and fluorescence-based assay. Consequently, a number of SH3 domains, including MAP3K and PI3K, were found to have moderate or high affinity for m1p and/or m2p. Interestingly, the two overlapping peptides exhibits a distinct binding profile to these identified domain partners, suggesting that the binding selectivity of m1p and m2p is optimized across the medulloblastoma expression spectrum by competing for domain candidates. In addition, two redesigned versions of m1p peptide ware obtained via a structure-based rational mutation approach, which exhibited an increased affinity for the domain as compared to native peptide.
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Affiliation(s)
- Jiangang Liu
- Department of Neurosurgery, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Dapeng Wang
- Department of Neurosurgery, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Yanyan Li
- Department of Neurosurgery, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Hui Yao
- Department of Neurosurgery, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Nan Zhang
- Department of Neurosurgery, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Xuewen Zhang
- Department of Neurosurgery, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Fangping Zhong
- Department of Neurosurgery, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Yulun Huang
- Department of Neurosurgery, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
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21
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Anselmi M, Pisabarro MT. Exploring Multiple Binding Modes Using Confined Replica Exchange Molecular Dynamics. J Chem Theory Comput 2016; 11:3906-18. [PMID: 26574471 DOI: 10.1021/acs.jctc.5b00253] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular docking is extensively applied to determine the position of a ligand on its receptor despite the rather poor correspondence between docking scores and experimental binding affinities found in several studies, especially for systems structurally unrelated with those used in the scoring functions' training sets. Here, we present a method for the prediction of binding modes and binding free energies, which uses replica exchange molecular dynamics in combination with a receptor-shaped piecewise potential, confining the ligand in the proximity of the receptor surface and limiting the accessible conformational space of interest. We assess our methodology with a set of protein receptor-ligand test cases. In every case studied, the method is able to locate the ligand on the experimentally known receptor binding site, and it gives as output the binding free energy. The added value of our approach with respect to other available methods is that it quickly performs a conformational space search, providing a set of bound (or unbound) configurations, which can be used to determine phenomenological structural and energetic properties of an experimental binding state as a result of contributions provided by diversified multiple binding poses.
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Affiliation(s)
- Massimiliano Anselmi
- Structural Bioinformatics, BIOTEC TU Dresden , Tatzberg 47-51, 01307 Dresden, Germany.,Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
| | - M Teresa Pisabarro
- Structural Bioinformatics, BIOTEC TU Dresden , Tatzberg 47-51, 01307 Dresden, Germany
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22
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Han S, Liu Q, Wang F, Yuan Z. Targeting the SH3 domain of human osteoclast-stimulating factor with rationally designed peptoid inhibitors. J Pept Sci 2016; 22:533-9. [PMID: 27443979 DOI: 10.1002/psc.2901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 05/24/2016] [Accepted: 05/31/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Shijie Han
- Department of Orthopedics; Shandong Provincial Hospital; Jinan 250021 China
| | - Qian Liu
- Department of Pain Management; Qilu Hospital of Shandong University; Jinan 250012 China
| | - Feng Wang
- Department of Orthopedics; Shandong Provincial Hospital; Jinan 250021 China
| | - Zenong Yuan
- Department of Orthopedics; Shandong Provincial Hospital; Jinan 250021 China
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23
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Badger J, Grover P, Shi H, Panjarian S, Engen JR, Smithgall T, Makowski L. c-Abl Tyrosine Kinase Adopts Multiple Active Conformational States in Solution. Biochemistry 2016; 55:3251-60. [PMID: 27166638 PMCID: PMC4910136 DOI: 10.1021/acs.biochem.6b00202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Indexed: 11/29/2022]
Abstract
Protein tyrosine kinases of the Abl family have diverse roles in normal cellular regulation and drive several forms of leukemia as oncogenic fusion proteins. In the crystal structure of the inactive c-Abl kinase core, the SH2 and SH3 domains dock onto the back of the kinase domain, resulting in a compact, assembled state. This inactive conformation is stabilized by the interaction of the myristoylated N-cap with a pocket in the C-lobe of the kinase domain. Mutations that perturb these intramolecular interactions result in kinase activation. Here, we present X-ray scattering solution structures of multidomain c-Abl kinase core proteins modeling diverse active states. Surprisingly, the relative positions of the regulatory N-cap, SH3, and SH2 domains in an active myristic acid binding pocket mutant (A356N) were virtually identical to those of the assembled wild-type kinase core, indicating that Abl kinase activation does not require dramatic reorganization of the downregulated core structure. In contrast, the positions of the SH2 and SH3 domains in a clinically relevant imatinib-resistant gatekeeper mutant (T315I) appear to be reconfigured relative to their positions in the wild-type protein. Our results demonstrate that c-Abl kinase activation can occur either with (T315I) or without (A356N) global allosteric changes in the core, revealing the potential for previously unrecognized signaling diversity.
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Affiliation(s)
- John Badger
- DeltaG
Technologies, San Diego, California 92122, United States
| | - Prerna Grover
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - Haibin Shi
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - Shoghag
B. Panjarian
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - John R. Engen
- Department of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas
E. Smithgall
- Department
of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, United States
| | - Lee Makowski
- Department of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
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24
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Vohidov F, Knudsen SE, Leonard PG, Ohata J, Wheadon MJ, Popp BV, Ladbury JE, Ball ZT. Potent and selective inhibition of SH3 domains with dirhodium metalloinhibitors. Chem Sci 2015; 6:4778-4783. [PMID: 29142714 PMCID: PMC5667506 DOI: 10.1039/c5sc01602a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 06/03/2015] [Indexed: 01/23/2023] Open
Abstract
Src-family kinases (SFKs) play important roles in human biology and are key drug targets as well. However, achieving selective inhibition of individual Src-family kinases is challenging due to the high similarity within the protein family. We describe rhodium(ii) conjugates that deliver both potent and selective inhibition of Src-family SH3 domains. Rhodium(ii) conjugates offer dramatic affinity enhancements due to interactions with specific and unique Lewis-basic histidine residues near the SH3 binding interface, allowing predictable, structure-guided inhibition of SH3 targets that are recalcitrant to traditional inhibitors. In one example, a simple metallopeptide binds the Lyn SH3 domain with 6 nM affinity and exhibits functional activation of Lyn kinase under biologically relevant concentrations (EC50 ∼ 200 nM).
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Affiliation(s)
- Farrukh Vohidov
- Department of Chemistry , Rice University , 6100 Main St. , Houston , Texas , USA .
| | - Sarah E Knudsen
- Department of Chemistry , Rice University , 6100 Main St. , Houston , Texas , USA .
| | - Paul G Leonard
- Department of Genomic Medicine , Core for Biomolecular Structure and Function , University of Texas , M.D. Anderson Cancer Center , Houston , Texas , USA
| | - Jun Ohata
- Department of Chemistry , Rice University , 6100 Main St. , Houston , Texas , USA .
| | - Michael J Wheadon
- Department of Chemistry , Rice University , 6100 Main St. , Houston , Texas , USA .
| | - Brian V Popp
- Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia , USA
| | - John E Ladbury
- Department of Molecular and Cellular Biology , University of Leeds , LS2 9JT , UK
| | - Zachary T Ball
- Department of Chemistry , Rice University , 6100 Main St. , Houston , Texas , USA .
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25
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Grover P, Shi H, Baumgartner M, Camacho CJ, Smithgall TE. Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function. PLoS One 2015. [PMID: 26222440 PMCID: PMC4519180 DOI: 10.1371/journal.pone.0133590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The ABL protein-tyrosine kinase regulates intracellular signaling pathways controlling diverse cellular processes and contributes to several forms of cancer. The kinase activity of ABL is repressed by intramolecular interactions involving its regulatory Ncap, SH3 and SH2 domains. Small molecules that allosterically regulate ABL kinase activity through its non-catalytic domains may represent selective probes of ABL function. Here we report a screening assay for chemical modulators of ABL kinase activity that target the regulatory interaction of the SH3 domain with the SH2-kinase linker. This fluorescence polarization (FP) assay is based on a purified recombinant ABL protein consisting of the N-cap, SH3 and SH2 domains plus the SH2-kinase linker (N32L protein) and a short fluorescein-labeled probe peptide that binds to the SH3 domain. In assay development experiments, we found that the probe peptide binds to the recombinant ABL N32L protein in vitro, producing a robust FP signal that can be competed with an excess of unlabeled peptide. The FP signal is not observed with control N32L proteins bearing either an inactivating mutation in the SH3 domain or enhanced SH3:linker interaction. A pilot screen of 1200 FDA-approved drugs identified four compounds that specifically reduced the FP signal by at least three standard deviations from the untreated controls. Secondary assays showed that one of these hit compounds, the antithrombotic drug dipyridamole, enhances ABL kinase activity in vitro to a greater extent than the previously described ABL agonist, DPH. Docking studies predicted that this compound binds to a pocket formed at the interface of the SH3 domain and the linker, suggesting that it activates ABL by disrupting this regulatory interaction. These results show that screening assays based on the non-catalytic domains of ABL can identify allosteric small molecule regulators of kinase function, providing a new approach to selective drug discovery for this important kinase system.
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Affiliation(s)
- Prerna Grover
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Matthew Baumgartner
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Carlos J. Camacho
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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26
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Huang F, Nie Y, Ye F, Zhang M, Xia J. Site Selective Azo Coupling for Peptide Cyclization and Affinity Labeling of an SH3 Protein. Bioconjug Chem 2015; 26:1613-22. [DOI: 10.1021/acs.bioconjchem.5b00238] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Feng Huang
- Department
of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yunyu Nie
- Department
of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fei Ye
- Division
of Life Science, The Hong Kong University of Science and Technology, Clear
Water Bay, Hong Kong SAR, China
| | - Mingjie Zhang
- Division
of Life Science, The Hong Kong University of Science and Technology, Clear
Water Bay, Hong Kong SAR, China
| | - Jiang Xia
- Department
of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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27
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The auto-inhibitory state of Rho guanine nucleotide exchange factor ARHGEF5/TIM can be relieved by targeting its SH3 domain with rationally designed peptide aptamers. Biochimie 2015; 111:10-8. [DOI: 10.1016/j.biochi.2015.01.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/22/2015] [Indexed: 11/20/2022]
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28
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Armendáriz BG, Masdeu MDM, Soriano E, Ureña JM, Burgaya F. The diverse roles and multiple forms of focal adhesion kinase in brain. Eur J Neurosci 2014; 40:3573-90. [DOI: 10.1111/ejn.12737] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/25/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Beatriz G. Armendáriz
- Department of Biologia Cellular; Fac Biologia; Universitat de Barcelona; Diagonal, 643 08028 Barcelona Spain
- Parc Científic de Barcelona; Barcelona Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Ciberned (ISC III); Madrid Spain
| | - Maria del Mar Masdeu
- Department of Biologia Cellular; Fac Biologia; Universitat de Barcelona; Diagonal, 643 08028 Barcelona Spain
- Parc Científic de Barcelona; Barcelona Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Ciberned (ISC III); Madrid Spain
| | - Eduardo Soriano
- Department of Biologia Cellular; Fac Biologia; Universitat de Barcelona; Diagonal, 643 08028 Barcelona Spain
- Parc Científic de Barcelona; Barcelona Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Ciberned (ISC III); Madrid Spain
| | - Jesús M. Ureña
- Department of Biologia Cellular; Fac Biologia; Universitat de Barcelona; Diagonal, 643 08028 Barcelona Spain
- Parc Científic de Barcelona; Barcelona Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Ciberned (ISC III); Madrid Spain
| | - Ferran Burgaya
- Department of Biologia Cellular; Fac Biologia; Universitat de Barcelona; Diagonal, 643 08028 Barcelona Spain
- Parc Científic de Barcelona; Barcelona Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Ciberned (ISC III); Madrid Spain
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29
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Lu Y, Huang F, Wang J, Xia J. Affinity-Guided Covalent Conjugation Reactions Based on PDZ–Peptide and SH3–Peptide Interactions. Bioconjug Chem 2014; 25:989-99. [DOI: 10.1021/bc500134w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yao Lu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Feng Huang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jianpeng Wang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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30
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Cámara-Artigas A, Martínez-Rodríguez S, Ortiz-Salmerón E, Martín-García JM. 3D domain swapping in a chimeric c-Src SH3 domain takes place through two hinge loops. J Struct Biol 2014; 186:195-203. [DOI: 10.1016/j.jsb.2014.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 11/29/2022]
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31
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Evolution of High-Affinity Peptide Probes to Detect the SH3 Domain of Cancer Biomarker BCR–ABL. Int J Pept Res Ther 2013. [DOI: 10.1007/s10989-013-9382-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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32
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Bacarizo J, Camara-Artigas A. Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:756-66. [PMID: 23633584 DOI: 10.1107/s0907444913001522] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/15/2013] [Indexed: 12/20/2022]
Abstract
The atomic resolution crystal structures of complexes between the SH3 domain of the c-Src tyrosine kinase and two high-affinity peptides belonging to class I and class II have been solved. The crystals of the Thr98Asp and Thr98Glu mutants in complex with the APP12 peptide (APPLPPRNRPRL) belonged to the trigonal space group P3121 and in both cases the asymmetric unit was composed of one molecule of the SH3-APP12 complex. The crystals of the Thr98Glu mutant in complex with the VSL12 peptide (VSLARRPLPLP) belonged to the trigonal space group P3221 and the asymmetric unit was also composed of a single molecule of the SH3-VSL12 complex. All crystals were obtained in the presence of PEG 300 under the same conditions as reported for the intertwined dimeric structure of the c-Src SH3 domain, but the presence of the peptide stabilizes the monomeric form of the domain. These structures allow a detailed analysis of the role of salt bridges, cation-π interactions and hydrogen bonds in the binding of proline-rich motifs to the c-Src SH3 domain. Moreover, these crystallographic structures allow the role of water molecules in the binding of these motifs to the c-Src SH3 domain to be studied for the first time.
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Affiliation(s)
- Julio Bacarizo
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence, Carretera de Sacramento, 04120 Almería, Spain
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33
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Kutyshenko VP, Prokhorov DA, Molochkov NV, Sharapov MG, Kolesnikov I, Uversky VN. Dancing retro: solution structure and micelle interactions of the retro-SH3-domain, retro-SHH-'Bergerac'. J Biomol Struct Dyn 2013; 32:257-72. [PMID: 23527530 DOI: 10.1080/07391102.2012.762724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A protein with the reversed direction of its polypeptide chain, retro-SHH, was analyzed by several spectroscopic techniques including circular dichroism and high-resolution NMR to understand its solution structure and structural consequences of interaction with the micelles formed by the zwitterionic detergent dodecylphosphocholine (DPC). This analysis revealed that retro-SHH does not contain rigid 3-D structure, but is characterized by the presence of residual secondary structure. Intriguingly, interaction with the DPC micelles affected the structures of SHH and retro-SHH very differently. In fact, micelles induce pronounced folding of retro-SHH, whereas micelle-bound SHH was noticeably disordered. Finally, we performed a disorder prediction with the PONDR-FIT algorithm and discovered that the reversal of the chain direction almost does not affect the propensity of a polypeptide for intrinsic disorder, since the disorder plot for retro-SHH was almost a mirror image of that for the normal SHH.
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Affiliation(s)
- Victor P Kutyshenko
- a Institute of Theoretical and Experimental Biophysics of Russian Academy of Science , Pushchino , Moscow Region , 142290 , Russia
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34
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A multiple reaction monitoring (MRM) method to detect Bcr-Abl kinase activity in CML using a peptide biosensor. PLoS One 2013; 8:e56627. [PMID: 23437189 PMCID: PMC3577862 DOI: 10.1371/journal.pone.0056627] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 01/14/2013] [Indexed: 11/19/2022] Open
Abstract
The protein kinase Bcr-Abl plays a major role in the pathogenesis of chronic myelogenous leukemia (CML), and is the target of the breakthrough drug imatinib (Gleevec™). While most patients respond well to imatinib, approximately 30% never achieve remission or develop resistance within 1–5 years of starting imatinib treatment. Evidence from clinical studies suggests that achieving at least 50% inhibition of a patient’s Bcr-Abl kinase activity (relative to their level at diagnosis) is associated with improved patient outcomes, including reduced occurrence of resistance and longer maintenance of remission. Accordingly, sensitive assays for detecting Bcr-Abl kinase activity compatible with small amounts of patient material are desirable as potential companion diagnostics for imatinib. Here we report the detection of Bcr-Abl activity and inhibition by imatinib in the human CML cell line K562 using a cell-penetrating peptide biosensor and multiple reaction monitoring (MRM) on a triple quadrupole mass spectrometer. MRM enabled reproducible, selective detection of the peptide biosensor at fmol levels from aliquots of cell lysate equivalent to ∼15,000 cells. This degree of sensitivity will facilitate the miniaturization of the entire assay procedure down to cell numbers approaching 15,000, making it practical for translational applications in patient cells in which the limited amount of available patient material often presents a major challenge.
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35
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Gumbart JC, Roux B, Chipot C. Standard binding free energies from computer simulations: What is the best strategy? J Chem Theory Comput 2012; 9:794-802. [PMID: 23794960 DOI: 10.1021/ct3008099] [Citation(s) in RCA: 239] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Accurate prediction of standard binding free energies describing protein:ligand association remains a daunting computational endeavor. This challenge is rooted to a large extent in the considerable changes in conformational, translational and rotational entropies underlying the binding process that atomistic simulations cannot easily capture. In spite of significant methodological advances, reflected in a continuously improving agreement with experiment, a characterization of alternate strategies aimed at measuring binding affinities, notably their respective advantages and drawbacks, is somewhat lacking. Here, two distinct avenues to determine the standard binding free energy are compared in the case of a short, proline-rich peptide associating to the Src homology domain 3 of tyrosine kinase Abl. These avenues - one relying upon alchemical transformations and the other on potentials of mean force (PMFs) - invoke a series of geometrical restraints acting on collective variables designed to alleviate sampling limitations inherent to classical molecular dynamics simulations. The experimental binding free energy of ΔGbind = -7.99 kcal/mol is well reproduced by the two strategies developed herein, with ΔGbind = -7.7 for the alchemical route and ΔGbind = -7.8 kcal/mol for the alternate PMF-based route. In detailing the underpinnings of these numerical strategies devised for the accurate determination of standard binding free energies, many practical elements of the proposed rigorous, conceptual framework are clarified, thereby paving way to tackle virtually any recognition and association phenomenon.
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Affiliation(s)
- James C Gumbart
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana IL 61801
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36
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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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37
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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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38
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Tang J, Wang JY, Parker LL. Detection of early Abl kinase activation after ionizing radiation by using a peptide biosensor. Chembiochem 2012; 13:665-73. [PMID: 22334513 PMCID: PMC3429332 DOI: 10.1002/cbic.201100763] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Indexed: 12/15/2022]
Abstract
The ubiquitously expressed Abl protein is a non-receptor tyrosine kinase that undergoes nuclear-cytoplasmic shuttling and is involved in many signaling pathways in the cell. Nuclear Abl is activated by DNA damage to regulate DNA repair, cell-cycle checkpoints and apoptosis. Previous studies have established that ataxia telangiectasia mutated (ATM) activates nuclear Abl by phosphorylating serine 465 (S465) in the kinase domain in response to ionizing radiation (IR). Using a peptide biosensor that specifically reports on the Abl kinase activity, we found that an Abl-S465A mutant, which is not capable of being activated by ATM through the canonical site, was still activated rapidly after IR. We established that DNA-dependent protein kinase (DNAPK) is likely to be responsible for a second pathway to activate Abl early on in the response to IR through phosphorylation at a site other than S465. Our findings show that nuclear and cytoplasmic Abl kinase is activated early on (within 5 min) in response to IR by both ATM and DNAPK, and that although one or the other of these kinases is required, either one is sufficient to activate Abl. These results support the concept of early Abl recruitment by both the ATM and the DNAPK pathways to regulate nuclear events triggered by DNA damage and potentially communicate them to proteins in the cytoplasm.
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Affiliation(s)
- Jiabin Tang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Center for Cancer Research, Purdue University, West Lafayette, IN 47907, Fax: (+001) 765-496-1496
| | - Jean Y. Wang
- Department of Medicine and Division of Hematology-Oncology, Moores Cancer Center, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Laurie L. Parker
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Center for Cancer Research, Purdue University, West Lafayette, IN 47907, Fax: (+001) 765-496-1496
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39
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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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Xu Z, Hou T, Li N, Xu Y, Wang W. Proteome-wide detection of Abl1 SH3-binding peptides by integrating computational prediction and peptide microarray. Mol Cell Proteomics 2011; 11:O111.010389. [PMID: 22023807 DOI: 10.1074/mcp.o111.010389] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Protein-protein interactions are essential for regulating almost all aspects of cellular functions. Many of these interactions are mediated by weak and transient protein domain-peptide binding, but they are often under-represented in high throughput screening of protein-protein interactions using techniques such as yeast two-hybrid and mass spectrometry. On the other hand, computational predictions and in vitro binding assays are valuable in providing clues of in vivo interactions. We present here a systematic approach that integrates computer modeling and a peptide microarray technology to identify binding peptides of the SH3 domain of the tyrosine kinase Abl1 in the human proteome. Our study provides a comprehensive list of candidate interacting partners for the Abl1 protein, among which the presence of numerous methyltransferases and RNA splicing proteins may suggest a novel function of Abl1 in chromatin remodeling and RNA processing. This study illustrates a powerful approach for integrating computational and experimental methods to detect protein interactions mediated by domain-peptide recognition.
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Affiliation(s)
- Zheng Xu
- Division of Biological Sciences, San Diego, California 92093-0359
| | - Tingjun Hou
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Nan Li
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093-0359
| | - Yang Xu
- Division of Biological Sciences, San Diego, California 92093-0359
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093-0359.
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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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Hill ZB, Perera BGK, Maly DJ. Bivalent inhibitors of the tyrosine kinases ABL and SRC: determinants of potency and selectivity. MOLECULAR BIOSYSTEMS 2010; 7:447-56. [PMID: 21060940 DOI: 10.1039/c0mb00108b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We recently reported a chemical genetic method for generating bivalent inhibitors of protein kinases. This method relies on the use of the DNA repair enzyme O(6)-alkylguanine-DNA alkyltransferase (AGT) to display an ATP-competitive inhibitor and a ligand that targets a secondary binding domain. With this method potent and selective inhibitors of the tyrosine kinases SRC and ABL were identified. Here, we dissect the molecular determinants of the potency and selectivity of these bivalent ligands. Systematic analysis of ATP-competitive inhibitors with varying linker lengths revealed that SRC and ABL have differential sensitivities to ligand presentation. Generation of bivalent constructs that contain ligands with differential affinities for the ATP-binding sites and SH3 domains of SRC and ABL demonstrated the modular nature of inhibitors based on the AGT scaffold. Furthermore, these studies revealed that the interaction between the SH3 domain ligand and the kinase SH3 domain is the major selectivity determinant amongst closely-related tyrosine kinases. Finally, the potency of bivalent inhibitors against distinct phospho-isoforms of SRC was determined. Overall, these results provide insight into how individual ligands can be modified to provide more potent and selective bivalent inhibitors of protein kinases.
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Affiliation(s)
- Zachary B Hill
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, USA
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43
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Wu D, Sylvester JE, Parker LL, Zhou G, Kron SJ. Peptide reporters of kinase activity in whole cell lysates. Biopolymers 2010; 94:475-86. [PMID: 20593469 DOI: 10.1002/bip.21401] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Kinase assays are used to screen for small-molecule inhibitors that may show promise as targeted pharmaceutical therapies. Using cell lysates instead of purified kinases provides a more accurate estimate of inhibitor sensitivity and selectivity in a biological setting. This review summarizes the range of homogeneous (solution-phase) and heterogeneous (solid-supported) formats available for using peptide substrates to monitor kinase activities in cell lysates. With a focus on heterogeneous kinase assays, the peptide substrate Abltide is used as a model to optimize presentation geometries and the modular arrangement of short sequences for kinase recognition. We present results from peptides immobilized on two- and three-dimensional surfaces such as hydrogels on 96-well plates and glass slides, and fluorescent Luminex beads. We discuss methods to increase assay sensitivity using chemifluorescent ELISAs, antibody-based recognition, and label-free mass spectrometry. Monitoring the activity of specific kinases in cell lysates presents challenges that can be overcome by manipulating peptide substrates to optimize assay conditions. In particular, signal-to-background ratios were improved by (1) adding long branched hydrophilic linkers between the substrate and the surface, (2) changing the orientation of peptides relative to the surface, and (3) including peptide ligands in cis or in trans to recruit kinases to the surface. By improving the accessibility of immobilized peptide substrates to kinases in solution, the apparent rate of phosphorylation increased and assays were more sensitive to changes in endogenous kinase activities. These strategies can be generalized to improve the reactivity of most peptide substrates used in heterogeneous kinase assays with cell lysates.
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Affiliation(s)
- Ding Wu
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
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Khristoforov VS, Prokhorov DA, Timchenko MA, Kudrevatykh YA, Gushchina LV, Filimonov VV, Kutyshenko VP. Chimeric SHA-D domain “SH3-Bergerac“: 3D structure and dynamics studies. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010. [DOI: 10.1134/s1068162010040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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45
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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: 61] [Impact Index Per Article: 4.4] [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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Sylvester JE, Kron SJ. A bead-based activity screen for small-molecule inhibitors of signal transduction in chronic myelogenous leukemia cells. Mol Cancer Ther 2010; 9:1469-81. [PMID: 20423990 DOI: 10.1158/1535-7163.mct-10-0157] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chronic myelogenous leukemia is characterized by the presence of the chimeric BCR-ABL gene, which is expressed as the constitutively active Bcr-Abl kinase. Although kinase activity is directly responsible for the clinical phenotype, current diagnostic and prognostic methods focus on a genetic classification system in which molecularly distinct subcategories are used to predict patient responses to small-molecule inhibitors of the Bcr-Abl kinase. Point mutations in the kinase domain are a central factor regulating inhibitor resistance; however, compensatory signaling caused by the activation of unrelated kinases can influence inhibitor efficacy. Kinase activity profiling can be used as a complementary approach to genetic screening and allows direct screening of small-molecule inhibitors. We developed a quantitative assay to monitor tyrosine kinase activities and inhibitor sensitivities in a model of chronic myelogenous leukemia using peptide reporters covalently immobilized on Luminex beads. Kinase activity is quantified by nonlinear regression from well-specific internal standard curves. Using optimized synthetic substrates and peptides derived from native substrates as probes, we measured kinase inhibition in cell lysates by the signal transduction inhibitors imatinib and dasatinib. Taking advantage of a convenient 96-well plate format, this assay also allows a straightforward and quantitative analysis of the differential effects of ATP and inhibitors on kinase activity. This method for analyzing a focused signaling network benefits from rigorous statistical analysis and short processing times, thereby offering a powerful tool for drug discovery and clinical testing.
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Affiliation(s)
- Juliesta E Sylvester
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA
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Mand MR, Wu D, Veach DR, Kron SJ. Cell treatment and lysis in 96-well filter-bottom plates for screening Bcr-Abl activity and inhibition in whole-cell extracts. ACTA ACUST UNITED AC 2010; 15:434-40. [PMID: 20237206 DOI: 10.1177/1087057110363307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although conventional high-throughput screens performed in vitro with purified protein kinases are powerful tools to discover new kinase inhibitors, they are far from ideal for determining efficacy in vivo. As a complementary approach, cell-based, target-driven secondary screens may help predict in vivo compound potency and specificity as well as evaluate bioavailability and toxicity. Here the authors report a simple protocol for treating K562 Bcr-Abl-expressing cells with small-molecule kinase inhibitors in 96-well filter-bottom plates followed by in-plate cell lysis. The lysates were assayed via a solid-phase kinase assay, allowing determination of apparent IC(50) for known Bcr-Abl inhibitors as well as facilitating the screening of a small kinase inhibitor library. This approach may have further applications in generating lysates for analyzing kinase activity and inhibition in other nonadherent suspension cell lines.
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Affiliation(s)
- Michael R Mand
- Institute of Cellular and Molecular Biology, University of Texas at Austin, USA
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48
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Tiwari R, Parang K. Protein conjugates of SH3-domain ligands and ATP-competitive inhibitors as bivalent inhibitors of protein kinases. Chembiochem 2010; 10:2445-8. [PMID: 19731277 DOI: 10.1002/cbic.200900462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rakesh Tiwari
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, 41 Lower College Road, Kingston, RI 02881, USA
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Kutyshenko VP, Prokhorov DA, Timchenko МА, Kudrevatykh YA, Gushchina LV, Khristoforov VS, Filimonov VV, Uversky VN. Solution structure and dynamics of the chimeric SH3 domains, SHH- and SHA-“Bergeracs”. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1813-22. [DOI: 10.1016/j.bbapap.2009.08.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 08/18/2009] [Accepted: 08/19/2009] [Indexed: 12/12/2022]
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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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