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Payliss BJ, Wyatt HDM. Protocol for in vitro phosphorylation of the MUS81-binding region of SLX4 using CDK1-cyclin B. STAR Protoc 2023; 4:102152. [PMID: 36917604 PMCID: PMC10025271 DOI: 10.1016/j.xpro.2023.102152] [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: 12/23/2022] [Revised: 01/23/2023] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
Phosphorylation is a post-translational modification that can alter protein structure and regulate protein-protein interactions. Here, we present a procedure for in vitro phosphorylation of the MUS81-binding region of SLX4 (SLX4MBR) using cyclin-dependent kinase 1-cyclin B. We describe steps for the dialysis and phosphorylation of target proteins followed by purification using size-exclusion chromatography. Finally, we detail a system to monitor phosphorylation effectiveness and identify phosphorylated residues. We anticipate this protocol to be readily adapted for other protein targets or kinases. For complete details on the use and execution of this protocol, please refer to Payliss et al. (2022).1.
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Affiliation(s)
- Brandon J Payliss
- Department of Biochemistry, University of Toronto, Toronto, ON M56 1A8, Canada.
| | - Haley D M Wyatt
- Department of Biochemistry, University of Toronto, Toronto, ON M56 1A8, Canada; Canada Research Chairs Program, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Payliss BJ, Tse YWE, Reichheld SE, Lemak A, Yun HY, Houliston S, Patel A, Arrowsmith CH, Sharpe S, Wyatt HD. Phosphorylation of the DNA repair scaffold SLX4 drives folding of the SAP domain and activation of the MUS81-EME1 endonuclease. Cell Rep 2022; 41:111537. [DOI: 10.1016/j.celrep.2022.111537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 11/03/2022] Open
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Ning S, Wang H, Zeng C, Zhao Y. Prediction of allosteric druggable pockets of cyclin-dependent kinases. Brief Bioinform 2022; 23:6643454. [PMID: 35830869 DOI: 10.1093/bib/bbac290] [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: 05/04/2022] [Revised: 06/07/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Cyclin-dependent kinase (Cdk) proteins play crucial roles in the cell cycle progression and are thus attractive drug targets for therapy against such aberrant cell cycle processes as cancer. Since most of the available Cdk inhibitors target the highly conserved catalytic ATP pocket and their lack of specificity often lead to side effects, it is imperative to identify and characterize less conserved non-catalytic pockets capable of interfering with the kinase activity allosterically. However, a systematic analysis of these allosteric druggable pockets is still in its infancy. Here, we summarize the existing Cdk pockets and their selectivity. Then, we outline a network-based pocket prediction approach (NetPocket) and illustrate its utility for systematically identifying the allosteric druggable pockets with case studies. Finally, we discuss potential future directions and their challenges.
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Affiliation(s)
- Shangbo Ning
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Huiwen Wang
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Chen Zeng
- Department of Physics, The George Washington University, Washington, DC 20052, USA
| | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China
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Rieloff E, Skepö M. The Effect of Multisite Phosphorylation on the Conformational Properties of Intrinsically Disordered Proteins. Int J Mol Sci 2021; 22:11058. [PMID: 34681718 PMCID: PMC8541499 DOI: 10.3390/ijms222011058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 02/06/2023] Open
Abstract
Intrinsically disordered proteins are involved in many biological processes such as signaling, regulation, and recognition. A common strategy to regulate their function is through phosphorylation, as it can induce changes in conformation, dynamics, and interactions with binding partners. Although phosphorylated intrinsically disordered proteins have received increased attention in recent years, a full understanding of the conformational and structural implications of phosphorylation has not yet been achieved. Here, we present all-atom molecular dynamics simulations of five disordered peptides originated from tau, statherin, and β-casein, in both phosphorylated and non-phosphorylated state, to compare changes in global dimensions and structural elements, in an attempt to gain more insight into the controlling factors. The changes are in qualitative agreement with experimental data, and we observe that the net charge is not enough to predict the impact of phosphorylation on the global dimensions. Instead, the distribution of phosphorylated and positively charged residues throughout the sequence has great impact due to the formation of salt bridges. In statherin, a preference for arginine-phosphoserine interaction over arginine-tyrosine accounts for a global expansion, despite a local contraction of the phosphorylated region, which implies that also non-charged residues can influence the effect of phosphorylation.
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Affiliation(s)
- Ellen Rieloff
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden;
| | - Marie Skepö
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden;
- LINXS—Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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Sieradzan AK, Korneev A, Begun A, Kachlishvili K, Scheraga HA, Molochkov A, Senet P, Niemi AJ, Maisuradze GG. Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics. J Chem Theory Comput 2021; 17:3203-3220. [PMID: 33909430 DOI: 10.1021/acs.jctc.1c00155] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Apart from being the most common mechanism of regulating protein function and transmitting signals throughout the cell, phosphorylation has an ability to induce disorder-to-order transition in an intrinsically disordered protein. In particular, it was shown that folding of the intrinsically disordered protein, eIF4E-binding protein isoform 2 (4E-BP2), can be induced by multisite phosphorylation. Here, the principles that govern the folding of phosphorylated 4E-BP2 (pT37pT46 4E-BP218-62) are investigated by analyzing canonical and replica exchange molecular dynamics trajectories, generated with the coarse-grained united-residue force field, in terms of local and global motions and the time dependence of formation of contacts between Cαs of selected pairs of residues. The key residues involved in the folding of the pT37pT46 4E-BP218-62 are elucidated by this analysis. The correlations between local and global motions are identified. Moreover, for a better understanding of the physics of the formation of the folded state, the experimental structure of the pT37pT46 4E-BP218-62 is analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. It is shown that without molecular dynamics simulations the kinks are able to identify not only the phosphorylated sites of protein, the key players in folding, but also the reasons for the weak stability of the pT37pT46 4E-BP218-62.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Anatolii Korneev
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia
| | - Alexander Begun
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia
| | - Khatuna Kachlishvili
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Alexander Molochkov
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia
| | - Patrick Senet
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States.,Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
| | - Antti J Niemi
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia.,Laboratoire de Mathematiques et Physique Theorique, CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200 Tours, France.,Nordita, Stockholm University and Uppsala University, Roslagstullsbacken 23, SE-106 91 Stockholm, Sweden.,School of Physics, Beijing Institute of Technology, Beijing 100081, P.R. China
| | - Gia G Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
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