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Yuan S, Han X, Zhang J, Xie Z, Fan C, Xiao Y, Gao YQ, Yang YI. Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms Using Molecular Configuration Transformer. J Phys Chem A 2024; 128:4378-4390. [PMID: 38759697 DOI: 10.1021/acs.jpca.4c01267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical calculations is the most commonly used method. However, this way is heavily dependent on individual experience and chemical intuition. In our previous study, we proposed a research paradigm that used enhanced sampling in molecular dynamics simulations to study chemical reactions. This approach can directly simulate the entire process of a chemical reaction. However, the computational speed limited the use of high-precision potential energy functions for simulations. To address this issue, we presented a scheme for training high-precision force fields for molecular modeling using a previously developed graph-neural-network-based molecular model, molecular configuration transformer. This potential energy function allowed for highly accurate simulations at a low computational cost, leading to more precise calculations of the mechanism of chemical reactions. We applied this approach to study a Claisen rearrangement reaction and a carbonyl insertion reaction catalyzed by manganese.
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Affiliation(s)
- Sihao Yuan
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xu Han
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jun Zhang
- Changping Laboratory, Beijing 102200, China
| | - Zhaoxin Xie
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Cheng Fan
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yunlong Xiao
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
- Changping Laboratory, Beijing 102200, China
| | - Yi Isaac Yang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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2
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Bahena Culhuac E, Bello M. Unveiling the Mechanisms of EGCG-p53 Interactions through Molecular Dynamics Simulations. ACS OMEGA 2024; 9:20066-20085. [PMID: 38737068 PMCID: PMC11080030 DOI: 10.1021/acsomega.3c10523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024]
Abstract
Green tea consumption is associated with protective and preventive effects against various types of cancer. These effects are attributed to polyphenols, particularly epigallocatechin-3-gallate (EGCG). EGCG acts by directly inhibiting tumor suppressor protein p53. The binding mechanism by which EGCG inhibits p53 activity is associated with residues Trp23-Lys24 and Pro47-Thr55 within the p53 N-terminal domain (NTD). However, the structural and thermodynamic aspects of the interaction between EGCG and p53 are poorly understood. Therefore, based on crystallographic data, we combine docking, molecular dynamics (MD) simulations, and molecular mechanics generalized Born surface area approaches to explore the intricacies of the EGCG-p53 binding mechanism. A triplicate microsecond MD simulation for each system is initially performed to capture diverse p53 NTD conformations. From the start, the most populated cluster of the second run (R2-1) stands out due to a unique opening between Trp23 and Trp53. During MD simulations, this conformation allows EGCG to sustain a high level of stability and affinity while interacting with both regions of interest and deepening the binding pocket. Structural analysis emphasizes the significance of pyrogallol motifs in EGCG binding. Therefore, the conformational shift in this gap is pivotal, enabling EGCG to impede p53 interactions and manifest its anticancer properties. These findings enhance the present comprehension of the anticancer properties of green tea polyphenols and pave the way for future therapeutic developments.
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Affiliation(s)
- Erick Bahena Culhuac
- Laboratorio
de Diseño y Desarrollo de Nuevos Fármacos e Innovación
Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
- Universidad
Autónoma del Estado de México Facultad de Ciencias, Toluca 50000, Mexico
| | - Martiniano Bello
- Laboratorio
de Diseño y Desarrollo de Nuevos Fármacos e Innovación
Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
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3
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Chepsergon J, Moleleki LN. "Order from disordered": Potential role of intrinsically disordered regions in phytopathogenic oomycete intracellular effector proteins. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102402. [PMID: 37329857 DOI: 10.1016/j.pbi.2023.102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 06/19/2023]
Abstract
There is a continuous arms race between pathogens and their host plants. However, successful pathogens, such as phytopathogenic oomycetes, secrete effector proteins to manipulate host defense responses for disease development. Structural analyses of these effector proteins reveal the existence of regions that fail to fold into three-dimensional structures, intrinsically disordered regions (IDRs). Because of their flexibility, these regions are involved in important biological functions of effector proteins, such as effector-host protein interactions that perturb host immune responses. Despite their significance, the role of IDRs in phytopathogenic oomycete effector-host protein interactions is not clear. This review, therefore, searched the literature for functionally characterized oomycete intracellular effectors with known host interactors. We further classify regions that mediate effector-host protein interactions into globular or disordered binding sites in these proteins. To fully appreciate the potential role of IDRs, five effector proteins encoding potential disordered binding sites were used as case studies. We also propose a pipeline that can be used to identify, classify as well as characterize potential binding regions in effector proteins. Understanding the role of IDRs in these effector proteins can aid in the development of new disease-control strategies.
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Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
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4
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Di Bartolo AL, Caparotta M, Masone D. Intrinsic Disorder in α-Synuclein Regulates the Exocytotic Fusion Pore Transition. ACS Chem Neurosci 2023. [PMID: 37192400 DOI: 10.1021/acschemneuro.3c00040] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023] Open
Abstract
Today, it is widely accepted that intrinsic disorder is strongly related to the cell cycle, during mitosis, differentiation, and apoptosis. Of particular interest are hybrid proteins possessing both structured and unstructured domains that are critical in human health and disease, such as α-synuclein. In this work, we describe how α-synuclein interacts with the nascent fusion pore as it evolves toward expansion. We unveil the key role played by its intrinsically disordered region as a thermodynamic regulator of the nucleation-expansion energy barrier. By analyzing a truncated variant of α-synuclein that lacks the disordered region, we find that the landscape of protein interactions with PIP2 and POPS lipids is highly altered, ultimately increasing the energy cost for the fusion pore to transit from nucleation to expansion. We conclude that the intrinsically disordered region in full-length α-synuclein recognizes and allocates pivotal protein:lipid interactions during membrane remodeling in the first stages of the fusion pore.
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Marcelo Caparotta
- Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
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5
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Chowdhury UD, Paul A, Bhargava BL. The effect of lipid composition on the dynamics of tau fibrils. Proteins 2022; 90:2103-2115. [DOI: 10.1002/prot.26401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/01/2022] [Accepted: 07/15/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Unmesh Dutta Chowdhury
- School of Chemical Sciences National Institute of Science Education & Research‐Bhubaneswar, OCC of Homi Bhabha National Institute Khurda Odisha India
| | - Arnav Paul
- School of Chemical Sciences National Institute of Science Education & Research‐Bhubaneswar, OCC of Homi Bhabha National Institute Khurda Odisha India
| | - B. L. Bhargava
- School of Chemical Sciences National Institute of Science Education & Research‐Bhubaneswar, OCC of Homi Bhabha National Institute Khurda Odisha India
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6
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Transcription Factor Movement and Exercise-Induced Mitochondrial Biogenesis in Human Skeletal Muscle: Current Knowledge and Future Perspectives. Int J Mol Sci 2022; 23:ijms23031517. [PMID: 35163441 PMCID: PMC8836245 DOI: 10.3390/ijms23031517] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
In response to exercise, the oxidative capacity of mitochondria within skeletal muscle increases through the coordinated expression of mitochondrial proteins in a process termed mitochondrial biogenesis. Controlling the expression of mitochondrial proteins are transcription factors—a group of proteins that regulate messenger RNA transcription from DNA in the nucleus and mitochondria. To fulfil other functions or to limit gene expression, transcription factors are often localised away from DNA to different subcellular compartments and undergo rapid movement or accumulation only when required. Although many transcription factors involved in exercise-induced mitochondrial biogenesis have been identified, numerous conflicting findings and gaps exist within our knowledge of their subcellular movement. This review aims to summarise and provide a critical analysis of the published literature regarding the exercise-induced movement of transcription factors involved in mitochondria biogenesis in skeletal muscle.
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7
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Röder K, Wales DJ. The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules. Front Mol Biosci 2022; 9:820792. [PMID: 35155579 PMCID: PMC8829389 DOI: 10.3389/fmolb.2022.820792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/07/2022] [Indexed: 12/02/2022] Open
Abstract
The energy landscape perspective is outlined with particular reference to biomolecules that perform multiple functions. We associate these multifunctional molecules with multifunnel energy landscapes, illustrated by some selected examples, where understanding the organisation of the landscape has provided new insight into function. Conformational selection and induced fit may provide alternative routes to realisation of multifunctionality, exploiting the possibility of environmental control and distinct binding modes.
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8
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Alston JJ, Soranno A, Holehouse AS. Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins. Methods 2021; 193:116-135. [PMID: 33831596 PMCID: PMC8713295 DOI: 10.1016/j.ymeth.2021.03.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/21/2022] Open
Abstract
Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have emerged from a niche corner of biophysics to be recognized as essential drivers of cellular function. Various techniques have provided fundamental insight into the function and dysfunction of IDRs. Among these techniques, single-molecule fluorescence spectroscopy and molecular simulations have played a major role in shaping our modern understanding of the sequence-encoded conformational behavior of disordered proteins. While both techniques are frequently used in isolation, when combined they offer synergistic and complementary information that can help uncover complex molecular details. Here we offer an overview of single-molecule fluorescence spectroscopy and molecular simulations in the context of studying disordered proteins. We discuss the various means in which simulations and single-molecule spectroscopy can be integrated, and consider a number of studies in which this integration has uncovered biological and biophysical mechanisms.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA.
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA.
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9
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Kozak F, Kurzbach D. How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations. Comput Struct Biotechnol J 2021; 19:2097-2105. [PMID: 33995905 PMCID: PMC8085671 DOI: 10.1016/j.csbj.2021.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
We review recent advances in modeling structural ensembles of transcription factors from nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopic data, integrated with molecular dynamics (MD) simulations. We focus on approaches that confirm computed conformational ensembles by sparse constraints obtained from magnetic resonance. This combination enables the deduction of functional and structural protein models even if nuclear Overhauser effects (NOEs) are too scarce for conventional structure determination. We highlight recent insights into the folding-upon-DNA binding transitions of intrinsically disordered transcription factors that could be assessed using such integrative approaches.
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Affiliation(s)
- Fanny Kozak
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
| | - Dennis Kurzbach
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
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10
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Beveridge R, Calabrese AN. Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins. Front Chem 2021; 9:603639. [PMID: 33791275 PMCID: PMC8006314 DOI: 10.3389/fchem.2021.603639] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and regions of intrinsic disorder (IDRs) are abundant in proteomes and are essential for many biological processes. Thus, they are often implicated in disease mechanisms, including neurodegeneration and cancer. The flexible nature of IDPs and IDRs provides many advantages, including (but not limited to) overcoming steric restrictions in binding, facilitating posttranslational modifications, and achieving high binding specificity with low affinity. IDPs adopt a heterogeneous structural ensemble, in contrast to typical folded proteins, making it challenging to interrogate their structure using conventional tools. Structural mass spectrometry (MS) methods are playing an increasingly important role in characterizing the structure and function of IDPs and IDRs, enabled by advances in the design of instrumentation and the development of new workflows, including in native MS, ion mobility MS, top-down MS, hydrogen-deuterium exchange MS, crosslinking MS, and covalent labeling. Here, we describe the advantages of these methods that make them ideal to study IDPs and highlight recent applications where these tools have underpinned new insights into IDP structure and function that would be difficult to elucidate using other methods.
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Affiliation(s)
- Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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11
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Frost CV, Zacharias M. From monomer to fibril: Abeta-amyloid binding to Aducanumab antibody studied by molecular dynamics simulation. Proteins 2020; 88:1592-1606. [PMID: 32666627 DOI: 10.1002/prot.25978] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/04/2020] [Accepted: 05/13/2020] [Indexed: 12/27/2022]
Abstract
Alzheimer's disease is one of the most common causes of dementia. It is believed that the aggregation of short Aβ-peptides to form oligomeric and protofibrillar amyloid assemblies plays a central role for disease-relevant neurotoxicity. In recent years, passive immunotherapy has been introduced as a potential treatment strategy with anti-amyloid antibodies binding to Aβ-amyloids and inducing their subsequent degradation by the immune system. Although so far mostly unsuccessful in clinical studies, the high-dosed application of the monoclonal antibody Aducanumab has shown therapeutic potential that might be attributed to its much greater affinity to Aβ-aggregates vs monomeric Aβ-peptides. In order to better understand how Aducanumab interacts with aggregated Aβ-forms compared to monomers, we have generated structural model complexes based on the known structure of Aducanumab in complex with an Aβ2 - 7 -eptitope. Structural models of Aducanumab bound to full-sequence Aβ1 - 40 -monomers, oligomers, protofilaments and mature fibrils were generated and investigated using extensive molecular dynamics simulations to characterize the flexibility and possible additional interactions. Indeed, an aggregate-specific N-terminal binding motif was found in case of Aducanumab binding to oligomers, protofilaments and fibrils that is located next to but not overlapping with the epitope binding site found in the crystal structure with Aβ2 - 7 . Analysis of binding energetics indicates that this motif binds weaker than the epitope but likely contributes to Aducanumab's preference for aggregated Aβ-species. The predicted aggregate-specific binding motif could potentially serve as a basis to reengineer Aducanumab for further enhanced preference to bind Aβ-aggregates vs monomers.
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Affiliation(s)
- Christina V Frost
- Physics Department T38, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, Garching, Germany
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12
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Zou R, Zhou Y, Wang Y, Kuang G, Ågren H, Wu J, Tu Y. Free Energy Profile and Kinetics of Coupled Folding and Binding of the Intrinsically Disordered Protein p53 with MDM2. J Chem Inf Model 2020; 60:1551-1558. [DOI: 10.1021/acs.jcim.9b00920] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Rongfeng Zou
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Yang Zhou
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Yong Wang
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Guanglin Kuang
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
- College of Chemistry and Chemical Engineering, Henan University, 475004 Kaifeng, Henan, P. R. China
| | - Junchen Wu
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237 Shanghai, China
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
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13
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Schuler B, Borgia A, Borgia MB, Heidarsson PO, Holmstrom ED, Nettels D, Sottini A. Binding without folding - the biomolecular function of disordered polyelectrolyte complexes. Curr Opin Struct Biol 2019; 60:66-76. [PMID: 31874413 DOI: 10.1016/j.sbi.2019.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
Abstract
Recent evidence shows that oppositely charged intrinsically disordered proteins (IDPs) can form high-affinity complexes that involve neither the formation of secondary or tertiary structure nor site-specific interactions between individual residues. Similar electrostatically dominated interactions have also been identified for positively charged IDPs binding to nucleic acids. These highly disordered polyelectrolyte complexes constitute an extreme case within the spectrum of biomolecular interactions involving disorder. Such interactions are likely to be widespread, since sequence analysis predicts proteins with highly charged disordered regions to be surprisingly numerous. Here, we summarize the insights that have emerged from the highly disordered polyelectrolyte complexes identified so far, and we highlight recent developments and future challenges in (i) establishing models for the underlying highly dynamic structural ensembles, (ii) understanding the novel binding mechanisms associated with them, and (iii) identifying the functional consequences.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Switzerland; Department of Physics, University of Zurich, Switzerland.
| | - Alessandro Borgia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Madeleine B Borgia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavík, Iceland
| | - Erik D Holmstrom
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside, Lawrence, KS 66045, USA; Department of Chemistry, University of Kansas, 1200 Sunnyside, Lawrence, KS 66045, USA
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Switzerland
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Switzerland
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14
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Yang J, Gao M, Xiong J, Su Z, Huang Y. Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding. Protein Sci 2019; 28:1952-1965. [PMID: 31441158 PMCID: PMC6798136 DOI: 10.1002/pro.3718] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
The sequence-structure-function paradigm of proteins has been revolutionized by the discovery of intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). In contrast to traditional ordered proteins, IDPs/IDRs are unstructured under physiological conditions. The absence of well-defined three-dimensional structures in the free state of IDPs/IDRs is fundamental to their function. Folding upon binding is an important mode of molecular recognition for IDPs/IDRs. While great efforts have been devoted to investigating the complex structures and binding kinetics and affinities, our knowledge on the binding mechanisms of IDPs/IDRs remains very limited. Here, we review recent advances on the binding mechanisms of IDPs/IDRs. The structures and kinetic parameters of IDPs/IDRs can vary greatly, and the binding mechanisms can be highly dependent on the structural properties of IDPs/IDRs. IDPs/IDRs can employ various combinations of conformational selection and induced fit in a binding process, which can be templated by the target and/or encoded by the IDP/IDR. Further studies should provide deeper insights into the molecular recognition of IDPs/IDRs and enable the rational design of IDP/IDR binding mechanisms in the future.
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Affiliation(s)
- Jing Yang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Meng Gao
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Junwen Xiong
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Zhengding Su
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Yongqi Huang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
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15
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Karlsson E, Andersson E, Jones NC, Hoffmann SV, Jemth P, Kjaergaard M. Coupled Binding and Helix Formation Monitored by Synchrotron-Radiation Circular Dichroism. Biophys J 2019; 117:729-742. [PMID: 31378314 PMCID: PMC6712486 DOI: 10.1016/j.bpj.2019.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/29/2019] [Accepted: 07/10/2019] [Indexed: 01/27/2023] Open
Abstract
Intrinsically disordered proteins organize interaction networks in the cell in many regulation and signaling processes. These proteins often gain structure upon binding to their target proteins in multistep reactions involving the formation of both secondary and tertiary structure. To understand the interactions of disordered proteins, we need to understand the mechanisms of these coupled folding and binding reactions. We studied helix formation in the binding of the molten globule-like nuclear coactivator binding domain and the disordered interaction domain from activator of thyroid hormone and retinoid receptors. We demonstrate that helix formation in a rapid binding reaction can be followed by stopped-flow synchrotron-radiation circular dichroism (CD) spectroscopy and describe the design of such a beamline. Fluorescence-monitored binding experiments of activator of thyroid hormone and retinoid receptors and nuclear coactivator binding domain display several kinetic phases, including one concentration-independent phase, which is consistent with an intermediate stabilized at high ionic strength. Time-resolved CD experiments show that almost all helicity is formed upon initial association of the proteins or separated from the encounter complex by only a small energy barrier. Through simulation of mechanistic models, we show that the intermediate observed at high ionic strength likely involves a structural rearrangement with minor overall changes in helicity. Our experiments provide a benchmark for simulations of coupled binding reactions and demonstrate the feasibility of using synchrotron-radiation CD for mechanistic studies of protein-protein interactions.
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Affiliation(s)
- Elin Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus, Denmark
| | | | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus, Denmark; Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark.
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16
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Han C, Cui C, Xing X, Lu Z, Zhang J, Liu J, Zhang Y. Functions of intrinsic disorder in proteins involved in DNA demethylation during pre-implantation embryonic development. Int J Biol Macromol 2019; 136:962-979. [PMID: 31229544 DOI: 10.1016/j.ijbiomac.2019.06.143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 01/21/2023]
Abstract
DNA demethylation is involved in many biological processes during pre-implantation embryonic development in mammals. To date, the complicated mechanism of DNA demethylation is still not fully understood. Ten-eleven translocation family (TET3, TET1 and TET2), thymine DNA glycosylase (TDG) and DNA methyltransferase 1 (DNMT1) are considered the major protein enzymes of DNA demethylation in pre-implantation embryos. TET3, TET1, TET2, TDG, and DNMT1 contain abundant levels of intrinsically disordered protein regions (IDPRs), which contribute to increasing the functional diversity of proteins. Thus we tried to explore the complicated DNA demethylation in pre-implantation embryos from the intrinsic disorder perspective. These five biological macromolecules all have DNA demethylation-related functional domains. They can work together to fulfill DNA demethylation in pre-implantation embryos through complex protein-protein interaction networks. Intrinsic disorder analysis results showed these proteins were partial intrinsically disordered proteins. Many identifiable disorder-based DNA-binding sites, protein-binding sites and post-translational modification sites located in the intrinsically disordered regions, and DNA demethylation deficiency point mutations in the IDPRs could significantly change the local disorder propensity of these proteins. To the best of our knowledge, this work provides a new viewpoint for studying the mechanism of DNA methylation reprogramming during mammalian pre-implantation embryonic development.
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Affiliation(s)
- Chengquan Han
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chenchen Cui
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xupeng Xing
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhenzhen Lu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China.
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17
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Efficient construction of a diverse conformational library for amyloid-β as an intrinsically disordered protein. J Mol Graph Model 2019; 88:183-193. [DOI: 10.1016/j.jmgm.2019.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/11/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
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18
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Semenyuk P, Muronetz V. Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications. Int J Mol Sci 2019; 20:E1252. [PMID: 30871103 PMCID: PMC6429204 DOI: 10.3390/ijms20051252] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/18/2022] Open
Abstract
Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for "generic" proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.
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Affiliation(s)
- Pavel Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Vladimir Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia.
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19
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Wu H, Wolynes PG, Papoian GA. AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins. J Phys Chem B 2018; 122:11115-11125. [PMID: 30091924 PMCID: PMC6713210 DOI: 10.1021/acs.jpcb.8b05791] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The associative memory, water-mediated, structure and energy model (AWSEM) has been successfully used to study protein folding, binding, and aggregation problems. In this work, we introduce AWSEM-IDP, a new AWSEM branch for simulating intrinsically disordered proteins (IDPs), where the weights of the potentials determining secondary structure formation have been finely tuned, and a novel potential is introduced that helps to precisely control both the average extent of protein chain collapse and the chain's fluctuations in size. AWSEM-IDP can efficiently sample large conformational spaces, while retaining sufficient molecular accuracy to realistically model proteins. We applied this new model to two IDPs, demonstrating that AWSEM-IDP can reasonably well reproduce higher-resolution reference data, thus providing the foundation for a transferable IDP force field. Finally, we used thermodynamic perturbation theory to show that, in general, the conformational ensembles of IDPs are highly sensitive to fine-tuning of force field parameters.
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Affiliation(s)
- Hao Wu
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Peter G. Wolynes
- Departments of Chemistry and Physics and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Garegin A. Papoian
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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20
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Joseph JA, Wales DJ. Intrinsically Disordered Landscapes for Human CD4 Receptor Peptide. J Phys Chem B 2018; 122:11906-11921. [DOI: 10.1021/acs.jpcb.8b08371] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Jerelle A. Joseph
- Department of Chemistry, University of Cambridge, Lenfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lenfield Road, Cambridge CB2 1EW, United Kingdom
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21
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Collins AP, Anderson PC. Complete Coupled Binding-Folding Pathway of the Intrinsically Disordered Transcription Factor Protein Brinker Revealed by Molecular Dynamics Simulations and Markov State Modeling. Biochemistry 2018; 57:4404-4420. [PMID: 29990433 DOI: 10.1021/acs.biochem.8b00441] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intrinsically disordered proteins (IDPs) make up a large class of proteins that lack stable structures in solution, existing instead as dynamic conformational ensembles. To perform their biological functions, many IDPs bind to other proteins or nucleic acids. Although IDPs are unstructured in solution, when they interact with binding partners, they fold into defined three-dimensional structures via coupled binding-folding processes. Because they frequently underlie IDP function, the mechanisms of this coupled binding-folding process are of great interest. However, given the flexibility inherent to IDPs and the sparse populations of intermediate states, it is difficult to reveal binding-folding pathways at atomic resolution using experimental methods. Computer simulations are another tool for studying these pathways at high resolution. Accordingly, we have applied 40 μs of unbiased molecular dynamics simulations and Markov state modeling to map the complete binding-folding pathway of a model IDP, the 59-residue C-terminal portion of the DNA binding domain of Drosophila melanogaster transcription factor Brinker (BrkDBD). Our modeling indicates that BrkDBD binds to its cognate DNA and folds in ∼50 μs by an induced fit mechanism, acquiring most of its stable secondary and tertiary structure only after it reaches the final binding site on the DNA. The protein follows numerous pathways en route to its bound and folded conformation, occasionally becoming stuck in kinetic traps. Each binding-folding pathway involves weakly bound, increasingly folded intermediate states located at different sites on the DNA surface. These findings agree with experimental data and provide additional insight into the BrkDBD folding mechanism and kinetics.
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Affiliation(s)
- Andrew P Collins
- Physical Sciences Division , University of Washington Bothell , Bothell , Washington 98011-8246 , United States
| | - Peter C Anderson
- Physical Sciences Division , University of Washington Bothell , Bothell , Washington 98011-8246 , United States
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22
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Karttunen M, Choy WY, Cino EA. Prediction of Binding Energy of Keap1 Interaction Motifs in the Nrf2 Antioxidant Pathway and Design of Potential High-Affinity Peptides. J Phys Chem B 2018; 122:5851-5859. [PMID: 29745220 DOI: 10.1021/acs.jpcb.8b03295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor and principal regulator of the antioxidant pathway. The Kelch domain of Kelch-like ECH-associated protein 1 (Keap1) binds to motifs in the N-terminal region of Nrf2, promoting its degradation. There is interest in developing ligands that can compete with Nrf2 for binding to Kelch, thereby activating its transcriptional activities and increasing antioxidant levels. Using experimental Δ Gbind values of Kelch-binding motifs determined previously, a revised hydrophobicity-based model was developed for estimating Δ Gbind from amino acid sequence and applied to rank potential uncharacterized Kelch-binding motifs identified from interaction databases and BLAST searches. Model predictions and molecular dynamics (MD) simulations suggested that full-length MAD2A binds Kelch more favorably than a high-affinity 20-mer Nrf2 E78P peptide, but that the motif in isolation is not a particularly strong binder. Endeavoring to develop shorter peptides for activating Nrf2, new designs were created based on the E78P peptide, some of which showed considerable propensity to form binding-competent structures in MD, and were predicted to interact with Kelch more favorably than the E78P peptide. The peptides could be promising new ligands for enhancing the oxidative stress response.
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Affiliation(s)
- Mikko Karttunen
- Department of Chemistry and Department of Applied Mathematics , The University of Western Ontario , London , Ontario , Canada N6A 5B7
| | - Wing-Yiu Choy
- Department of Biochemistry , The University of Western Ontario , London , Ontario , Canada N6A 5C1
| | - Elio A Cino
- Department of Biochemistry and Immunology , Federal University of Minas Gerais , Belo Horizonte 31270-901 , Brazil
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23
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Mascarenhas NM, Terse VL, Gosavi S. Intrinsic Disorder in a Well-Folded Globular Protein. J Phys Chem B 2018; 122:1876-1884. [PMID: 29304275 DOI: 10.1021/acs.jpcb.7b12546] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The folded structure of the heterodimeric sweet protein monellin mimics single-chain proteins with topology β1-α1-β2-β3-β4-β5 (chain A: β3-β4-β5; chain B: β1-α1-β2). Furthermore, like naturally occurring single-chain proteins of a similar size, monellin folds cooperatively with no detectable intermediates. However, the two monellin chains, A and B, are marginally structured in isolation and fold only upon binding to each other. Thus, monellin presents a unique opportunity to understand the design of intrinsically disordered proteins that fold upon binding. Here, we study the folding of a single-chain variant of monellin (scMn) using simulations of an all heavy-atom structure-based model. These simulations can explain mechanistic details derived from scMn experiments performed using several different structural probes. scMn folds cooperatively in our structure-based simulations, as is also seen in experiments. We find that structure formation near the transition-state ensemble of scMn is not uniformly distributed but is localized to a hairpin-like structure which contains one strand from each chain (β2, β3). Thus, the sequence and the underlying energetics of heterodimeric monellin promote the early formation of the interchain interface (β2-β3). By studying computational scMn mutants whose "interchain" interactions are deleted, we infer that this energy distribution allows the two protein chains to remain largely disordered when this interface is not folded. From these results, we suggest that cutting the protein backbone of a globular protein between residues which lie within its folding nucleus may be one way to construct two disordered fragments which fold upon binding.
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Affiliation(s)
| | - Vishram L Terse
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
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24
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Kosciolek T, Buchan DWA, Jones DT. Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment-Based Protein Structure Predictions. Sci Rep 2017; 7:6999. [PMID: 28765603 PMCID: PMC5539115 DOI: 10.1038/s41598-017-07156-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/23/2017] [Indexed: 11/08/2022] Open
Abstract
Intrinsically disordaered proteins (IDPs) are a prevalent phenomenon with over 30% of human proteins estimated to have long disordered regions. Computational methods are widely used to study IDPs, however, nearly all treat disorder in a binary fashion, not accounting for the structural heterogeneity present in disordered regions. Here, we present a new de novo method, FRAGFOLD-IDP, which addresses this problem. Using 200 protein structural ensembles derived from NMR, we show that FRAGFOLD-IDP achieves superior results compared to methods which can predict related data (NMR order parameter, or crystallographic B-factor). FRAGFOLD-IDP produces very good predictions for 33.5% of cases and helps to get a better insight into the dynamics of the disordered ensembles. The results also show it is not necessary to predict the correct fold of the protein to reliably predict per-residue fluctuations. It implies that disorder is a local property and it does not depend on the fold. Our results are orthogonal to DynaMine, the only other method significantly better than the naïve prediction. We therefore combine these two using a neural network. FRAGFOLD-IDP enables better insight into backbone dynamics in IDPs and opens exciting possibilities for the design of disordered ensembles, disorder-to-order transitions, or design for protein dynamics.
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Affiliation(s)
- Tomasz Kosciolek
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel W A Buchan
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - David T Jones
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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25
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Hughes ZE, Kochandra R, Walsh TR. Facet-Specific Adsorption of Tripeptides at Aqueous Au Interfaces: Open Questions in Reconciling Experiment and Simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3742-3754. [PMID: 28358489 DOI: 10.1021/acs.langmuir.6b04558] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The adsorption of three homo-tripeptides, HHH, YYY, and SSS, at the aqueous Au interface is investigated, using molecular dynamics simulations. We find that consideration of surface facet effects, relevant to experimental conditions, opens up new questions regarding interpretations of current experimental findings. Our well-tempered metadynamics simulations predict the rank ordering of the tripeptide binding affinities at aqueous Au(111) to be YYY > HHH > SSS. This ranking differs with that obtained from existing experimental data which used surface-immobilized Au nanoparticles as the target substrate. The influence of Au facet on these experimental findings is then considered, via our binding strength predictions of the relevant amino acids at aqueous Au(111) and Au(100)(1 × 1). The Au(111) interface supports an amino acid ranking of Tyr > HisA ≃ HisH > Ser, matching that of the tripeptides on Au(111), while the ranking on Au(100) is HisA > Ser ≃ Tyr ≃ HisH, with only HisA showing non-negligible binding. The substantial reduction in Tyr amino acid affinity for Au(100) vs Au(111) offers one possible explanation for the experimentally observed weaker adsorption of YYY on the nanoparticle-immobilized substrate compared with HHH. In a separate set of simulations, we predict the structures of the adsorbed tripeptides at the two aqueous Au facets, revealing facet-dependent differences in the adsorbed conformations. Our findings suggest that Au facet effects, where relevant, may influence the adsorption structures and energetics of biomolecules, highlighting the possible influence of the structural model used to interpret experimental binding data.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia
| | - Raji Kochandra
- Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University , Geelong, Victoria 3216, Australia
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26
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Masone D, Uhart M, Bustos DM. On the role of residue phosphorylation in 14-3-3 partners: AANAT as a case study. Sci Rep 2017; 7:46114. [PMID: 28387381 PMCID: PMC5384239 DOI: 10.1038/srep46114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/08/2017] [Indexed: 01/14/2023] Open
Abstract
Twenty years ago, a novel concept in protein structural biology was discovered: the intrinsically disordered regions (IDRs). These regions remain largely unstructured under native conditions and the more are studied, more properties are attributed to them. Possibly, one of the most important is their ability to conform a new type of protein-protein interaction. Besides the classical domain-to-domain interactions, IDRs follow a 'fly-casting' model including 'induced folding'. Unfortunately, it is only possible to experimentally explore initial and final states. However, the complete movie of conformational changes of protein regions and their characterization can be addressed by in silico experiments. Here, we simulate the binding of two proteins to describe how the phosphorylation of a single residue modulates the entire process. 14-3-3 protein family is considered a master regulator of phosphorylated proteins and from a modern point-of-view, protein phosphorylation is a three component system, with writers (kinases), erasers (phosphatases) and readers. This later biological role is attributed to the 14-3-3 protein family. Our molecular dynamics results show that phosphorylation of the key residue Thr31 in a partner of 14-3-3, the aralkylamine N-acetyltransferase, releases the fly-casting mechanism during binding. On the other hand, the non-phosphorylation of the same residue traps the proteins, systematically and repeatedly driving the simulations into wrong protein-protein conformations.
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Affiliation(s)
- Diego Masone
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Marina Uhart
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
| | - Diego M. Bustos
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
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27
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Chu WT, Clarke J, Shammas SL, Wang J. Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1. PLoS Comput Biol 2017; 13:e1005468. [PMID: 28369057 PMCID: PMC5400261 DOI: 10.1371/journal.pcbi.1005468] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/21/2017] [Accepted: 03/20/2017] [Indexed: 11/23/2022] Open
Abstract
PUMA, which belongs to the BH3-only protein family, is an intrinsically disordered protein (IDP). It binds to its cellular partner Mcl-1 through its BH3 motif, which folds upon binding into an α helix. We have applied a structure-based coarse-grained model, with an explicit Debye-Hückel charge model, to probe the importance of electrostatic interactions both in the early and the later stages of this model coupled folding and binding process. This model was carefully calibrated with the experimental data on helical content and affinity, and shown to be consistent with previously published experimental data on binding rate changes with respect to ionic strength. We find that intramolecular electrostatic interactions influence the unbound states of PUMA only marginally. Our results further suggest that intermolecular electrostatic interactions, and in particular non-native electrostatic interactions, are involved in formation of the initial encounter complex. We are able to reveal the binding mechanism in more detail than is possible using experimental data alone however, and in particular we uncover the role of non-native electrostatic interactions. We highlight the potential importance of such electrostatic interactions for describing the binding reactions of IDPs. Such approaches could be used to provide predictions for the results of mutational studies.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
| | - Sarah L. Shammas
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, New York, United States of America
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28
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Computational and theoretical advances in studies of intrinsically disordered proteins. Curr Opin Struct Biol 2017; 42:147-154. [PMID: 28259050 DOI: 10.1016/j.sbi.2017.01.006] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/16/2017] [Accepted: 01/21/2017] [Indexed: 01/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) are increasingly realized to play diverse biological roles, ranging from molecular signaling to the formation of membraneless organelles. Their high degree of disorder makes them more challenging to study using the techniques of conventional structural biology, because any observable will be averaged over a heterogeneous ensemble of structures. Molecular simulations and theory are therefore a natural complement to experiment for studying the structure, dynamics and function of IDPs. The diverse time and length scales relevant to the roles played by IDPs require flexibility in the techniques applied. Here, I summarize some of the developments in simulation and theory in recent years, which have been driven by the desire to better capture IDP properties at different time- and length-scales. I also provide an outlook for how methods can be improved in the future and emerging problems which may be addressed by theory and simulation.
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29
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Han M, Xu J, Ren Y. Compromise in competition between free energy and binding effect of intrinsically disordered protein p53 C-terminal domain. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1237023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mengzhi Han
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, R.C. China
- University of Chinese Academy of Sciences, Beijing, R.C. China
| | - Ji Xu
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, R.C. China
| | - Ying Ren
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, R.C. China
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30
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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31
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Rajasekaran N, Gopi S, Narayan A, Naganathan AN. Quantifying Protein Disorder through Measures of Excess Conformational Entropy. J Phys Chem B 2016; 120:4341-50. [PMID: 27111521 DOI: 10.1021/acs.jpcb.6b00658] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intrinsically disordered proteins (IDPs) and proteins with a large degree of disorder are abundant in the proteomes of eukaryotes and viruses, and play a vital role in cellular homeostasis and disease. One fundamental question that has been raised on IDPs is the process by which they offset the entropic penalty involved in transitioning from a heterogeneous ensemble of conformations to a much smaller collection of binding-competent states. However, this has been a difficult problem to address, as the effective entropic cost of fixing residues in a folded-like conformation from disordered amino acid neighborhoods is itself not known. Moreover, there are several examples where the sequence complexity of disordered regions is as high as well-folded regions. Disorder in such cases therefore arises from excess conformational entropy determined entirely by correlated sequence effects, an entropic code that is yet to be identified. Here, we explore these issues by exploiting the order-disorder transitions of a helix in Pbx-Homeodomain together with a dual entropy statistical mechanical model to estimate the magnitude and sign of the excess conformational entropy of residues in disordered regions. We find that a mere 2.1-fold increase in the number of allowed conformations per residue (∼0.7kBT favoring the unfolded state) relative to a well-folded sequence, or ∼2(N) additional conformations for a N-residue sequence, is sufficient to promote disorder under physiological conditions. We show that this estimate is quite robust and helps in rationalizing the thermodynamic signatures of disordered regions in important regulatory proteins, modeling the conformational folding-binding landscapes of IDPs, quantifying the stability effects characteristic of disordered protein loops and their subtle roles in determining the partitioning of folding flux in ordered domains. In effect, the dual entropy model we propose provides a statistical thermodynamic basis for the relative conformational propensities of amino acids in folded and disordered environments in proteins. Our work thus lays the foundation for understanding and quantifying protein disorder through measures of excess conformational entropy.
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Affiliation(s)
- Nandakumar Rajasekaran
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras , Chennai 600036, India
| | - Soundhararajan Gopi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras , Chennai 600036, India
| | - Abhishek Narayan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras , Chennai 600036, India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras , Chennai 600036, India
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32
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Neale C, Pomès R, García AE. Peptide Bond Isomerization in High-Temperature Simulations. J Chem Theory Comput 2016; 12:1989-99. [PMID: 26866899 DOI: 10.1021/acs.jctc.5b01022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Force fields for molecular simulation are generally optimized to model macromolecules such as proteins at ambient temperature and pressure. Nevertheless, elevated temperatures are frequently used to enhance conformational sampling, either during system setup or as a component of an advanced sampling technique such as temperature replica exchange. Because macromolecular force fields are now put upon to simulate temperatures and time scales that greatly exceed their original design specifications, it is appropriate to re-evaluate whether these force fields are up to the task. Here, we quantify the rates of peptide bond isomerization in high-temperature simulations of three octameric peptides and a small fast-folding protein. We show that peptide octamers with and without proline residues undergo cis/trans isomerization every 1-5 ns at 800 K with three classical atomistic force fields (AMBER99SB-ILDN, CHARMM22/CMAP, and OPLS-AA/L). On the low microsecond time scale, these force fields permit isomerization of nonprolyl peptide bonds at temperatures ≥500 K, and the CHARMM22/CMAP force field permits isomerization of prolyl peptide bonds ≥400 K. Moreover, the OPLS-AA/L force field allows chiral inversion about the Cα atom at 800 K. Finally, we show that temperature replica exchange permits cis peptide bonds developed at 540 K to subsequently migrate back to the 300 K ensemble, where cis peptide bonds are present in 2 ± 1% of the population of Trp-cage TC5b, including up to 4% of its folded state. Further work is required to assess the accuracy of cis/trans isomerization in the current generation of protein force fields.
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Affiliation(s)
- Chris Neale
- Center for NonLinear Studies (CNLS), MS B258, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children , 686 Bay Street, Toronto, Ontario M5G 0A4, Canada.,Department of Biochemistry, University of Toronto , 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Angel E García
- Center for NonLinear Studies (CNLS), MS B258, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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33
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Yuwen T, Xue Y, Skrynnikov NR. Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets: 2. The Model of Encounter Complex Involving the Double Mutant of the c-Crk N-SH3 Domain and Peptide Sos. Biochemistry 2016; 55:1784-800. [PMID: 26910732 DOI: 10.1021/acs.biochem.5b01283] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tairan Yuwen
- Department
of Chemistry, Purdue University, West Lafayette Indiana 47907, United States
| | - Yi Xue
- Department
of Chemistry, Purdue University, West Lafayette Indiana 47907, United States
| | - Nikolai R. Skrynnikov
- Department
of Chemistry, Purdue University, West Lafayette Indiana 47907, United States
- Laboratory
of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
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34
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Do TN, Choy WY, Karttunen M. Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations. J Chem Theory Comput 2015; 12:395-404. [PMID: 26636721 DOI: 10.1021/acs.jctc.5b00868] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Keap1 protein plays an essential role in regulating cellular oxidative stress response and is a crucial binding hub for multiple proteins, several of which are intrinsically disordered proteins (IDP). Among Kelch's IDP binding partners, NRF2 and PTMA are the two most interesting cases. They share a highly similar binding motif; however, NRF2 binds to Kelch with a binding affinity of approximately 100-fold higher than that of PTMA. In this study, we perform an exhaustive sampling composed of 6 μs well-tempered metadynamics and 2 μs unbiased molecular dynamics (MD) simulations aiming at characterizing the binding mechanisms and structural properties of these two peptides. Our results agree with previous experimental observations that PTMA is remarkably more disordered than NRF2 in both the free and bound states. This explains PTMA's lower binding affinity. Our extensive sampling also provides valuable insights into the vast conformational ensembles of both NRF2 and PTMA, supports the hypothesis of coupled folding-binding, and confirms the essential role of linear motifs in IDP binding.
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Affiliation(s)
- Trang Nhu Do
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, ON, Canada N2L 3G1
| | - Wing-Yiu Choy
- Department of Biochemistry, University of Western Ontario , 1151 Richmond Street, London, ON, Canada N6A 3K7
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, MetaForum, 5600 MB, Eindhoven, The Netherlands
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35
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Do TN, Choy WY, Karttunen M. Accelerating the Conformational Sampling of Intrinsically Disordered Proteins. J Chem Theory Comput 2015; 10:5081-94. [PMID: 26584388 DOI: 10.1021/ct5004803] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) are a class of proteins lacking a well-defined secondary structure. Instead, they are able to attain multiple conformations, bind to multiple targets, and respond to changes in their surroundings. Functionally, IDPs have been associated with molecular recognition, cell regulation, and signal transduction. The dynamic conformational ensemble of IDPs is highly environmental and binding partner dependent, rendering the characterization of IDPs extremely challenging. Here, we compare the sampling efficiencies of conventional molecular dynamics (MD), well-tempered metadynamics (WT-META), and bias-exchange metadynamics (BE-META). The total simulation time was over 10 μs, and a 20-mer peptide derived from the Neh2 domain of the Nuclear factor erythroid 2-related factor 2 (Nrf2) protein was simulated. BE-META, with a neutral replica and seven biased replicas employing a set of seven relevant collective variables (CVs), provided the most reliable and efficient sampling. Finally, we propose a free-energy reconstruction method based on the probability distribution of the secondary structure contents. This postprocessing analysis confirms the presence of not only the β-hairpin conformation of the free Neh2 peptide but also its rare bound-state-like conformation, both of that have been experimentally observed. In addition, our simulations also predict other possible conformations to be verified with future experiments.
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Affiliation(s)
- Trang Nhu Do
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, University of Western Ontario , 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Mikko Karttunen
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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36
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Bedford NM, Hughes ZE, Tang Z, Li Y, Briggs BD, Ren Y, Swihart MT, Petkov VG, Naik RR, Knecht MR, Walsh TR. Sequence-Dependent Structure/Function Relationships of Catalytic Peptide-Enabled Gold Nanoparticles Generated under Ambient Synthetic Conditions. J Am Chem Soc 2015; 138:540-8. [DOI: 10.1021/jacs.5b09529] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Nicholas M. Bedford
- Applied
Chemical and Materials Division, National Institute of Standards and Technology, Boulder, Colorado 80305, United States
- Materials
and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson
AFB, Ohio 45433, United States
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Zak E. Hughes
- Institute
for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Zhenghua Tang
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
- New
Energy Research Institute, School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Yue Li
- Chemical
and Biological Engineering, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Beverly D. Briggs
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Yang Ren
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Mark T. Swihart
- Chemical
and Biological Engineering, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Valeri G. Petkov
- Department
of Physics, Central Michigan University, Mt. Pleasant, Michigan 48858, United States
| | - Rajesh R. Naik
- Materials
and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson
AFB, Ohio 45433, United States
| | - Marc R. Knecht
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Tiffany R. Walsh
- Institute
for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
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37
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Feng T, Li M, Zhou J, Zhuang H, Chen F, Ye R, Campanella O, Fang Z. Application of molecular dynamics simulation in food carbohydrate research—a review. INNOV FOOD SCI EMERG 2015. [DOI: 10.1016/j.ifset.2015.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Gruber MF, Wood E, Truelsen S, Østergaard T, Hélix-Nielsen C. Computational Design of Biomimetic Phosphate Scavengers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:9469-9478. [PMID: 25920519 DOI: 10.1021/es506214c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Phosphorus has long been the target of much research, but in recent years the focus has shifted from being limited only to reducing its detrimental environmental impact, to also looking at how it is linked to the global food security. Therefore, the interest in finding novel techniques for phosphorus recovery, as well as improving existing techniques, has increased. In this study we apply a hybrid simulation approach of molecular dynamics and quantum mechanics to investigate the binding modes of phosphate anions by a small intrinsically disordered peptide. Our results confirm that the conformational ensemble of the peptide is significantly changed, or stabilized, by the binding of phosphate anions and that binding does not take place purely as a result of a stable P-loop binding nest, but rather that multiple binding modes may be involved. Such small synthetic peptides capable of binding phosphate could be the starting point of new novel technological approaches toward phosphorus recovery, and they represent an excellent model system for investigating the nature and dynamics of functional de novo designed intrinsically disordered proteins.
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Affiliation(s)
- Mathias F Gruber
- †The Biomimetic Membrane Group, Department of Environmental Engineering, Technical University of Denmark, DK 2800 Kgs. Lyngby Denmark
| | - Elizabeth Wood
- †The Biomimetic Membrane Group, Department of Environmental Engineering, Technical University of Denmark, DK 2800 Kgs. Lyngby Denmark
| | - Sigurd Truelsen
- †The Biomimetic Membrane Group, Department of Environmental Engineering, Technical University of Denmark, DK 2800 Kgs. Lyngby Denmark
| | - Thomas Østergaard
- †The Biomimetic Membrane Group, Department of Environmental Engineering, Technical University of Denmark, DK 2800 Kgs. Lyngby Denmark
| | - Claus Hélix-Nielsen
- †The Biomimetic Membrane Group, Department of Environmental Engineering, Technical University of Denmark, DK 2800 Kgs. Lyngby Denmark
- ‡University of Maribor, Faculty of Chemistry and Chemical Engineering, Smetanova ulica 17, SI-2000 Maribor, Slovenia
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39
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Pastor N, Amero C. Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations. FRONTIERS IN PLANT SCIENCE 2015; 6:306. [PMID: 25999971 PMCID: PMC4419604 DOI: 10.3389/fpls.2015.00306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/17/2015] [Indexed: 06/04/2023]
Abstract
Proteins participate in information pathways in cells, both as links in the chain of signals, and as the ultimate effectors. Upon ligand binding, proteins undergo conformation and motion changes, which can be sensed by the following link in the chain of information. Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations represent powerful tools for examining the time-dependent function of biological molecules. The recent advances in NMR and the availability of faster computers have opened the door to more detailed analyses of structure, dynamics, and interactions. Here we briefly describe the recent applications that allow NMR spectroscopy and MD simulations to offer unique insight into the basic motions that underlie information transfer within and between cells.
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Affiliation(s)
- Nina Pastor
- Laboratorio de Dinámica de Proteínas y Ácidos Nucleicos, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Carlos Amero
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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40
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Blöchliger N, Xu M, Caflisch A. Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges. Biophys J 2015; 108:2362-70. [PMID: 25954893 PMCID: PMC4423040 DOI: 10.1016/j.bpj.2015.03.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 03/11/2015] [Accepted: 03/17/2015] [Indexed: 12/15/2022] Open
Abstract
We have captured the binding of a peptide to a PDZ domain by unbiased molecular dynamics simulations. Analysis of the trajectories reveals on-pathway encounter complex formation, which is driven by electrostatic interactions between negatively charged carboxylate groups in the peptide and positively charged side chains surrounding the binding site. In contrast, the final stereospecific complex, which matches the crystal structure, features completely different interactions, namely the burial of the hydrophobic side chain of the peptide C-terminal residue and backbone hydrogen bonds. The simulations show that nonnative salt bridges stabilize kinetically the encounter complex during binding. Unbinding follows the inverse sequence of events with the same nonnative salt bridges in the encounter complex. Thus, in contrast to protein folding, which is driven by native interactions, the binding of charged peptides can be steered by nonnative interactions, which might be a general mechanism, e.g., in the recognition of histone tails by bromodomains.
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Affiliation(s)
| | - Min Xu
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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41
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Baker CM. Polarizable force fields for molecular dynamics simulations of biomolecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2015. [DOI: 10.1002/wcms.1215] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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42
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Chen T, Song J, Chan HS. Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding. Curr Opin Struct Biol 2014; 30:32-42. [PMID: 25544254 DOI: 10.1016/j.sbi.2014.12.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/02/2014] [Accepted: 12/02/2014] [Indexed: 11/29/2022]
Abstract
The diverse biological functions of intrinsically disordered proteins (IDPs) have markedly raised our appreciation of protein conformational versatility, whereas the existence of energetically favorable yet functional detrimental nonnative interactions underscores the physical limitations of evolutionary optimization. Here we survey recent advances in using biophysical modeling to gain insight into experimentally observed nonnative behaviors and IDP properties. Simulations of IDP interactions to date focus mostly on coupled folding-binding, which follows essentially the same organizing principle as the local-nonlocal coupling mechanism in cooperative folding of monomeric globular proteins. By contrast, more innovative theories of electrostatic and aromatic interactions are needed for the conceptually novel but less-explored 'fuzzy' complexes in which the functionally bound IDPs remain largely disordered.
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Affiliation(s)
- Tao Chen
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Jianhui Song
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada.
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43
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Rogers JM, Oleinikovas V, Shammas SL, Wong CT, De Sancho D, Baker CM, Clarke J. Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein. Proc Natl Acad Sci U S A 2014; 111:15420-5. [PMID: 25313042 PMCID: PMC4217413 DOI: 10.1073/pnas.1409122111] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein-protein interactions are at the heart of regulatory and signaling processes in the cell. In many interactions, one or both proteins are disordered before association. However, this disorder in the unbound state does not prevent many of these proteins folding to a well-defined, ordered structure in the bound state. Here we examine a typical system, where a small disordered protein (PUMA, p53 upregulated modulator of apoptosis) folds to an α-helix when bound to a groove on the surface of a folded protein (MCL-1, induced myeloid leukemia cell differentiation protein). We follow the association of these proteins using rapid-mixing stopped flow, and examine how the kinetic behavior is perturbed by denaturant and carefully chosen mutations. We demonstrate the utility of methods developed for the study of monomeric protein folding, including β-Tanford values, Leffler α, Φ-value analysis, and coarse-grained simulations, and propose a self-consistent mechanism for binding. Folding of the disordered protein before binding does not appear to be required and few, if any, specific interactions are required to commit to association. The majority of PUMA folding occurs after the transition state, in the presence of MCL-1. We also examine the role of the side chains of folded MCL-1 that make up the binding groove and find that many favor equilibrium binding but, surprisingly, inhibit the association process.
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Affiliation(s)
- Joseph M Rogers
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | | | - Sarah L Shammas
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Chi T Wong
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - David De Sancho
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Christopher M Baker
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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44
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Villoutreix BO, Kuenemann MA, Poyet JL, Bruzzoni-Giovanelli H, Labbé C, Lagorce D, Sperandio O, Miteva MA. Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. Mol Inform 2014; 33:414-437. [PMID: 25254076 PMCID: PMC4160817 DOI: 10.1002/minf.201400040] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 04/21/2014] [Indexed: 12/13/2022]
Abstract
[Formula: see text] Fundamental processes in living cells are largely controlled by macromolecular interactions and among them, protein-protein interactions (PPIs) have a critical role while their dysregulations can contribute to the pathogenesis of numerous diseases. Although PPIs were considered as attractive pharmaceutical targets already some years ago, they have been thus far largely unexploited for therapeutic interventions with low molecular weight compounds. Several limiting factors, from technological hurdles to conceptual barriers, are known, which, taken together, explain why research in this area has been relatively slow. However, this last decade, the scientific community has challenged the dogma and became more enthusiastic about the modulation of PPIs with small drug-like molecules. In fact, several success stories were reported both, at the preclinical and clinical stages. In this review article, written for the 2014 International Summer School in Chemoinformatics (Strasbourg, France), we discuss in silico tools (essentially post 2012) and databases that can assist the design of low molecular weight PPI modulators (these tools can be found at www.vls3d.com). We first introduce the field of protein-protein interaction research, discuss key challenges and comment recently reported in silico packages, protocols and databases dedicated to PPIs. Then, we illustrate how in silico methods can be used and combined with experimental work to identify PPI modulators.
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Affiliation(s)
- Bruno O Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Melaine A Kuenemann
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - Jean-Luc Poyet
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- IUH, Hôpital Saint-LouisParis, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Heriberto Bruzzoni-Giovanelli
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CIC, Clinical investigation center, Hôpital Saint-LouisParis, France
| | - Céline Labbé
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - David Lagorce
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
| | - Olivier Sperandio
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
- CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse59000 Lille, France
| | - Maria A Miteva
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 InsermParis 75013, France
- Inserm, U973Paris 75013, France
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45
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Knott M, Best RB. Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model. J Chem Phys 2014; 140:175102. [PMID: 24811666 PMCID: PMC4032430 DOI: 10.1063/1.4873710] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/17/2014] [Indexed: 12/31/2022] Open
Abstract
Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an "induced fit" or "conformational selection" mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.
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Affiliation(s)
- Michael Knott
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Robert B Best
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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