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Qin S, Zhou HX. Predicting the Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.02.526886. [PMID: 36778236 PMCID: PMC9915584 DOI: 10.1101/2023.02.02.526886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
How the sequences of intrinsically disordered proteins (IDPs) code for functions is still an enigma. Dynamics, in particular residue-specific dynamics, holds crucial clues. Enormous efforts have been spent to characterize residue-specific dynamics of IDPs, mainly through NMR spin relaxation experiments. Here we present a sequence-based method, SeqDYN, for predicting residue-specific backbone dynamics of IDPs. SeqDYN employs a mathematical model with 21 parameters: one is a correlation length and 20 are the contributions of the amino acids to slow dynamics. Training on a set of 45 IDPs reveals aromatic, Arg, and long-branched aliphatic amino acids as the most active in slow dynamics whereas Gly and short polar amino acids as the least active. SeqDYN predictions not only provide an accurate and insightful characterization of sequence-dependent IDP dynamics but may also serve as indicators in a host of biophysical processes, including the propensities of IDP sequences to undergo phase separation.
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Affiliation(s)
- Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago, IL 60607, USA
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2
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McIvor JAP, Larsen DS, Mercadante D. Charge Relaying within a Phospho-Motif Rescue Binding Competency of a Disordered Transcription Factor. J Chem Inf Model 2024; 64:6041-6052. [PMID: 39074869 DOI: 10.1021/acs.jcim.4c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Structural disorder in proteins is central to cellular signaling, where conformational plasticity equips molecules to promiscuously interact with different partners. By engaging with multiple binding partners via the rearrangement of its three helices, the nuclear coactivator binding domain (NCBD) of the CBP/p300 transcription factor is a paradigmatic example of promiscuity. Recently, molecular simulations and experiments revealed that, through the establishment of long-range electrostatic interactions, intended as salt-bridges formed between the post-translationally inserted phosphate and positively charged residues in helix H3 of NCBD, phosphorylation triggers NCBD compaction, lowering its affinity for binding partners. By means of extensive molecular simulations, we here investigated the effect of short-range electrostatics on the conformational ensemble of NCBD, by monitoring the interactions between a phosphorylated serine and conserved positively charged residues within the NCBD phospho-motif. We found that empowering proximal electrostatic interactions, as opposed to long-range electrostatics, can reshape the NCBD ensemble rescuing the binding competency of phosphorylated NCBD. Given the conservation of positive charges in phospho-motifs, proximal electrostatic interactions might dampen the effects of phosphorylation and act as a relay to regulate phosphorylated intrinsically disordered proteins, ultimately tuning the binding affinity for different cellular partners.
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Affiliation(s)
- Jordan A P McIvor
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Danaé S Larsen
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
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Savva L, Platts JA. Evaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein. J Biomol Struct Dyn 2022:1-16. [PMID: 35670576 DOI: 10.1080/07391102.2022.2082534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report conventional and accelerated molecular dynamics simulations of α-Synuclein, designed to assess performance of using different starting conformation, solvation environment and force field combination. Backbone and sidechain chemical shifts, radius of gyration, presence of β-hairpin structures in KTK(E/Q)GV repeats and secondary structure percentages were used to evaluate how variations in forcefield, solvation model and simulation protocol provide results that correlate with experimental findings. We show that with suitable choice of forcefield and solvent, ff03ws and OBC implicit model, respectively, acceptable reproduction of experimental data on size and secondary structure is obtained by both conventional and accelerated MD. In contrast to the implicit solvent model, simulations in explicit TIP4P/2005 solvent do not properly represent size or secondary structure of α-Synuclein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Loizos Savva
- School of Chemistry, Cardiff University, Cardiff, UK
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Biophysical Reviews’ “Meet the Councilor Series”—a profile of Kandala V. R. Chary. Biophys Rev 2021; 13:821-824. [DOI: 10.1007/s12551-021-00898-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022] Open
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Patel S, Hosur RV. Replica exchange molecular dynamics simulations reveal self-association sites in M-crystallin caused by mutations provide insights of cataract. Sci Rep 2021; 11:23270. [PMID: 34857812 PMCID: PMC8639718 DOI: 10.1038/s41598-021-02728-8] [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: 06/21/2021] [Accepted: 11/09/2021] [Indexed: 11/09/2022] Open
Abstract
Crystallins are ubiquitous, however, prevalence is seen in eye lens. Eye lens crystallins are long-lived and structural intactness is required for maintaining lens transparency and protein solubility. Mutations in crystallins often lead to cataract. In this study, we performed mutations at specific sites of M-crystallin, a close homologue of eye lens crystallin and studied by using replica exchange molecular dynamics simulation with generalized Born implicit solvent model. Mutations were made on the Ca2+ binding residues (K34D and S77D) and in the hydrophobic core (W45R) which is known to cause congenital cataract in homologous γD-crystallin. The chosen mutations caused large motion of the N-terminal Greek key, concomitantly broke the interlocking Greek keys interactions and perturbed the compact core resulting in several folded and partially unfolded states. Partially unfolded states exposed large hydrophobic patches that could act as precursors for self-aggregation. Accumulation of such aggregates is the potential cause of cataract in homologous eye lens crystallins.
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Affiliation(s)
- Sunita Patel
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Vidyanagari, Mumbai, 400098, India.
| | - Ramakrishna V. Hosur
- grid.452882.1UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Vidyanagari, Mumbai, 400098 India
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Patel S, Krishnan B, Hosur RV, Chary KVR. Mechanistic Insights from Replica Exchange Molecular Dynamics Simulations into Mutation Induced Disordered-to-Ordered Transition in Hahellin, a βγ-Crystallin. J Phys Chem B 2019; 123:5086-5098. [DOI: 10.1021/acs.jpcb.9b03845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sunita Patel
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai 400098, India
- Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Bal Krishnan
- Indian Institute of Science Education and Research, Berhampur, 760010, India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai 400098, India
- Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kandala V. R. Chary
- Tata Institute of Fundamental Research, Hyderabad 500107, India
- Tata Institute of Fundamental Research, Mumbai 400005, India
- Indian Institute of Science Education and Research, Berhampur, 760010, India
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Gao M, Yang F, Zhang L, Su Z, Huang Y. Exploring the sequence-structure-function relationship for the intrinsically disordered βγ-crystallin Hahellin. J Biomol Struct Dyn 2017; 36:1171-1181. [PMID: 28393629 DOI: 10.1080/07391102.2017.1316519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
βγ-Crystallins are a superfamily of proteins containing crystallin-type Greek key motifs. Some βγ-crystallin domains have been shown to bind Ca2+. Hahellin is a newly identified intrinsically disordered βγ-crystallin domain from Hahella chejuensis. It folds into a typical βγ-crystallin structure upon Ca2+ binding and acts as a Ca2+-regulated conformational switch. Besides Hahellin, another two putative βγ-crystallins from Caulobacter crescentus and Yersinia pestis are shown to be partially disordered in their apo-form and undergo large conformational changes upon Ca2+ binding, although whether they acquire a βγ-crystallin fold is not known. The extent of conformational disorder/order of a protein is determined by its amino acid sequence. To date how this sequence-structure relationship is reflected in the βγ-crystallin superfamily has not been investigated. In this work, we comparatively studied the sequence and structure of Hahellin with those of Protein S, an ordered βγ-crystallin, via various computational biophysical techniques. We found that several factors, including presence of a C-terminal disorder prone region, high content of energetic frustrations, and low contact density, may promote the formation of the disordered state of apo-Hahellin. We also analyzed the disorder propensities for other putative disordered βγ-crystallin domains. This study provides new clues for further understanding the sequence-structure-function relationship of βγ-crystallins.
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Affiliation(s)
- Meng Gao
- a Department of Biological Engineering and Institute of Biomedical and Pharmaceutical Sciences , Hubei University of Technology , Wuhan , Hubei 430068 , China
| | - Fei Yang
- a Department of Biological Engineering and Institute of Biomedical and Pharmaceutical Sciences , Hubei University of Technology , Wuhan , Hubei 430068 , China
| | - Lei Zhang
- a Department of Biological Engineering and Institute of Biomedical and Pharmaceutical Sciences , Hubei University of Technology , Wuhan , Hubei 430068 , China
| | - Zhengding Su
- a Department of Biological Engineering and Institute of Biomedical and Pharmaceutical Sciences , Hubei University of Technology , Wuhan , Hubei 430068 , China
| | - Yongqi Huang
- a Department of Biological Engineering and Institute of Biomedical and Pharmaceutical Sciences , Hubei University of Technology , Wuhan , Hubei 430068 , China
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Ambadipudi S, Zweckstetter M. Targeting intrinsically disordered proteins in rational drug discovery. Expert Opin Drug Discov 2015; 11:65-77. [DOI: 10.1517/17460441.2016.1107041] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Susmitha Ambadipudi
- German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center Göttingen, 37073 Göttingen, Germany
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