1
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Han ISM, Thayer KM. Reconnaissance of Allostery via the Restoration of Native p53 DNA-Binding Domain Dynamics in Y220C Mutant p53 Tumor Suppressor Protein. ACS OMEGA 2024; 9:19837-19847. [PMID: 38737036 PMCID: PMC11079909 DOI: 10.1021/acsomega.3c08509] [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: 10/27/2023] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 05/14/2024]
Abstract
Allosteric regulation of protein dynamics infers a long-range deliberate propagation of information via micro- and macroscale interactions. The Y220C structural mutant is one of the most frequent cancerous p53 mutants. The mutation is distally located from the DNA-binding site of the p53 DNA-binding domain yet causes changes in DNA recognition. This system presents a unique opportunity to examine the allosteric control of mutated proteins under a drug design paradigm. We focus on the key case study of p53 Y220C mutation restoration by a series of new compounds suggested to have Y220C reactivation properties in comparison to our previous findings on the restorative potential of PK11000, a compound studied extensively for reactivation in vitro and in vivo. Previously, we implemented all-atom molecular dynamics (MD) simulations and our lab's techniques of MD-Sectors and MD-Markov state models on the wild type, the Y220C mutant, and Y220C with PK11000 to characterize the effector's restorative properties in terms of conformational dynamics and hydrogen bonding. In this study, we turn to probing the effects made by docking the battery of a new but less well-tested set of aminobenzothiazole derivative compounds reported by Baud et al., which show promise of Y220C rescue. We find that while complete and precise reconstitution of p53 WT molecular dynamics may not be observed as was the case with PK11000, dispersed local reconstitution of loop dynamics provides evidence of rescuing effects by aminobenzothiazole derivative N,2-dihydroxy-3,5-diiodo-4-(1H-pyrrol-1-yl)benzamide, Effector 22, like what we observed for PK11000. Generalizable insights into the mutation and allosteric reactivation of p53 by various effectors by reconstitution of WT dynamics observed in statistical conformational ensemble analysis and network inference are discussed, considering the development of allosteric drug design rooted in first principles.
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Affiliation(s)
- In Sub M. Han
- College of Integrated Sciences, Wesleyan University, Hall-Atwater Laboratories, Middletown, Connecticut 06459-0180, United States
| | - Kelly M. Thayer
- College of Integrated Sciences, Wesleyan University, Hall-Atwater Laboratories, Middletown, Connecticut 06459-0180, United States
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2
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Ma C, Chung DJ, Abramson D, Langley DR, Thayer KM. Mutagenic Activation of Glutathione Peroxidase-4: Approaches toward Rational Design of Allosteric Drugs. ACS OMEGA 2022; 7:29587-29597. [PMID: 36061715 PMCID: PMC9434792 DOI: 10.1021/acsomega.2c01289] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Glutathione peroxidase 4 (GPX4) reduces lipid hydroperoxides in lipid membranes, effectively inhibiting iron-dependent cell death or ferroptosis. The upregulation of the enzyme by the mutations at residues D21 and D23 has been suggested to be associated with higher protein activity, which confers more protection against neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's diseases. Therefore, it has become an attractive target for treating and preventing neurodegenerative diseases. However, identifying means of mimicking the beneficial effects of these mutations distant from the active site constitutes a formidable challenge in moving toward therapeutics. In this study, we explore using molecular dynamics simulations to computationally map the conformational and energetic landscape of the wild-type GPX4 protein and three mutant variants to identify the allosteric networks of the enzyme. We present the conformational dynamic profile providing the desired signature behavior of the enzyme. We also discuss the implications of these findings for drug design efforts.
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Affiliation(s)
- Chunyue Ma
- Department
of Mathematics & Computer Science, Wesleyan
University, Middletown, Connecticut 06459, United States
| | - Daniel J. Chung
- Department
of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
- Molecular
Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Dylan Abramson
- Department
of Mathematics & Computer Science, Wesleyan
University, Middletown, Connecticut 06459, United States
| | - David R. Langley
- Department
of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
- Molecular
Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
- Arvinas
Inc., New Haven, Connecticut 06511, United States
| | - Kelly M. Thayer
- Department
of Mathematics & Computer Science, Wesleyan
University, Middletown, Connecticut 06459, United States
- Department
of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
- Molecular
Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
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3
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Han ISM, Abramson D, Thayer KM. Insights into Rational Design of a New Class of Allosteric Effectors with Molecular Dynamics Markov State Models and Network Theory. ACS OMEGA 2022; 7:2831-2841. [PMID: 35097279 PMCID: PMC8792916 DOI: 10.1021/acsomega.1c05624] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/16/2021] [Indexed: 05/12/2023]
Abstract
The development of drugs to restore protein function has been a major advance facilitated by molecular medicine. Allosteric regulation, a phenomenon widely observed in nature, in which a molecule binds to control a distance active site, holds great promise for regulating proteins, yet how to rationally design such a molecule remains a mystery. Over the past few years, we and others have developed several techniques based on molecular dynamics (MD) simulations: MD-Markov state models to capture global conformational substates, and network theory approach utilizing the interaction energy within the protein to confer local allosteric control. We focus on the key case study of the p53 Y220C mutation restoration by PK11000, a compound experimentally shown to reactivate p53 native function in Y220C mutant present tumors. We gain insights into the mutation and allosteric reactivation of the protein, which we anticipate will be applicable to de novo design to engineer new compounds not only for this mutation, but in other macromolecular systems as well.
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4
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Wang H, Song L, Zhou T, Zeng C, Jia Y, Zhao Y. A computational study of Tat-CDK9-Cyclin binding dynamics and its implication in transcription-dependent HIV latency. Phys Chem Chem Phys 2020; 22:25474-25482. [PMID: 33043947 DOI: 10.1039/d0cp03662e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
HIV is a virus that attacks the T cells. HIV may either actively replicate or become latent within host cells for years. Since HIV uses its own protein Tat to hijack the host CDK9-Cyclin complex for transcription, Tat is implicated in transcription-dependent HIV latency. To quantify the impact of Tat binding, we propose a computational framework to probe the dynamics of the CDK9-Cyclin interface and the ATP pocket reorganization upon binding by different Tat mutants. Specifically, we focus on mutations at three Tat residues P10, W11, and N12 that are known to interact directly with CDK9 based on the crystal structure of the Tat-CDK9-Cyclin complex. Our molecular dynamics simulations show that the CDK9-Cyclin interface becomes slightly weaker for P10S and W11R mutants but tighter for the K12N mutant. Furthermore, the side chain orientation of residue K48 in the ATP pocket of CDK9 is similar to the inactive state in P10S and W11R simulations, but similar to the active state in K12N simulations. These are consistent with some existing but puzzling observations of latency for these mutants. This framework may hence help gain a better understanding of the role of Tat in the transcription-dependent HIV latency establishment.
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Affiliation(s)
- Huiwen Wang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China.
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5
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Lakhani B, Thayer KM, Black E, Beveridge DL. Spectral analysis of molecular dynamics simulations on PDZ: MD sectors. J Biomol Struct Dyn 2020; 38:781-790. [PMID: 31262238 PMCID: PMC7307555 DOI: 10.1080/07391102.2019.1588169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 02/23/2019] [Indexed: 02/06/2023]
Abstract
The idea of protein "sectors" posits that sparse subsets of amino acid residues form cooperative networks that are key elements of protein stability, ligand binding, and allosterism. To date, protein sectors have been calculated by the statistical coupling analysis (SCA) method of Ranganathan and co-workers via the spectral analysis of conservation-weighted evolutionary covariance matrices obtained from a multiple sequence alignments of homologous families of proteins. SCA sectors, a knowledge-based protocol, have been indentified with functional properties and allosterism for a number of systems. In this study, we investigate the utility of the sector idea for the analysis of physics-based molecular dynamics (MD) trajectories of proteins. Our test case for this procedure is PSD95- PDZ3, one of the smallest proteins for which allosterism has been observed. It has served previously as a model system for a number of prediction algorithms, and is well characterized by X-ray crystallography, NMR spectroscopy and site specific mutagenisis. All-atom MD simulations were performed for a total of 500 nanoseconds using AMBER, and MD-calculated covariance matrices for the fluctuations of residue displacements and non-bonded interaction energies were subjected to spectral analysis in a manner analogous to that of SCA. The composition of MD sectors was compared with results from SCA, site specific mutagenesis, and allosterism. The concordance indicates that MD sectors are a viable protocol for analyzing MD trajectories and provide insight into the physical origin of the phenomenon.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharat Lakhani
- Program in Molecular Biophysics, Wesleyan University, Middletown CT 06459, USA
- Department of Molecular Biology & Biochemistry, Wesleyan University, Middletown CT 06459, USA
| | - Kelly M. Thayer
- Program in Molecular Biophysics, Wesleyan University, Middletown CT 06459, USA
- Chemistry Department, Wesleyan University, Middletown CT 06459, USA
- Department of Mathematics and Computer Science, Wesleyan University, Middletown CT 06459, USA
| | - Emily Black
- Program in Molecular Biophysics, Wesleyan University, Middletown CT 06459, USA
| | - David L. Beveridge
- Program in Molecular Biophysics, Wesleyan University, Middletown CT 06459, USA
- Chemistry Department, Wesleyan University, Middletown CT 06459, USA
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6
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LeBlanc SJ, Gauer JW, Hao P, Case BC, Hingorani MM, Weninger KR, Erie DA. Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS. Nucleic Acids Res 2019; 46:10782-10795. [PMID: 30272207 PMCID: PMC6237781 DOI: 10.1093/nar/gky865] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022] Open
Abstract
MutS homologs identify base-pairing errors made in DNA during replication and initiate their repair. In the presence of adenosine triphosphate, MutS induces DNA bending upon mismatch recognition and subsequently undergoes conformational transitions that promote its interaction with MutL to signal repair. In the absence of MutL, these transitions lead to formation of a MutS mobile clamp that can move along the DNA. Previous single-molecule FRET (smFRET) studies characterized the dynamics of MutS DNA-binding domains during these transitions. Here, we use protein–DNA and DNA–DNA smFRET to monitor DNA conformational changes, and we use kinetic analyses to correlate DNA and protein conformational changes to one another and to the steps on the pathway to mobile clamp formation. The results reveal multiple sequential structural changes in both MutS and DNA, and they suggest that DNA dynamics play a critical role in the formation of the MutS mobile clamp. Taking these findings together with data from our previous studies, we propose a unified model of coordinated MutS and DNA conformational changes wherein initiation of mismatch repair is governed by a balance of DNA bending/unbending energetics and MutS conformational changes coupled to its nucleotide binding properties.
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Affiliation(s)
- Sharonda J LeBlanc
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Jacob W Gauer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pengyu Hao
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Brandon C Case
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Manju M Hingorani
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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7
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Maffeo C, Chou HY, Aksimentiev A. Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations. ADVANCED THEORY AND SIMULATIONS 2019; 2:1800191. [PMID: 31728433 PMCID: PMC6855400 DOI: 10.1002/adts.201800191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/15/2022]
Abstract
Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein-nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. In this review, we describe recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. We highlight the use of diverse computational methods to address specific problems of the fields and discuss unexplored possibilities that lie ahead for the computational approaches in these areas.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Han-Yi Chou
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign,1110 W Green St, Urbana, IL 61801, USA
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8
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Lin K, Zhao ZZ, Bo HB, Hao XJ, Wang JQ. Applications of Ruthenium Complex in Tumor Diagnosis and Therapy. Front Pharmacol 2018; 9:1323. [PMID: 30510511 PMCID: PMC6252376 DOI: 10.3389/fphar.2018.01323] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/29/2018] [Indexed: 12/27/2022] Open
Abstract
Ruthenium complexes are a new generation of metal antitumor drugs that are currently of great interest in multidisciplinary research. In this review article, we introduce the applications of ruthenium complexes in the diagnosis and therapy of tumors. We focus on the actions of ruthenium complexes on DNA, mitochondria, and endoplasmic reticulum of cells, as well as signaling pathways that induce tumor cell apoptosis, autophagy, and inhibition of angiogenesis. Furthermore, we highlight the use of ruthenium complexes as specific tumor cell probes to dynamically monitor the active biological component of the microenvironment and as excellent photosensitizer, catalyst, and bioimaging agents for phototherapies that significantly enhance the diagnosis and therapeutic effect on tumors. Finally, the combinational use of ruthenium complexes with existing clinical antitumor drugs to synergistically treat tumors is discussed.
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Affiliation(s)
- Ke Lin
- School of Bioscience and Biopharmaceutics, Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zi-Zhuo Zhao
- Department of Ultrasound, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hua-Ben Bo
- School of Bioscience and Biopharmaceutics, Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiao-Juan Hao
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - Jin-Quan Wang
- School of Bioscience and Biopharmaceutics, Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, China
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9
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Thayer KM, Galganov JC, Stein AJ. Dependence of prevalence of contiguous pathways in proteins on structural complexity. PLoS One 2017; 12:e0188616. [PMID: 29232711 PMCID: PMC5726733 DOI: 10.1371/journal.pone.0188616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/10/2017] [Indexed: 12/15/2022] Open
Abstract
Allostery is a regulatory mechanism in proteins where an effector molecule binds distal from an active site to modulate its activity. Allosteric signaling may occur via a continuous path of residues linking the active and allosteric sites, which has been suggested by large conformational changes evident in crystal structures. An alternate possibility is that the signal occurs in the realm of ensemble dynamics via an energy landscape change. While the latter was first proposed on theoretical grounds, increasing evidence suggests that such a control mechanism is plausible. A major difficulty for testing the two methods is the ability to definitively determine that a residue is directly involved in allosteric signal transduction. Statistical Coupling Analysis (SCA) is a method that has been successful at predicting pathways, and experimental tests involving mutagenesis or domain substitution provide the best available evidence of signaling pathways. However, ascertaining energetic pathways which need not be contiguous is far more difficult. To date, simple estimates of the statistical significance of a pathway in a protein remain to be established. The focus of this work is to estimate such benchmarks for the statistical significance of contiguous pathways for the null model of selecting residues at random. We found that when 20% of residues in proteins are randomly selected, contiguous pathways at the 6 Å cutoff level were found with success rates of 51% in PDZ, 30% in p53, and 3% in MutS. The results suggest that the significance of pathways may have system specific factors involved. Furthermore, the possible existence of false positives for contiguous pathways implies that signaling could be occurring via alternate routes including those consistent with the energetic landscape model.
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Affiliation(s)
- Kelly M. Thayer
- Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT, United States of America
- Program in Molecular Biophysics, Wesleyan University, Middletown, CT, United States of America
- Department of Chemistry, Wesleyan University, Middletown, CT, United States of America
- * E-mail:
| | - Jesse C. Galganov
- Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT, United States of America
- Program in Bioinformatics, Wesleyan University, Middletown, CT, United States of America
| | - Avram J. Stein
- Department of Astronomy, Wesleyan University, Middletown, CT, United States of America
- Department of Earth and Environmental Sciences, Wesleyan University, Middletown, CT, United States of America
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10
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Hayakawa D, Yamaotsu N, Nakagome I, Ozawa SI, Yoshida T, Hirono S. In silico analyses of the effects of a point mutation and a pharmacological chaperone on the thermal fluctuation of phenylalanine hydroxylase. Biophys Chem 2017; 228:47-54. [DOI: 10.1016/j.bpc.2017.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/28/2017] [Accepted: 06/28/2017] [Indexed: 10/19/2022]
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11
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Lakhani B, Thayer KM, Hingorani MM, Beveridge DL. Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein. J Phys Chem B 2017; 121:2049-2061. [PMID: 28135092 PMCID: PMC5346969 DOI: 10.1021/acs.jpcb.6b11976] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Mismatch
repair (MMR) is an essential, evolutionarily conserved
pathway that maintains genome stability by correcting base-pairing
errors in DNA. Here we examine the sequence and structure of MutS
MMR protein to decipher the amino acid framework underlying its two
key activities—recognizing mismatches in DNA and using ATP
to initiate repair. Statistical coupling analysis (SCA) identified
a network (sector) of coevolved amino acids in the MutS protein family.
The potential functional significance of this SCA sector was assessed
by performing molecular dynamics (MD) simulations for alanine mutants
of the top 5% of 160 residues in the distribution, and control nonsector
residues. The effects on three independent metrics were monitored:
(i) MutS domain conformational dynamics, (ii) hydrogen bonding between
MutS and DNA/ATP, and (iii) relative ATP binding free energy. Each
measure revealed that sector residues contribute more substantively
to MutS structure–function than nonsector residues. Notably,
sector mutations disrupted MutS contacts with DNA and/or ATP from
a distance via contiguous pathways and correlated motions, supporting
the idea that SCA can identify amino acid networks underlying allosteric
communication. The combined SCA/MD approach yielded novel, experimentally
testable hypotheses for unknown roles of many residues distributed
across MutS, including some implicated in Lynch cancer syndrome.
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Affiliation(s)
- Bharat Lakhani
- Molecular Biology and Biochemistry Department, ‡Molecular Biophysics Program, §Chemistry Department, and ∥Computer Science Department, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Kelly M Thayer
- Molecular Biology and Biochemistry Department, ‡Molecular Biophysics Program, §Chemistry Department, and ∥Computer Science Department, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Manju M Hingorani
- Molecular Biology and Biochemistry Department, ‡Molecular Biophysics Program, §Chemistry Department, and ∥Computer Science Department, Wesleyan University , Middletown, Connecticut 06459, United States
| | - David L Beveridge
- Molecular Biology and Biochemistry Department, ‡Molecular Biophysics Program, §Chemistry Department, and ∥Computer Science Department, Wesleyan University , Middletown, Connecticut 06459, United States
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12
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Foster CA, West AH. Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems. Proteins 2016; 85:155-176. [PMID: 27802580 PMCID: PMC5242315 DOI: 10.1002/prot.25207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/22/2016] [Accepted: 10/25/2016] [Indexed: 01/22/2023]
Abstract
Two‐component signaling (TCS) is the primary means by which bacteria, as well as certain plants and fungi, respond to external stimuli. Signal transduction involves stimulus‐dependent autophosphorylation of a sensor histidine kinase and phosphoryl transfer to the receiver domain of a downstream response regulator. Phosphorylation acts as an allosteric switch, inducing structural and functional changes in the pathway's components. Due to their transient nature, phosphorylated receiver domains are challenging to characterize structurally. In this work, we provide a methodology for simulating receiver domain phosphorylation to predict conformations that are nearly identical to experimental structures. Using restrained molecular dynamics, phosphorylated conformations of receiver domains can be reliably sampled on nanosecond timescales. These simulations also provide data on conformational dynamics that can be used to identify regions of functional significance related to phosphorylation. We first validated this approach on several well‐characterized receiver domains and then used it to compare the upstream and downstream components of the fungal Sln1 phosphorelay. Our results demonstrate that this technique provides structural insight, obtained in the absence of crystallographic or NMR information, regarding phosphorylation‐induced conformational changes in receiver domains that regulate the output of their associated signaling pathway. To our knowledge, this is the first time such a protocol has been described that can be broadly applied to TCS proteins for predictive purposes. Proteins 2016; 85:155–176. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Clay A Foster
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Ann H West
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
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13
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Wang B, Francis J, Sharma M, Law SM, Predeus AV, Feig M. Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways. PLoS Comput Biol 2016; 12:e1005159. [PMID: 27768684 PMCID: PMC5074593 DOI: 10.1371/journal.pcbi.1005159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/21/2016] [Indexed: 11/19/2022] Open
Abstract
Allostery is conformation regulation by propagating a signal from one site to another distal site. This study focuses on the long-range communication in DNA mismatch repair proteins MutS and its homologs where intramolecular signaling has to travel over 70 Å to couple lesion detection to ATPase activity and eventual downstream repair. Using dynamic network analysis based on extensive molecular dynamics simulations, multiple preserved communication pathways were identified that would allow such long-range signaling. The pathways appear to depend on the nucleotides bound to the ATPase domain as well as the type of DNA substrate consistent with previously proposed functional cycles of mismatch recognition and repair initiation by MutS and homologs. A mechanism is proposed where pathways are switched without major conformational rearrangements allowing for efficient long-range signaling and allostery.
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Affiliation(s)
- Beibei Wang
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Joshua Francis
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Monika Sharma
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Sean M. Law
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Alexander V. Predeus
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Michael Feig
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
- * E-mail:
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14
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Ishida H, Matsumoto A. Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations. Proteins 2016; 84:1287-303. [PMID: 27238299 DOI: 10.1002/prot.25077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/13/2016] [Accepted: 05/24/2016] [Indexed: 11/10/2022]
Abstract
In order to understand how MutS recognizes mismatched DNA and induces the reaction of DNA repair using ATP, the dynamics of the complexes of MutS (bound to the ADP and ATP nucleotides, or not) and DNA (with mismatched and matched base-pairs) were investigated using molecular dynamics simulations. As for DNA, the structure of the base-pairs of the homoduplex DNA which interacted with the DNA recognition site of MutS was intermittently disturbed, indicating that the homoduplex DNA was unstable. As for MutS, the disordered loops in the ATPase domains, which are considered to be necessary for the induction of DNA repair, were close to (away from) the nucleotide-binding sites in the ATPase domains when the nucleotides were (not) bound to MutS. This indicates that the ATPase domains changed their structural stability upon ATP binding using the disordered loop. Conformational analysis by principal component analysis showed that the nucleotide binding changed modes which have structurally solid ATPase domains and the large bending motion of the DNA from higher to lower frequencies. In the MutS-mismatched DNA complex bound to two nucleotides, the bending motion of the DNA at low frequency modes may play a role in triggering the formation of the sliding clamp for the following DNA-repair reaction step. Moreover, MM-PBSA/GBSA showed that the MutS-homoduplex DNA complex bound to two nucleotides was unstable because of the unfavorable interactions between MutS and DNA. This would trigger the ATP hydrolysis or separation of MutS and DNA to continue searching for mismatch base-pairs. Proteins 2016; 84:1287-1303. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hisashi Ishida
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai Kizugawa-Shi, Kyoto, 619-0215, Japan
| | - Atsushi Matsumoto
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai Kizugawa-Shi, Kyoto, 619-0215, Japan
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15
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Lu Y, Salsbury FR. Recapturing the Correlated Motions of Protein Using Coarse- Grained Models. Protein Pept Lett 2016; 22:654-9. [PMID: 26100687 DOI: 10.2174/0929866522666150511150332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 03/24/2015] [Accepted: 05/07/2015] [Indexed: 11/22/2022]
Abstract
Long-range interactions and allostery are important for many biological processes. Increasing numbers of studies, both experimental and computational, show that internal dynamics may play an important role in such behaviors. Investigating the dynamical effects of proteins, how- ever, is a challenging problem using all-atom molecular dynamics because of the length-scales and timescales involved. As a result, coarse-grained models are often implemented. Herein, we use three well-defined coarse-grained models: Go, Martini and Cafemol, and a small model protein Eglin C, which is readily studied via all-atom molecular dynamics, to examine if these coarse grained models can explore the dynamics of Eglin C accurately as well as to see how these models respond to mutations. We found that all three models can recapture the dynamics of Eglin C to a significant extent - where we focus on root-mean square fluctuations and correlated motions as dynamical measures - but that the Cafemol and Go models are superior. The best agreement with all-atom simulations is for structured regions of Eglin C.
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Affiliation(s)
| | - Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, NC 27106, USA.
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16
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Hingorani MM. Mismatch binding, ADP-ATP exchange and intramolecular signaling during mismatch repair. DNA Repair (Amst) 2016; 38:24-31. [PMID: 26704427 PMCID: PMC4740199 DOI: 10.1016/j.dnarep.2015.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 09/08/2015] [Accepted: 11/30/2015] [Indexed: 12/16/2022]
Abstract
The focus of this article is on the DNA binding and ATPase activities of the mismatch repair (MMR) protein, MutS-our current understanding of how this protein uses ATP to fuel its actions on DNA and initiate repair via interactions with MutL, the next protein in the pathway. Structure-function and kinetic studies have yielded detailed views of the MutS mechanism of action in MMR. How MutS and MutL work together after mismatch recognition to enable strand-specific nicking, which leads to strand excision and synthesis, is less clear and remains an active area of investigation.
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17
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Wan H, Chang S, Hu JP, Tian YX, Tian XH. Molecular Dynamics Simulations of Ternary Complexes: Comparisons of LEAFY Protein Binding to Different DNA Motifs. J Chem Inf Model 2015; 55:784-94. [PMID: 25734970 DOI: 10.1021/ci500705j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LEAFY (LFY) is a plant-specific transcription factor, with a variety of roles in different species. LFY contains a conserved DNA-binding domain (DBD) that determines its DNA-binding specificity. Recently, the structures of the dimeric LFY-DBD bound to different DNA motifs were successively solved by X-ray crystallography. In this article, molecular dynamics (MD) simulations are employed to study two crystal structures of DNA-bound LFY protein from angiosperms and the moss Physcomitrella patens, respectively. The comparison of stabilities of the two systems is consistent with the experimental data of binding affinities. The calculation of hydrogen bonds showed that position 312 in LFY determines the difference of DNA-binding specificity. By using principal component analysis (PCA) and free energy landscape (FEL) methods, the open-close conformational change of the dimerization interface was found to be important for the system stability. At the dimerization interface, the protein-protein interaction has multiple influences on the cooperative DNA binding of LFY. The following analysis of DNA structural parameters further revealed that the protein-protein interaction contributes varying roles according to the specific DNA-binding efficiency. We propose that the protein-protein interaction serves a dual function as a connector between LFY monomers and a regulator of DNA-binding specificity. It will improve the robustness and adaptivity of the LFY-DNA ternary structure. This study provides some new insights into the understanding of the dynamics and interaction mechanism of dimeric LFY-DBD bound to DNA at the atomic level.
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Affiliation(s)
- Hua Wan
- †College of Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Shan Chang
- ‡Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Jian-ping Hu
- §Faculty of Biotechnology Industry, Chengdu University, Chengdu 610106, China
| | - Yuan-xin Tian
- ∥School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xu-hong Tian
- †College of Informatics, South China Agricultural University, Guangzhou 510642, China
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18
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Kumar C, Eichmiller R, Wang B, Williams GM, Bianco PR, Surtees JA. ATP binding and hydrolysis by Saccharomyces cerevisiae Msh2-Msh3 are differentially modulated by mismatch and double-strand break repair DNA substrates. DNA Repair (Amst) 2014; 18:18-30. [PMID: 24746922 DOI: 10.1016/j.dnarep.2014.03.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 03/24/2014] [Accepted: 03/31/2014] [Indexed: 01/08/2023]
Abstract
In Saccharomyces cerevisiae, Msh2-Msh3-mediated mismatch repair (MMR) recognizes and targets insertion/deletion loops for repair. Msh2-Msh3 is also required for 3' non-homologous tail removal (3'NHTR) in double-strand break repair. In both pathways, Msh2-Msh3 binds double-strand/single-strand junctions and initiates repair in an ATP-dependent manner. However, we recently demonstrated that the two pathways have distinct requirements with respect to Msh2-Msh3 activities. We identified a set of aromatic residues in the nucleotide binding pocket (FLY motif) of Msh3 that, when mutated, disrupted MMR, but left 3'NHTR largely intact. One of these mutations, msh3Y942A, was predicted to disrupt the nucleotide sandwich and allow altered positioning of ATP within the pocket. To develop a mechanistic understanding of the differential requirements for ATP binding and/or hydrolysis in the two pathways, we characterized Msh2-Msh3 and Msh2-msh3Y942A ATP binding and hydrolysis activities in the presence of MMR and 3'NHTR DNA substrates. We observed distinct, substrate-dependent ATP hydrolysis and nucleotide turnover by Msh2-Msh3, indicating that the MMR and 3'NHTR DNA substrates differentially modify the ATP binding/hydrolysis activities of Msh2-Msh3. Msh2-msh3Y942A retained the ability to bind DNA and ATP but exhibited altered ATP hydrolysis and nucleotide turnover. We propose that both ATP and structure-specific repair substrates cooperate to direct Msh2-Msh3-mediated repair and suggest an explanation for the msh3Y942A separation-of-function phenotype.
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Affiliation(s)
- Charanya Kumar
- Department of Biochemistry, Immunology, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Robin Eichmiller
- Department of Biochemistry, Immunology, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Bangchen Wang
- Department of Biochemistry, Immunology, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Gregory M Williams
- Department of Biochemistry, Immunology, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Piero R Bianco
- Department of Microbiology and Immunology, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Jennifer A Surtees
- Department of Biochemistry, Immunology, University at Buffalo (SUNY), Buffalo, NY 14214, USA.
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19
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Davis BC, Thorpe IF. Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase. Proteins 2012; 81:40-52. [PMID: 22855387 DOI: 10.1002/prot.24154] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/12/2012] [Accepted: 07/23/2012] [Indexed: 11/09/2022]
Abstract
Hepatitis C virus (HCV) has infected almost 200 million people worldwide, typically causing chronic liver damage and severe complications such as liver failure. Currently, there are few approved treatments for viral infection. Thus, the HCV RNA-dependent RNA polymerase (gene product NS5B) has emerged as an important target for small molecule therapeutics. Potential therapeutic agents include allosteric inhibitors that bind distal to the enzyme active site. While their mechanism of action is not conclusively known, it has been suggested that certain inhibitors prevent a conformational change in NS5B that is crucial for RNA replication. To gain insight into the molecular origin of long-range allosteric inhibition of NS5B, we employed molecular dynamics simulations of the enzyme with and without an inhibitor bound to the thumb domain. These studies indicate that the presence of an inhibitor in the thumb domain alters both the structure and internal motions of NS5B. Principal components analysis identified motions that are severely attenuated by inhibitor binding. These motions may have functional relevance by facilitating interactions between NS5B and RNA template or nascent RNA duplex, with presence of the ligand leading to enzyme conformations with narrower and thus less accessible RNA binding channels. This study provides the first evidence for a mechanistic basis of allosteric inhibition in NS5B. Moreover, we present evidence that allosteric inhibition of NS5B results from intrinsic features of the enzyme free energy landscape, suggesting a common mechanism for the action of diverse allosteric ligands.
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Affiliation(s)
- Brittny C Davis
- Department of Chemistry and Biochemistry, University of Maryland-Baltimore County, Baltimore, Maryland 21250, USA
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