1
|
Alterio V, Langella E, Buonanno M, Esposito D, Nocentini A, Berrino E, Bua S, Polentarutti M, Supuran CT, Monti SM, De Simone G. Zeta-carbonic anhydrases show CS 2 hydrolase activity: A new metabolic carbon acquisition pathway in diatoms? Comput Struct Biotechnol J 2021; 19:3427-3436. [PMID: 34194668 PMCID: PMC8217695 DOI: 10.1016/j.csbj.2021.05.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 05/30/2021] [Indexed: 12/26/2022] Open
Abstract
CDCA1 is a carbonic anhydrase that can utilize Zn(II) or Cd(II) as catalytic metal. CDCA1 has been the first enzyme to show an efficient utilization of Cd(II) ions in Nature. By using a multidisciplinary approach, we discovered that CS2 is a substrate for this enzyme. CDCA1 is the unique enzyme, known so far, able to use both CS2 and CO2 as substrates.
CDCA1 is a very peculiar member of the Carbonic Anhydrase (CA) family. It has been the first enzyme to show an efficient utilization of Cd(II) ions in Nature and a unique adaptation capability to live on the surface ocean. Indeed, in this environment, which is extremely depleted in essential metal ions, CDCA1 can utilize Zn(II) or Cd(II) as catalytic metal to support the metabolic needs of fast growing diatoms. In this paper we demonstrate a further catalytic versatility of this enzyme by using a combination of X-ray crystallography, molecular dynamics simulations and enzymatic experiments. First we identified the CO2 binding site and the way in which this substrate travels from the environment to the enzyme active site. Then, starting from the observation of a structural similarity with the substrate entry route of CS2 hydrolase from Acidanius A1-3, we hypothesized and demonstrated that also CS2 is a substrate for CDCA1. This finding is new and unexpected since until now only few CS2 hydrolases have been characterized, and none of them is reported to have any CO2 hydratase action. The physiological implications of this supplementary catalytic activity still remain to be unveiled. We suggest here that it could represent another ability of diatoms expressing CDCA1 to adapt to the external environment. Indeed, the ability of this enzyme to convert CS2 could represent an alternative source of carbon acquisition for diatoms, in addition to CO2.
Collapse
Key Words
- AAZ, Acetazolamide
- CA, Carbonic Anhydrase
- CAI, Carbonic Anhydrase Inhibitor
- CCD, Charge Coupled Device
- CDCA1, Cadmium-specific Carbonic Anhydrase
- CO2
- CS2
- CS2H, S. solfataricus CS2 hydrolase
- Cambialistic enzyme
- Carbonic Anhydrase
- DMSO, Dimethyl Sulfoxide
- FbiCA, Flaveria bidentis Carbonic Anhydrase
- HEPES, 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
- IPTG, Isopropyl-β-D-1-thiogalactopyranoside
- MD, Molecular Dynamics
- Molecular dynamics
- NCS, Non-Crystallographic Symmetry
- PDB, Protein Data Bank
- PEG, Polyethylene glycol
- SDS-PAGE, Sodium Dodecyl Sulphate - PolyAcrylamide Gel Electrophoresis
- Tris-HCl, Tris(hydroxymethyl)aminomethane hydrochloride
- bCA, bovine Carbonic Anhydrase
- hCA, human Carbonic Anhydrase
- psCA3, Pseudomonas aeruginosa Carbonic Anhydrase 3
Collapse
Affiliation(s)
- Vincenzo Alterio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Emma Langella
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Martina Buonanno
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Davide Esposito
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Alessio Nocentini
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Emanuela Berrino
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Silvia Bua
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Maurizio Polentarutti
- Elettra - Sincrotrone Trieste, s.s. 14 Km 163.5 in Area Science Park, Basovizza (Trieste) 34149, Trieste, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Simona Maria Monti
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Giuseppina De Simone
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| |
Collapse
|
2
|
Zhang Z, Duan FX, Gu GL, Yu PF. Mutation analysis of related genes in hamartoma polyp tissue of Peutz-Jeghers syndrome. World J Gastroenterol 2020; 26:1926-1937. [PMID: 32390703 PMCID: PMC7201153 DOI: 10.3748/wjg.v26.i16.1926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/29/2020] [Accepted: 04/04/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Peutz-Jeghers syndrome (PJS) is a rare disease with clinical manifestations of pigmented spots on the lips, mucous membranes and extremities, scattered gastrointestinal polyps, and susceptibility to tumors. The clinical heterogeneity of PJS is obvious, and the relationship between clinical phenotype and genotype is still unclear.
AIM To investigate the mutation status of hereditary colorectal tumor-associated genes in hamartoma polyp tissue of PJS patients and discuss its relationship with the clinicopathological data of PJS.
METHODS Twenty patients with PJS were randomly selected for this study and were treated in the Air Force Medical Center (former Air Force General Hospital) PLA between 2008 and 2017. Their hamartoma polyp tissues were used for APC, AXIN2, BMPR1A, EPCAM, MLH1, MLH3, MSH2, MSH6, MUTYH, PMS1, PMS2, PTEN, SMAD4, and LKB1/STK11 gene sequencing using next-generation sequencing technology. The correlations between the sequencing results and clinical pathological data of PJS were analyzed.
RESULTS Fourteen types of LKB1/STK11 mutations were detected in 16 cases (80.0%), of which 8 new mutations were found (3 types of frameshift deletion mutations: c.243delG, c.363_364delGA, and c.722delC; 2 types of frameshift insertions: c. 144_145insGCAAG, and c.454_455insC; 3 types of splice site mutations: c.464+1G>T, c.464+1G>A, and c.598-1G>A); 9 cases (45.0%) were found to have 18 types of heterozygous mutations in the remaining 13 genes except LKB1/STK11. Of these, MSH2: c.792+1G>A, MSH6: c.3689C>G, c.4001+13C>CTTAC, PMS1: c.46C>t, and c.922G>A were new mutations.
CONCLUSION The genetic mutations in hamartoma polyp tissue of PJS are complex and diverse. Moreover, other gene mutations in PJS hamartoma polyp tissue were observed, with the exception of LKB1/STK11 gene, especially the DNA mismatch repair gene (MMR). Colorectal hamartoma polyps with LKB1/STK11 mutations were larger in diameter than those with other gene mutations.
Collapse
Affiliation(s)
- Zhi Zhang
- Air Force Clinical College (Air Force Medical Center) of Anhui Medical University, Beijing 100142, China
| | - Fu-Xiao Duan
- Department of General Surgery, the General Hospital of Northern Theater Command PLA, Shenyang 110016, Liaoning Province, China
| | - Guo-Li Gu
- Department of General Surgery, Air Force Medical Center, PLA, Beijing 100142, China
| | - Peng-Fei Yu
- Department of General Surgery, Air Force Medical Center, PLA, Beijing 100142, China
| |
Collapse
|
3
|
Yu M, Chen Y, Wang ZL, Liu Z. Fluctuation correlations as major determinants of structure- and dynamics-driven allosteric effects. Phys Chem Chem Phys 2019; 21:5200-5214. [DOI: 10.1039/c8cp07859a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Both structure- and dynamics-driven allosteric effects are determined by the correlation of distance fluctuations in proteins.
Collapse
Affiliation(s)
- Miao Yu
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Yixin Chen
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Zi-Le Wang
- Department of Physics
- Tsinghua University
- Beijing 100084
- China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
- Center for Quantitative Biology
| |
Collapse
|
4
|
Duan FX, Gu GL, Yang HR, Yu PF, Zhang Z. Must Peutz-Jeghers syndrome patients have the LKB1/STK11 gene mutation? A case report and review of the literature. World J Clin Cases 2018; 6:224-232. [PMID: 30148152 PMCID: PMC6107527 DOI: 10.12998/wjcc.v6.i8.224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/23/2018] [Accepted: 05/13/2018] [Indexed: 02/05/2023] Open
Abstract
Peutz-Jeghers syndrome (PJS) is an autosomal dominant inherited disease, which is characterized by mucocutaneous pigmentation and multiple gastrointestinal hamartoma polyps. The germline mutation of LKB1/STK11 gene on chromosome 19p13.3 is considered to be the hereditary cause of PJS. However, must a patient with PJS have the LKB1/STK11 gene mutation? We here report a case of a male patient who had typical manifestations of PJS and a definite family history, but did not have LKB1/STK11 gene mutation. By means of high-throughput sequencing technology, only mutations in APC gene (c.6662T > C: p.Met2221Thr) and MSH6 gene (c.3488A > T: p.Glu1163Val) were detected. The missense mutations in APC and MSH6 gene may lead to abnormalities in structure and function of their expression products, and may result in the occurrence of PJS. This study suggests that some other genetic disorders may cause PJS besides LKB1/STK11 gene mutation.
Collapse
Affiliation(s)
- Fu-Xiao Duan
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Guo-Li Gu
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Hai-Rui Yang
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Peng-Fei Yu
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| | - Zhi Zhang
- Department of General Surgery, Air Force General Hospital of Chinese PLA, Beijing 100142, China
| |
Collapse
|
5
|
Melvin RL, Xiao J, Godwin RC, Berenhaut KS, Salsbury FR. Visualizing correlated motion with HDBSCAN clustering. Protein Sci 2018; 27:62-75. [PMID: 28799290 PMCID: PMC5734272 DOI: 10.1002/pro.3268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 12/22/2022]
Abstract
Correlated motion analysis provides a method for understanding communication between and dynamic similarities of biopolymer residues and domains. The typical equal-time correlation matrices-frequently visualized with pseudo-colorings or heat maps-quickly convey large regions of highly correlated motion but hide more subtle similarities of motion. Here we propose a complementary method for visualizing correlations within proteins (or general biopolymers) that quickly conveys intuition about which residues have a similar dynamic behavior. For grouping residues, we use the recently developed non-parametric clustering algorithm HDBSCAN. Although the method we propose here can be used to group residues using correlation as a similarity matrix-the most straightforward and intuitive method-it can also be used to more generally determine groups of residues which have similar dynamic properties. We term these latter groups "Dynamic Domains", as they are based not on spatial closeness but rather closeness in the column space of a correlation matrix. We provide examples of this method across three human proteins of varying size and function-the Nf-Kappa-Beta essential modulator, the clotting promoter Thrombin and the mismatch repair protein (dimer) complex MutS-alpha. Although the examples presented here are from all-atom molecular dynamics simulations, this visualization technique can also be used on correlations matrices built from any ensembles of conformations from experiment or computation.
Collapse
Affiliation(s)
- Ryan L. Melvin
- Department of PhysicsWake Forest UniversityWinston SalemNorth Carolina
- Department of Mathematics and StatisticsWake Forest UniversityWinston‐SalemNorth Carolina27109
| | - Jiajie Xiao
- Department of PhysicsWake Forest UniversityWinston SalemNorth Carolina
- Department of Computer ScienceWake Forest UniversityWinston‐SalemNorth Carolina27109
| | - Ryan C. Godwin
- Department of PhysicsWake Forest UniversityWinston SalemNorth Carolina
| | - Kenneth S. Berenhaut
- Department of Mathematics and StatisticsWake Forest UniversityWinston‐SalemNorth Carolina27109
| | | |
Collapse
|
6
|
Kulandaisamy A, Srivastava A, Nagarajan R, Gromiha MM. Dissecting and analyzing key residues in protein-DNA complexes. J Mol Recognit 2017; 31. [DOI: 10.1002/jmr.2692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 02/03/2023]
Affiliation(s)
- A. Kulandaisamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences; Indian Institute of Technology Madras; Chennai 600 036 Tamilnadu India
| | - Ambuj Srivastava
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences; Indian Institute of Technology Madras; Chennai 600 036 Tamilnadu India
| | - R. Nagarajan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences; Indian Institute of Technology Madras; Chennai 600 036 Tamilnadu India
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences; Indian Institute of Technology Madras; Chennai 600 036 Tamilnadu India
| |
Collapse
|
7
|
Ma H, Li A, Gao K. Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Carbonic Anhydrase II Apo-Enzyme. ACS OMEGA 2017; 2:8414-8420. [PMID: 30023582 PMCID: PMC6045336 DOI: 10.1021/acsomega.7b01414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/15/2017] [Indexed: 05/30/2023]
Abstract
Human carbonic anhydrase II (HCA II) is an enzyme that catalyzes the reversible hydration of CO2 into bicarbonate (HCO3-) and a proton (H+) as well as other reactions at an extremely high rate. This enzyme plays fundamental roles in human physiology/pathology, such as controlling the pH level in cells and so on. However, the binding mechanism between apo-HCA II and CO2 or other ligands as well as related conformational changes remains poorly understood, and atomic investigation into it could promote our understanding of related internal physiological/pathological mechanisms. In this study, long-time atomic molecular dynamics simulations as well as the clustering and free-energy analysis were performed to reveal the dynamics of apo-HCA II as well as the mechanism upon ligand binding. Our simulations indicate that the crystallographic B-factors considerably underestimate the loop dynamics: multiple conformations can be adopted by loops 1 and 2, especially for loop 1 because loop 1 is one side of the binding pocket, and its left-to-right movement can compress or extend the binding pocket, leading to one inactive (closed) state, three intermediate (semiopen) states, and one active (open) state; CO2 cannot get into the binding pocket of the inactive state but can get into those of intermediate and active states. The coexistence of multiple conformational states proposes a possible conformational selection model for the binding mechanism between apo-HCA II and CO2 or other ligands, revising our previous view of its functional mechanism of conformational change upon ligand binding and offering valuable structural insights into the workings of HCA II.
Collapse
Affiliation(s)
- Huishu Ma
- Institute of Biophysics and Department
of Physics, Central China Normal University, Wuhan 430079, P. R. China
| | - Anbang Li
- Institute of Biophysics and Department
of Physics, Central China Normal University, Wuhan 430079, P. R. China
| | - Kaifu Gao
- Institute of Biophysics and Department
of Physics, Central China Normal University, Wuhan 430079, P. R. China
| |
Collapse
|
8
|
Xiao J, Salsbury FR. Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin. J Biomol Struct Dyn 2017; 35:3354-3369. [PMID: 27794633 PMCID: PMC6876308 DOI: 10.1080/07391102.2016.1254682] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/21/2016] [Indexed: 01/11/2023]
Abstract
Thrombin is an attractive target for antithrombotic therapy due to its central role in thrombosis and hemostasis as well as its role in inducing tumor growth, metastasis, and tumor invasion. The thrombin-binding DNA aptamer (TBA), is under investigation for anticoagulant drugs. Although aptamer binding experiments have been revealed various effects on thrombin's enzymatic activities, the detailed picture of the thrombin's allostery from TBA binding is still unclear. To investigate thrombin's response to the aptamer-binding at the molecular level, we compare the mechanical properties and free energy landscapes of the free and aptamer-bound thrombin using microsecond-scale all-atom GPU-based molecular dynamics simulations. Our calculations on residue fluctuations and coupling illustrate the allosteric effects of aptamer-binding at the atomic level, highlighting the exosite II, 60s, γ and the sodium loops, and the alpha helix region in the light chains involved in the allosteric changes. This level of details clarifies the mechanisms of previous experimentally demonstrated phenomena, and provides a prediction of the reduced autolysis rate after aptamer-binding. The shifts in thrombin's ensemble of conformations and free energy surfaces after aptamer-binding demonstrate that the presence of bound-aptamer restricts the conformational freedom of thrombin suggesting that conformational selection, i.e. generalized allostery, is the dominant mechanism of thrombin-aptamer binding. The profound perturbation on thrombin's mechanical and thermodynamic properties due to the aptamer-binding, which was revealed comprehensively as a generalized allostery in this work, may be exploited in further drug discovery and development.
Collapse
Affiliation(s)
- Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | | |
Collapse
|
9
|
Melvin RL, Thompson WG, Godwin RC, Gmeiner WH, Salsbury FR. MutS α's Multi-Domain Allosteric Response to Three DNA Damage Types Revealed by Machine Learning. FRONTIERS IN PHYSICS 2017; 5:10. [PMID: 31938712 PMCID: PMC6959842 DOI: 10.3389/fphy.2017.00010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
MutSα is a key component in the mismatch repair (MMR) pathway. This protein is responsible for initiating the signaling pathways for DNA repair or cell death. Herein we investigate this heterodimer's post-recognition, post-binding response to three types of DNA damage involving cytotoxic, anti-cancer agents-carboplatin, cisplatin, and FdU. Through a combination of supervised and unsupervised machine learning techniques along with more traditional structural and kinetic analysis applied to all-atom molecular dynamics (MD) calculations, we predict that MutSα has a distinct response to each of the three damage types. Via a binary classification tree (a supervised machine learning technique), we identify key hydrogen bond motifs unique to each type of damage and suggest residues for experimental mutation studies. Through a combination of a recently developed clustering (unsupervised learning) algorithm, RMSF calculations, PCA, and correlated motions we predict that each type of damage causes MutSα to explore a specific region of conformation space. Detailed analysis suggests a short range effect for carboplatin-primarily altering the structures and kinetics of residues within 10 angstroms of the damaged DNA-and distinct longer-range effects for cisplatin and FdU. In our simulations, we also observe that a key phenylalanine residue-known to stack with a mismatched or unmatched bases in MMR-stacks with the base complementary to the damaged base in 88.61% of MD frames containing carboplatinated DNA. Similarly, this Phe71 stacks with the base complementary to damage in 91.73% of frames with cisplatinated DNA. This residue, however, stacks with the damaged base itself in 62.18% of trajectory frames with FdU-substituted DNA and has no stacking interaction at all in 30.72% of these frames. Each drug investigated here induces a unique perturbation in the MutSα complex, indicating the possibility of a distinct signaling event and specific repair or death pathway (or set of pathways) for a given type of damage.
Collapse
Affiliation(s)
- Ryan L. Melvin
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - William G. Thompson
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - Ryan C. Godwin
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - William H. Gmeiner
- Gmeiner Laboratory, Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Freddie R. Salsbury
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Melvin RL, Godwin RC, Xiao J, Thompson WG, Berenhaut KS, Salsbury FR. Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge. J Chem Theory Comput 2016; 12:6130-6146. [PMID: 27802394 PMCID: PMC5719493 DOI: 10.1021/acs.jctc.6b00757] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the length of molecular dynamics (MD) trajectories grows with increasing computational power, so does the importance of clustering methods for partitioning trajectories into conformational bins. Of the methods available, the vast majority require users to either have some a priori knowledge about the system to be clustered or to tune clustering parameters through trial and error. Here we present non-parametric uses of two modern clustering techniques suitable for first-pass investigation of an MD trajectory. Being non-parametric, these methods require neither prior knowledge nor parameter tuning. The first method, HDBSCAN, is fast-relative to other popular clustering methods-and is able to group unstructured or intrinsically disordered systems (such as intrinsically disordered proteins, or IDPs) into bins that represent global conformational shifts. HDBSCAN is also useful for determining the overall stability of a system-as it tends to group stable systems into one or two bins-and identifying transition events between metastable states. The second method, iMWK-Means, with explicit rescaling followed by K-Means, while slower than HDBSCAN, performs well with stable, structured systems such as folded proteins and is able to identify higher resolution details such as changes in relative position of secondary structural elements. Used in conjunction, these clustering methods allow a user to discern quickly and without prior knowledge the stability of a simulated system and identify both local and global conformational changes.
Collapse
Affiliation(s)
- Ryan L. Melvin
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Ryan C. Godwin
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - William G. Thompson
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Kenneth S. Berenhaut
- Department of Mathematics & Statistics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Freddie R. Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| |
Collapse
|
12
|
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.
Collapse
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:
| |
Collapse
|
13
|
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.
Collapse
Affiliation(s)
| | - Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, NC 27106, USA.
| |
Collapse
|
14
|
Gao K, He H, Yang M, Yan H. Molecular dynamics simulations of the Escherichia coli HPPK apo-enzyme reveal a network of conformational transitions. Biochemistry 2015; 54:6734-42. [PMID: 26492157 DOI: 10.1021/acs.biochem.5b01012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that even when confined by crystal contacts, loops 2 and 3 remain rather flexible when the enzyme is in its apo form, raising questions about the putative large-scale induced-fit conformational change of HPPK. To investigate the loop dynamics in a crystal-free environment, we performed conventional molecular dynamics simulations of the apo-enzyme at two different temperatures (300 and 350 K). Our simulations show that the crystallographic B-factors considerably underestimate the loop dynamics; multiple conformations of loops 2 and 3, including the open, semi-open, and closed conformations that an enzyme must adopt throughout its catalytic cycle, are all accessible to the apo-enzyme. These results revise our previous view of the functional mechanism of conformational change upon MgATP binding and offer valuable structural insights into the workings of HPPK. In this paper, conformational network analysis and principal component analysis related to the loops are discussed to support the presented conclusions.
Collapse
Affiliation(s)
- Kaifu Gao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
| | - Hongqing He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
| |
Collapse
|
15
|
Godwin R, Gmeiner W, Salsbury FR. Importance of long-time simulations for rare event sampling in zinc finger proteins. J Biomol Struct Dyn 2015; 34:125-34. [PMID: 25734227 DOI: 10.1080/07391102.2015.1015168] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Molecular dynamics (MD) simulation methods have seen significant improvement since their inception in the late 1950s. Constraints of simulation size and duration that once impeded the field have lessened with the advent of better algorithms, faster processors, and parallel computing. With newer techniques and hardware available, MD simulations of more biologically relevant timescales can now sample a broader range of conformational and dynamical changes including rare events. One concern in the literature has been under which circumstances it is sufficient to perform many shorter timescale simulations and under which circumstances fewer longer simulations are necessary. Herein, our simulations of the zinc finger NEMO (2JVX) using multiple simulations of length 15, 30, 1000, and 3000 ns are analyzed to provide clarity on this point.
Collapse
Affiliation(s)
- Ryan Godwin
- a Department of Physics , Wake Forest University , Winston-Salem , NC 27109 , USA
| | - William Gmeiner
- b Department of Cancer Biology , Wake Forest University Health Sciences , Winston-Salem , NC 27107 , USA
| | - Freddie R Salsbury
- a Department of Physics , Wake Forest University , Winston-Salem , NC 27109 , USA
| |
Collapse
|
16
|
Godwin RC, Melvin R, Salsbury FR. Molecular Dynamics Simulations and Computer-Aided Drug Discovery. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2015. [DOI: 10.1007/7653_2015_41] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
17
|
Wan H, Hu JP, Li KS, Tian XH, Chang S. Molecular dynamics simulations of DNA-free and DNA-bound TAL effectors. PLoS One 2013; 8:e76045. [PMID: 24130757 PMCID: PMC3794935 DOI: 10.1371/journal.pone.0076045] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 08/22/2013] [Indexed: 12/05/2022] Open
Abstract
TAL (transcriptional activator-like) effectors (TALEs) are DNA-binding proteins, containing a modular central domain that recognizes specific DNA sequences. Recently, the crystallographic studies of TALEs revealed the structure of DNA-recognition domain. In this article, molecular dynamics (MD) simulations are employed to study two crystal structures of an 11.5-repeat TALE, in the presence and absence of DNA, respectively. The simulated results indicate that the specific binding of RVDs (repeat-variable diresidues) with DNA leads to the markedly reduced fluctuations of tandem repeats, especially at the two ends. In the DNA-bound TALE system, the base-specific interaction is formed mainly by the residue at position 13 within a TAL repeat. Tandem repeats with weak RVDs are unfavorable for the TALE-DNA binding. These observations are consistent with experimental studies. By using principal component analysis (PCA), the dominant motions are open-close movements between the two ends of the superhelical structure in both DNA-free and DNA-bound TALE systems. The open-close movements are found to be critical for the recognition and binding of TALE-DNA based on the analysis of free energy landscape (FEL). The conformational analysis of DNA indicates that the 5′ end of DNA target sequence has more remarkable structural deformability than the other sites. Meanwhile, the conformational change of DNA is likely associated with the specific interaction of TALE-DNA. We further suggest that the arrangement of N-terminal repeats with strong RVDs may help in the design of efficient TALEs. This study provides some new insights into the understanding of the TALE-DNA recognition mechanism.
Collapse
Affiliation(s)
- Hua Wan
- College of Informatics, South China Agricultural University, Guangzhou, China
| | - Jian-ping Hu
- College of Chemistry, Leshan Normal University, Leshan, China
| | - Kang-shun Li
- College of Informatics, South China Agricultural University, Guangzhou, China
| | - Xu-hong Tian
- College of Informatics, South China Agricultural University, Guangzhou, China
| | - Shan Chang
- College of Informatics, South China Agricultural University, Guangzhou, China
- * E-mail:
| |
Collapse
|
18
|
Negureanu L, Salsbury FR. Destabilization of the MutSα's protein-protein interface due to binding to the DNA adduct induced by anticancer agent carboplatin via molecular dynamics simulations. J Mol Model 2013; 19:4969-89. [PMID: 24061854 DOI: 10.1007/s00894-013-1998-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/05/2013] [Indexed: 12/22/2022]
Abstract
DNA mismatch repair (MMR) proteins maintain genetic integrity in all organisms by recognizing and repairing DNA errors. Such alteration of hereditary information can lead to various diseases, including cancer. Besides their role in DNA repair, MMR proteins detect and initiate cellular responses to certain type of DNA damage. Its response to the damaged DNA has made the human MMR pathway a useful target for anticancer agents such as carboplatin. This study indicates that strong, specific interactions at the interface of MutSα in response to the mismatched DNA recognition are replaced by weak, non-specific interactions in response to the damaged DNA recognition. Data suggest a severe impairment of the dimerization of MutSα in response to the damaged DNA recognition. While the core of MutSα is preserved in response to the damaged DNA recognition, the loss of contact surface and the rearrangement of contacts at the protein interface suggest a different packing in response to the damaged DNA recognition. Coupled in response to the mismatched DNA recognition, interaction energies, hydrogen bonds, salt bridges, and solvent accessible surface areas at the interface of MutSα and within the subunits are uncoupled or asynchronously coupled in response to the damaged DNA recognition. These pieces of evidence suggest that the loss of a synchronous mode of response in the MutSα's surveillance for DNA errors would possibly be one of the mechanism(s) of signaling the MMR-dependent programed cell death much wanted in anticancer therapies. The analysis was drawn from dynamics simulations.
Collapse
|
19
|
Negureanu L, Salsbury FR. Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex. J Biomol Struct Dyn 2013; 32:969-92. [PMID: 23799640 DOI: 10.1080/07391102.2013.799437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
MutSα is the most abundant mismatch-binding factor of human DNA mismatch repair (MMR) proteins. MMR maintains genetic stability by recognizing and repairing DNA defects. Failure to accomplish their function may lead to cancer. In addition, MutSα recognizes at least some types of DNA damage making it a target for anticancer agents. Here, complementing scarce experimental data, we report unique hydrogen-bonding motifs associated with the recognition of the carboplatin induced DNA damage by MutSα. These data predict that carboplatin and cisplatin induced damaging DNA adducts are recognized by MutSα in a similar manner. Our simulations also indicate that loss of base pairing at the damage site results in (1) non-specific binding and (2) changes in the atomic flexibility at the lesion site and beyond. To further quantify alterations at MutSα-DNA interface in response to damage recognition, non-bonding interactions and salt bridges were investigated. These data indicate (1) possible different packing and (2) disruption of the salt bridges at the MutSα-DNA interface in the damaged complex. These findings (1) underscore the general observation of disruptions at the MutSα-DNA interface and (2) highlight the nature of the anticancer effect of the carboplatin agent. The analysis was carried out from atomistic simulations.
Collapse
|
20
|
AbdelHafez EMN, Diamanduros A, Negureanu L, Luy Y, Bean JH, Zielke K, Crowe B, Vasilyeva A, Clodfelter JE, Aly OM, Abuo-Rahma GEDAA, Scarpinato KD, Salsbury FR, King SB. Computational and synthetic studies towards improving rescinnamine as an inducer of MSH2-dependent apoptosis in cancer treatment. MOLECULAR CANCER BIOLOGY 2013; 1:44. [PMID: 25485184 PMCID: PMC4254817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
We, and others, have previously shown that mismatch repair proteins, in addition to their repair function, contribute to cell death initiation. In response to some drugs, this cell death activity is independent of the repair function of the proteins. Rescinnamine, a derivative of the indole alkaloid reserpine, a drug used to treat hypertension several decades ago, was shown to target the cell death-initiating activity of mismatch repair proteins. When used in animals, the hypotensive action of this drug prevents applying appropriate concentrations for statistically significant tumor reduction. Using a combination of computational modeling, chemical synthesis and cell assays, we determine how rescinnamine can be structurally modified and what effect these modifications have on cell survival. These results inform further computational modeling to suggest new synthetic lead molecules to move toward further biological testing.
Collapse
Affiliation(s)
| | | | | | - Yan Luy
- Department of Physics, Wake Forest University, Winston-Salem, NC
| | - J. Hayley Bean
- Department of Biology, Georgia Southern University, Statesboro, GA
| | - Katherine Zielke
- Department of Biology, Georgia Southern University, Statesboro, GA
| | - Brittany Crowe
- Department of Biology, Georgia Southern University, Statesboro, GA
| | - Aksana Vasilyeva
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC; now: St. Jude Hospital, Memphis, TN
| | - Jill E. Clodfelter
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Omar M. Aly
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia , Egypt
| | | | | | | | - S. Bruce King
- Department of Chemistry, Wake Forest University, Winston-Salem, NC
| |
Collapse
|
21
|
Negureanu L, Salsbury F. 212 Shifting interfaces: changes in protein–protein and protein–DNA interfaces probed via molecular dynamics. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.790143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
22
|
Negureanu L, Salsbury FR. The molecular origin of the MMR-dependent apoptosis pathway from dynamics analysis of MutSα-DNA complexes. J Biomol Struct Dyn 2012; 30:347-61. [PMID: 22712459 PMCID: PMC3389999 DOI: 10.1080/07391102.2012.680034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The cellular response to DNA damage signaling by mismatch-repair (MMR) proteins is incompletely understood. It is generally accepted that MMR-dependent apoptosis pathway in response to DNA damage detection is independent of MMR's DNA repair function. In this study, we investigate correlated motions in response to the binding of mismatched and platinum cross-linked DNA fragments by MutSα, as derived from 50 ns molecular dynamics simulations. The protein dynamics in response to the mismatched and damaged DNA recognition suggests that MutSα signals their recognition through independent pathways providing evidence for the molecular origin of the MMR-dependent apoptosis. MSH2 subunit is indicated to play a key role in signaling both mismatched and damaged DNA recognition; localized and collective motions within the protein allow identifying sites on the MSH2 surface possible involved in recruiting proteins responsible for downstream events. Unlike in the mismatch complex, predicted key communication sites specific for the damage recognition are on the list of known cancer-causing mutations or deletions. This confirms MSH2's role in signaling DNA damage-induced apoptosis and suggests that defects in MMR alone is sufficient to trigger tumorigenesis, supporting the experimental evidence that MMR-damage response function could protect from the early occurrence of tumors. Identifying these particular communication sites may have implications for the treatment of cancers that are not defective for MMR, but are unable to function optimally for MMR-dependent responses following DNA damage such as the case of resistance to cisplatin.
Collapse
|