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Chandrasekhar G, Pengyong H, Pravallika G, Hailei L, Caixia X, Rajasekaran R. Defensin-based therapeutic peptide design in attenuating V30M TTR-induced Familial Amyloid Polyneuropathy. 3 Biotech 2023; 13:227. [PMID: 37304406 PMCID: PMC10250285 DOI: 10.1007/s13205-023-03646-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
In the present study, we aimed to formulate an effective therapeutic candidate against V30M mutant transthyretin (TTR) protein to hinder its pathogenic misfolding. Nicotiana alata Defensin 1 (NaD1) Antimicrobial Peptide (AMP) was availed due to its tendency to aggregate, which may compete for aggregation-prone regions of pathogenic TTR protein. Based on NaD1's potential to bind to V30M TTR, we proposed NaD1-derived tetra peptides: CKTE and SKIL to be initial therapeutic candidates. Based on their association with mutant TTR protein, CKTE tetra peptide showed considerable interaction and curative potential as compared to SKIL tetra peptide. Further analyses from discrete molecular dynamics simulation corroborate CKTE tetra peptide's effectiveness as a 'beta-sheet breaker' against V30M TTR. Various post-simulation trajectory analyses suggested that CKTE tetra peptide alters the structural dynamics of pathogenic V30M TTR protein, thereby potentially attenuating its beta-sheets and impeding its aggregation. Normal mode analysis simulation corroborated that V30M TTR conformation is altered upon its interaction with CKTE peptide. Moreover, simulated thermal denaturation findings suggested that CKTE-V30M TTR complex is more susceptible to simulated denaturation, relative to pathogenic V30M TTR; further substantiating CKTE peptide's potential to alter V30M TTR's pathogenic conformation. Moreover, the residual frustration analysis augmented CKTE tetra peptide's proclivity in reorienting the conformation of V30M TTR. Therefore, we predicted that the tetra peptide, CKTE could be a promising therapeutic candidate in mitigating the amyloidogenic detrimental effects of V30M TTR-mediated familial amyloid polyneuropathy (FAP). Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03646-4.
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Affiliation(s)
- G. Chandrasekhar
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu 632014 India
| | - H. Pengyong
- Changzhi Medical College, Changzhi, 046000 China
| | - G. Pravallika
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu 632014 India
| | - L. Hailei
- Changzhi Medical College, Changzhi, 046000 China
| | - X. Caixia
- Changzhi Medical College, Changzhi, 046000 China
| | - R. Rajasekaran
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu 632014 India
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2
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Chandrasekhar G, Chandra Sekar P, Srinivasan E, Amarnath A, Pengyong H, Rajasekaran R. Molecular simulation unravels the amyloidogenic misfolding of nascent ApoA1 protein, driven by deleterious point mutations occurring in between 170-178 hotspot region. J Biomol Struct Dyn 2022; 40:13278-13290. [PMID: 34613891 DOI: 10.1080/07391102.2021.1986134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein ApoA1 is extensively studied for its role in lipid metabolism. Its seedy dark side of amyloid formulation remains relatively understudied yet. Due to genetic mutations, the protein pathologically misshapes into its amyloid form that gets accumulated in various organs, including the heart. To contrive effective therapeutics against this debilitating congenital disorder, it is imperative to comprehend the structural ramifications induced by mutations in APoA1's dynamic conformation. Till now, several point mutations have been implicated in ApoA1's amyloidosis, although only a handful has been examined considerably. Especially, the single nucleotide polymorphisms (SNPs) that occur in-between 170-178 mutation hotspot site of APoA1 needs to be investigated, since most of them are culpable of amyloid deposition in the heart. To that effect, in the present study, we have computationally quantified and studied the ApoA1's biomolecular modifications fostered by SNPs in the 170-178 mutation hotspot. Findings from discrete molecular dynamics simulation studies indicate that the SNPs have noticeably steered the ApoA1's behaviour from its native structural dynamics. Analysis of protein's secondary structural changes exhibits a considerable change upon mutations. Further, subjecting the protein structures to simulated thermal denaturation shows increased resistance to denaturation among mutants when compared to native. Further, normal mode analysis of protein's dynamic motion also shows discrepancy in its dynamic structural change upon SNP. These structural digressions induced by SNPs can very well be the biomolecular incendiary that drives ApoA1 into its amyloidogenesis. And, understanding these structural modifications initiates a better understanding of SNP's amyloidogenic pathology on APoA1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- G Chandrasekhar
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, India
| | - P Chandra Sekar
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, India
| | - E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, India
| | - A Amarnath
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, India
| | - H Pengyong
- Central Lab, Changzhi Medical College, Changzhi, China
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, India
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3
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Bayarri G, Andrio P, Hospital A, Orozco M, Gelpí JL. BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. Nucleic Acids Res 2022; 50:W99-W107. [PMID: 35639735 PMCID: PMC9252775 DOI: 10.1093/nar/gkac380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/19/2022] [Accepted: 05/02/2022] [Indexed: 11/15/2022] Open
Abstract
We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library. Available workflows include Molecular Dynamics setup, protein-ligand docking, trajectory analyses and small molecule parameterization. Workflows can be launched in the platform or downloaded to be run in the users’ own premises. Remote launching of long executions to user's available High-Performance computers is possible, only requiring configuration of the appropriate access credentials. The web-based graphical user interface offers a high level of interactivity, with integration with the NGL viewer to visualize and check 3D structures, MDsrv to visualize trajectories, and Plotly to explore 2D plots. The server requires no login but is recommended to store the users’ projects and manage sensitive information such as remote credentials. Private projects can be made public and shared with colleagues with a simple URL. The tool will help biomolecular simulation users with the most common and repetitive processes by means of a very intuitive and interactive graphical user interface. The server is accessible at https://mmb.irbbarcelona.org/biobb-wfs.
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Affiliation(s)
- Genís Bayarri
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Pau Andrio
- Barcelona Supercomputing Center (BSC), Jordi Girona 29, 08034, Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain.,Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Josep Lluís Gelpí
- Barcelona Supercomputing Center (BSC), Jordi Girona 29, 08034, Barcelona, Spain.,Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain
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4
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Castillo F, Corbi-Verge C, Murciano-Calles J, Candel AM, Han Z, Iglesias-Bexiga M, Ruiz-Sanz J, Kim PM, Harty RN, Martinez JC, Luque I. Phage display identification of nanomolar ligands for human NEDD4-WW3: Energetic and dynamic implications for the development of broad-spectrum antivirals. Int J Biol Macromol 2022; 207:308-323. [PMID: 35257734 DOI: 10.1016/j.ijbiomac.2022.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022]
Abstract
The recognition of PPxY viral Late domains by the third WW domain of the human HECT-E3 ubiquitin ligase NEDD4 (NEDD4-WW3) is essential for the budding of many viruses. Blocking these interactions is a promising strategy to develop broad-spectrum antivirals. As all WW domains, NEDD4-WW3 is a challenging therapeutic target due to the low binding affinity of its natural interactions, its high conformational plasticity, and its complex thermodynamic behavior. In this work, we set out to investigate whether high affinity can be achieved for monovalent ligands binding to the isolated NEDD4-WW3 domain. We show that a competitive phage-display set-up allows for the identification of high-affinity peptides showing inhibitory activity of viral budding. A detailed biophysical study combining calorimetry, nuclear magnetic resonance, and molecular dynamic simulations reveals that the improvement in binding affinity does not arise from the establishment of new interactions with the domain, but is associated to conformational restrictions imposed by a novel C-terminal -LFP motif in the ligand, unprecedented in the PPxY interactome. These results, which highlight the complexity of WW domain interactions, provide valuable insight into the key elements for high binding affinity, of interest to guide virtual screening campaigns for the identification of novel therapeutics targeting NEDD4-WW3 interactions.
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Affiliation(s)
- Francisco Castillo
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Carles Corbi-Verge
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain; Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics & Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Javier Murciano-Calles
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Adela M Candel
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Ziying Han
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 19104, USA
| | - Manuel Iglesias-Bexiga
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Javier Ruiz-Sanz
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics & Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ronald N Harty
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 19104, USA
| | - Jose C Martinez
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain
| | - Irene Luque
- Department of Physical Chemistry, Institute of Biotechnology and Excelence Unit in Chemistry Applied to Biomedicine and Environment, School of Sciences, University of Granada, Campus Fuentenueva s/n 18071, Granada, Spain.
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5
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Krieger JM, Sorzano COS, Carazo JM, Bahar I. Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:399-409. [PMID: 35362464 PMCID: PMC8972803 DOI: 10.1107/s2059798322001966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/18/2022] [Indexed: 11/24/2022]
Abstract
New computational biophysics pipelines for analysing the global dynamics of structural ensembles and large, dynamic complexes resolved by cryoEM are reviewed. Cryo-electron microscopy (cryoEM) has become a well established technique with the potential to produce structures of large and dynamic supramolecular complexes that are not amenable to traditional approaches for studying structure and dynamics. The size and low resolution of such molecular systems often make structural modelling and molecular dynamics simulations challenging and computationally expensive. This, together with the growing wealth of structural data arising from cryoEM and other structural biology methods, has driven a trend in the computational biophysics community towards the development of new pipelines for analysing global dynamics using coarse-grained models and methods. At the centre of this trend has been a return to elastic network models, normal mode analysis (NMA) and ensemble analyses such as principal component analysis, and the growth of hybrid simulation methodologies that make use of them. Here, this field is reviewed with a focus on ProDy, the Python application programming interface for protein dynamics, which has been developed over the last decade. Two key developments in this area are highlighted: (i) ensemble NMA towards extracting and comparing the signature dynamics of homologous structures, aided by the recent SignDy pipeline, and (ii) pseudoatom fitting for more efficient global dynamics analyses of large and low-resolution supramolecular assemblies from cryoEM, revisited in the CryoDy pipeline. It is believed that such a renewal and extension of old models and methods in new pipelines will be critical for driving the field forward into the next cryoEM revolution.
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Klaewkla M, Pichyangkura R, Chunsrivirot S. Computational Design of Oligosaccharide-Producing Levansucrase from Bacillus licheniformis RN-01 to Increase Its Stability at High Temperature. J Phys Chem B 2021; 125:5766-5774. [PMID: 34047564 DOI: 10.1021/acs.jpcb.1c02016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Levan-type fructooligosaccharides (LFOs) and levan can potentially be used as ingredients in prebiotics, skincare products, and antitumor agents. The Y246S mutant of Bacillus licheniformis RN-01 levansucrase (oligosaccharide-producing levansucrase, OPL) was reported to productively synthesize LFOs; however, OPL's thermostability is low at high temperatures. To enhance OPL structural stability, this study employed molecular dynamics (AMBER) to identify a highly flexible region, as measured by its average root-mean-square fluctuation (RMSF) value, on the OPL surface and computational protein design (Rosetta) to rigidify and increase favorable interactions to increase its structural stability. AMBER identified region nine (residues 277-317) as a highly flexible region that was selected for design because it has the highest number of residues and the second-highest average RMSF, and it is farthest from the active site. Rosetta designed 14 mutants with the best ΔΔG value in each position, where three mutants have better ΔG than OPL. To determine whether their flexibilities and stabilities are lower than those of OPL, all 14 designed mutants were simulated at high temperature (500 K), and we found that K296E, G309S, and A310W mutants were predicted to be more stable and could retain their native structures better than OPL. Our results suggest that enhanced structural stabilities of these mutants are caused by increased hydrogen bond strengths of the designed residues and their neighboring residues. This study designed K296E, G309S, and A310W mutants of OPL with high potential for stability improvement, and they could potentially be used for the effective production of LFOs.
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Affiliation(s)
- Methus Klaewkla
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Surasak Chunsrivirot
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
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7
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Planas-Iglesias J, Marques SM, Pinto GP, Musil M, Stourac J, Damborsky J, Bednar D. Computational design of enzymes for biotechnological applications. Biotechnol Adv 2021; 47:107696. [PMID: 33513434 DOI: 10.1016/j.biotechadv.2021.107696] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/14/2022]
Abstract
Enzymes are the natural catalysts that execute biochemical reactions upholding life. Their natural effectiveness has been fine-tuned as a result of millions of years of natural evolution. Such catalytic effectiveness has prompted the use of biocatalysts from multiple sources on different applications, including the industrial production of goods (food and beverages, detergents, textile, and pharmaceutics), environmental protection, and biomedical applications. Natural enzymes often need to be improved by protein engineering to optimize their function in non-native environments. Recent technological advances have greatly facilitated this process by providing the experimental approaches of directed evolution or by enabling computer-assisted applications. Directed evolution mimics the natural selection process in a highly accelerated fashion at the expense of arduous laboratory work and economic resources. Theoretical methods provide predictions and represent an attractive complement to such experiments by waiving their inherent costs. Computational techniques can be used to engineer enzymatic reactivity, substrate specificity and ligand binding, access pathways and ligand transport, and global properties like protein stability, solubility, and flexibility. Theoretical approaches can also identify hotspots on the protein sequence for mutagenesis and predict suitable alternatives for selected positions with expected outcomes. This review covers the latest advances in computational methods for enzyme engineering and presents many successful case studies.
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Affiliation(s)
- Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic; IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 61266 Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
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8
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Cirauqui Diaz N, Frezza E, Martin J. Using normal mode analysis on protein structural models. How far can we go on our predictions? Proteins 2020; 89:531-543. [PMID: 33349977 DOI: 10.1002/prot.26037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/12/2020] [Indexed: 01/01/2023]
Abstract
Normal mode analysis (NMA) is a fast and inexpensive approach that is largely used to gain insight into functional protein motions, and more recently to create conformations for further computational studies. However, when the protein structure is unknown, the use of computational models is necessary. Here, we analyze the capacity of NMA in internal coordinate space to predict protein motion, its intrinsic flexibility, and atomic displacements, using protein models instead of native structures, and the possibility to use it for model refinement. Our results show that NMA is quite insensitive to modeling errors, but that calculations are strictly reliable only for very accurate models. Our study also suggests that internal NMA is a more suitable tool for the improvement of structural models, and for integrating them with experimental data or in other computational techniques, such as protein docking or more refined molecular dynamics simulations.
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Affiliation(s)
- Nuria Cirauqui Diaz
- CNRS, UMR 5086 Molecular Microbiology and Structural Biochemistry, Université de Lyon, Lyon, France
| | - Elisa Frezza
- CiTCoM, CNRS, Université de Paris, Paris, France
| | - Juliette Martin
- CNRS, UMR 5086 Molecular Microbiology and Structural Biochemistry, Université de Lyon, Lyon, France
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9
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Khan FI, Hassan F, Anwer R, Juan F, Lai D. Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2. Biomolecules 2020; 10:biom10091286. [PMID: 32906690 PMCID: PMC7564321 DOI: 10.3390/biom10091286] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/27/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Two photoactivatable near infrared fluorescent proteins (NIR FPs) named “PAiRFP1” and “PAiRFP2” are formed by directed molecular evolution from Agp2, a bathy bacteriophytochrome of Agrobacterium tumefaciens C58. There are 15 and 24 amino acid substitutions in the structure of PAiRFP1 and PAiRFP2, respectively. A comprehensive molecular exploration of these bacteriophytochrome photoreceptors (BphPs) are required to understand the structure dynamics. In this study, the NIR fluorescence emission spectra for PAiRFP1 were recorded upon repeated excitation and the fluorescence intensity of PAiRFP1 tends to increase as the irradiation time was prolonged. We also predicted that mutations Q168L, V244F, and A480V in Agp2 will enhance the molecular stability and flexibility. During molecular dynamics (MD) simulations, the average root mean square deviations of Agp2, PAiRFP1, and PAiRFP2 were found to be 0.40, 0.49, and 0.48 nm, respectively. The structure of PAiRFP1 and PAiRFP2 were more deviated than Agp2 from its native conformation and the hydrophobic regions that were buried in PAiRFP1 and PAiRFP2 core exposed to solvent molecules. The eigenvalues and the trace of covariance matrix were found to be high for PAiRFP1 (597.90 nm2) and PAiRFP2 (726.74 nm2) when compared with Agp2 (535.79 nm2). It was also found that PAiRFP1 has more sharp Gibbs free energy global minima than Agp2 and PAiRFP2. This comparative analysis will help to gain deeper understanding on the structural changes during the evolution of photoactivatable NIR FPs. Further work can be carried out by combining PCR-based directed mutagenesis and spectroscopic methods to provide strategies for the rational designing of these PAiRFPs.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China;
| | - Fakhrul Hassan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China; (F.H.); (F.J.)
| | - Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad ibn Saud Islamic University (IMSIU), Riyadh 13317, Saudi Arabia;
| | - Feng Juan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China; (F.H.); (F.J.)
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China;
- Correspondence: ; Tel.: +86-182-0052-9516
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10
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Basak N, Krishnan V, Pandey V, Punjabi M, Hada A, Marathe A, Jolly M, Palaka BK, Ampasala DR, Sachdev A. Expression profiling and in silico homology modeling of Inositol penta kisphosphate 2-kinase, a potential candidate gene for low phytate trait in soybean. 3 Biotech 2020; 10:268. [PMID: 32523862 DOI: 10.1007/s13205-020-02260-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/14/2020] [Indexed: 11/27/2022] Open
Abstract
Low phytate soybeans are desirable both from a nutritional and economic standpoint. Inositol 1, 3, 4, 5, 6-pentakisphosphate 2-kinase (IPK1), optimizes the metabolic flux of phytate generation in soybean and thus shows much promise as a likely candidate for pathway regulation. In the present study, the differential spatial and temporal expression profiling of GmIpk1 and its two homologs Glyma06g03310 and Glyma04g03310 were carried out in Glycine max L. var Pusa 9712 revealing the early stages of seed development to be the potential target for gene manipulation. NCBI databank was screened using BLASTp to retrieve 32 plant IPK1 sequences showing high homology to GmIPK1 and its homologs. Bio-computational tools were employed to predict the protein's properties, conserved domains, and secondary structures. Using state-of-the-art in silico physicochemical approach, the three-dimensional (3D) GmIPK1 protein model (PMD ID-PM0079931), was developed based on Arabidopsis thaliana (PDB ID: 4AQK). Superimposition of 4AQK and best model of GmIPK1 revealed that the GmIPK1 aligned well and shows a sequence identity score of 54.32% with 4AQK and a low RMSD of 0.163 nm and almost similar structural features. The modeled structure was further refined considering the stereochemical geometry, energy and packing environment between the model and the template along with validation of its intrinsic dynamics. Molecular dynamics simulation studies of GmIPK1 were carried out to obtain structural insights and to understand the interactive behavior of this enzyme with ligands ADP and IP6. The results of this study provide some fundamental knowledge on the distinct mechanistic step performed by the key residues to elucidate the structure-function relationship of GmIPK1, as an initiative towards engineering "low phytate soybean".
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Affiliation(s)
- Nabaneeta Basak
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | - Veda Krishnan
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Vanita Pandey
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Quality and Basic Sciences Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - Mansi Punjabi
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Alkesh Hada
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Ashish Marathe
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Biotechnology Lab, ICAR-National Institute of Biotic Stress Management, Raipur, Chattisgarh 493225 India
| | - Monica Jolly
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Dinakara R Ampasala
- Centre for Bioinformatics, Pondicherry University, Puducherry, 605 014 India
| | - Archana Sachdev
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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11
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Klaewkla M, Pichyangkura R, Charoenwongpaiboon T, Wangpaiboon K, Chunsrivirot S. Computational design of oligosaccharide producing levansucrase from Bacillus licheniformis RN-01 to improve its thermostability for production of levan-type fructooligosaccharides from sucrose. Int J Biol Macromol 2020; 160:252-263. [PMID: 32439436 DOI: 10.1016/j.ijbiomac.2020.05.102] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022]
Abstract
Levansucrase catalyzes production of levan and levan-type fructooligosaccharides (LFOs) with potential applications in food and pharmaceutical industries such as prebiotics and anti-tumor agents. Previous study found that Y246S mutant of Bacillus licheniformis RN-01 levansucrase (oligosaccharide producing levansucrase, OPL) could effectively produce LFOs but its thermostability is limited at high temperature. In this study, molecular dynamics (MD) and computational protein design were used to create mutants with higher thermostability than OPL by rigidifying highly flexible residues on enzyme surface. MD results show that highly flexible residues suitable for design are K82, N83, D179, and Q308. Two approaches were employed to improve their interactions by allowing them to be amino acids that could potentially form favorable interactions with their neighboring residues or natural amino acids except G, P and C. Flexibilities of designed residues of K82H, N83R, Q308S and K82H/N83R mutants are lower than those of OPL. Experimental results show that characteristics and product patterns of designed mutants are relatively similar to those of OPL. K82H/N83R mutant has higher thermostability than OPL with 1.7-fold increase in t1/2. Circular dichroism result suggests that designed mutations do not drastically affect secondary structures. This study shows how computational technique can engineer enzyme for thermostability improvement.
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Affiliation(s)
- Methus Klaewkla
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand; Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | | | - Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Surasak Chunsrivirot
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand; Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand.
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12
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Schaduangrat N, Lampa S, Simeon S, Gleeson MP, Spjuth O, Nantasenamat C. Towards reproducible computational drug discovery. J Cheminform 2020; 12:9. [PMID: 33430992 PMCID: PMC6988305 DOI: 10.1186/s13321-020-0408-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022] Open
Abstract
The reproducibility of experiments has been a long standing impediment for further scientific progress. Computational methods have been instrumental in drug discovery efforts owing to its multifaceted utilization for data collection, pre-processing, analysis and inference. This article provides an in-depth coverage on the reproducibility of computational drug discovery. This review explores the following topics: (1) the current state-of-the-art on reproducible research, (2) research documentation (e.g. electronic laboratory notebook, Jupyter notebook, etc.), (3) science of reproducible research (i.e. comparison and contrast with related concepts as replicability, reusability and reliability), (4) model development in computational drug discovery, (5) computational issues on model development and deployment, (6) use case scenarios for streamlining the computational drug discovery protocol. In computational disciplines, it has become common practice to share data and programming codes used for numerical calculations as to not only facilitate reproducibility, but also to foster collaborations (i.e. to drive the project further by introducing new ideas, growing the data, augmenting the code, etc.). It is therefore inevitable that the field of computational drug design would adopt an open approach towards the collection, curation and sharing of data/code.
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Affiliation(s)
- Nalini Schaduangrat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, 10700, Bangkok, Thailand
| | - Samuel Lampa
- Department of Pharmaceutical Biosciences, Uppsala University, 751 24, Uppsala, Sweden
| | - Saw Simeon
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 10900, Bangkok, Thailand
| | - Matthew Paul Gleeson
- Department of Biomedical Engineering, Faculty of Engineering, King Mongkut's Institute of Technology Ladkrabang, 10520, Bangkok, Thailand.
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, 751 24, Uppsala, Sweden.
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, 10700, Bangkok, Thailand.
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13
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Sheik Amamuddy O, Veldman W, Manyumwa C, Khairallah A, Agajanian S, Oluyemi O, Verkhivker GM, Tastan Bishop Ö. Integrated Computational Approaches and Tools forAllosteric Drug Discovery. Int J Mol Sci 2020; 21:E847. [PMID: 32013012 PMCID: PMC7036869 DOI: 10.3390/ijms21030847] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/16/2022] Open
Abstract
Understanding molecular mechanisms underlying the complexity of allosteric regulationin proteins has attracted considerable attention in drug discovery due to the benefits and versatilityof allosteric modulators in providing desirable selectivity against protein targets while minimizingtoxicity and other side effects. The proliferation of novel computational approaches for predictingligand-protein interactions and binding using dynamic and network-centric perspectives has ledto new insights into allosteric mechanisms and facilitated computer-based discovery of allostericdrugs. Although no absolute method of experimental and in silico allosteric drug/site discoveryexists, current methods are still being improved. As such, the critical analysis and integration ofestablished approaches into robust, reproducible, and customizable computational pipelines withexperimental feedback could make allosteric drug discovery more efficient and reliable. In this article,we review computational approaches for allosteric drug discovery and discuss how these tools can beutilized to develop consensus workflows for in silico identification of allosteric sites and modulatorswith some applications to pathogen resistance and precision medicine. The emerging realization thatallosteric modulators can exploit distinct regulatory mechanisms and can provide access to targetedmodulation of protein activities could open opportunities for probing biological processes and insilico design of drug combinations with improved therapeutic indices and a broad range of activities.
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Affiliation(s)
- Olivier Sheik Amamuddy
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Colleen Manyumwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Afrah Khairallah
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Steve Agajanian
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Odeyemi Oluyemi
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
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14
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Kuriata A, Gierut AM, Oleniecki T, Ciemny MP, Kolinski A, Kurcinski M, Kmiecik S. CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures. Nucleic Acids Res 2019; 46:W338-W343. [PMID: 29762700 PMCID: PMC6031000 DOI: 10.1093/nar/gky356] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/27/2018] [Indexed: 11/13/2022] Open
Abstract
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.
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Affiliation(s)
- Aleksander Kuriata
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Aleksandra Maria Gierut
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.,Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Krakow, Poland
| | - Tymoteusz Oleniecki
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Maciej Pawel Ciemny
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.,Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Andrzej Kolinski
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Mateusz Kurcinski
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Sebastian Kmiecik
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
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15
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Rodrigues CH, Pires DE, Ascher DB. DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. Nucleic Acids Res 2019; 46:W350-W355. [PMID: 29718330 PMCID: PMC6031064 DOI: 10.1093/nar/gky300] [Citation(s) in RCA: 615] [Impact Index Per Article: 123.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/16/2018] [Indexed: 12/31/2022] Open
Abstract
Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based approaches for assessing the impact of mutations on protein structure and function relying upon static structures. Here we present DynaMut, a web server implementing two distinct, well established normal mode approaches, which can be used to analyze and visualize protein dynamics by sampling conformations and assess the impact of mutations on protein dynamics and stability resulting from vibrational entropy changes. DynaMut integrates our graph-based signatures along with normal mode dynamics to generate a consensus prediction of the impact of a mutation on protein stability. We demonstrate our approach outperforms alternative approaches to predict the effects of mutations on protein stability and flexibility (P-value < 0.001), achieving a correlation of up to 0.70 on blind tests. DynaMut also provides a comprehensive suite for protein motion and flexibility analysis and visualization via a freely available, user friendly web server at http://biosig.unimelb.edu.au/dynamut/.
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Affiliation(s)
- Carlos Hm Rodrigues
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | | | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia.,Instituto René Rachou, Fundação Oswaldo Cruz, Brazil.,Department of Biochemistry, University of Cambridge, UK
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16
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Astl L, Verkhivker GM. Data-driven computational analysis of allosteric proteins by exploring protein dynamics, residue coevolution and residue interaction networks. Biochim Biophys Acta Gen Subj 2019:S0304-4165(19)30179-5. [PMID: 31330173 DOI: 10.1016/j.bbagen.2019.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Computational studies of allosteric interactions have witnessed a recent renaissance fueled by the growing interest in modeling of the complex molecular assemblies and biological networks. Allosteric interactions in protein structures allow for molecular communication in signal transduction networks. METHODS In this work, we performed a large scale comprehensive and multi-faceted analysis of >300 diverse allosteric proteins and complexes with allosteric modulators. By modeling and exploring coarse-grained dynamics, residue coevolution, and residue interaction networks for allosteric proteins, we have determined unifying molecular signatures shared by allosteric systems. RESULTS The results of this study have suggested that allosteric inhibitors and allosteric activators may differentially affect global dynamics and network organization of protein systems, leading to diverse allosteric mechanisms. By using structural and functional data on protein kinases, we present a detailed case study that that included atomic-level analysis of coevolutionary networks in kinases bound with allosteric inhibitors and activators. CONCLUSIONS We have found that coevolutionary networks can form direct communication pathways connecting functional regions and can recapitulate key regulatory sites and interactions responsible for allosteric signaling in the studied protein systems. The results of this computational investigation are compared with the experimental studies and reveal molecular signatures of known regulatory hotspots in protein kinases. GENERAL SIGNIFICANCE This study has shown that allosteric inhibitors and allosteric activators can have a different effect on residue interaction networks and can exploit distinct regulatory mechanisms, which could open up opportunities for probing allostery and new drug combinations with broad range of activities.
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Affiliation(s)
- Lindy Astl
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States of America
| | - Gennady M Verkhivker
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States of America; Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States of America.
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17
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Mayank, Kaur N, Singh N. Structural insights and influence of V599 mutations on the overall dynamics of BRAF protein against its kinase domains. Integr Biol (Camb) 2019; 10:646-657. [PMID: 30229251 DOI: 10.1039/c8ib00095f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutations in the BRAF gene are well known for their oncogenic effects. Point mutations in V599 are particularly oncogenic and are considered important for therapeutic purposes. Along with wild type, other V599 mutated BRAF variants viz. V599E, V599D and V599R are reported and crystals of the former two with inhibitor (BAY43-9006) are further detailed. Both wild-type and mutated BRAF forms show similar interaction patterns with BAY43-9006, but the 599th residue did not show any involvement in the interactions. Upon BAY43-9006 binding, kinase domains of both forms were found adopting essentially identical conformations. However, BAY43-9006 shows a varied activity profile in the case of the wild and V599E variant of the BRAF protein. Furthermore, MMGBSA binding energy results for all four BRAF variants, further revealed the importance of the 599th residue. In-depth analysis viz. molecular dynamics, residue correlation studies and residue interaction network (RIN) analyses were conducted, providing a deep insight into the 599th residue and its impact on the overall dynamics of BRAF protein. Our findings reveal that the mutated residue at the 599th position not only changed the BAY43-9006-BRAF binding behaviour but also produced a massive impact on the overall dynamic behaviour of the protein. The insights obtained herein could be of great relevance for designing new BRAF inhibitors aimed at getting ideal activity against all BRAF forms.
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Affiliation(s)
- Mayank
- Department of Chemistry, Indian Institute of Technology Ropar, Punjab 140001, India.
| | - Navneet Kaur
- Department of Chemistry, Punjab University Chandigarh, Punjab, India.
| | - Narinder Singh
- Department of Chemistry, Indian Institute of Technology Ropar, Punjab 140001, India.
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18
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Pal A, Levy Y. Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins. PLoS Comput Biol 2019; 15:e1006768. [PMID: 30933978 PMCID: PMC6467422 DOI: 10.1371/journal.pcbi.1006768] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 04/16/2019] [Accepted: 01/01/2019] [Indexed: 02/06/2023] Open
Abstract
Recognition of single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA) is important for many fundamental cellular functions. A variety of single-stranded DNA-binding proteins (ssDBPs) and single-stranded RNA-binding proteins (ssRBPs) have evolved that bind ssDNA and ssRNA, respectively, with varying degree of affinities and specificities to form complexes. Structural studies of these complexes provide key insights into their recognition mechanism. However, computational modeling of the specific recognition process and to predict the structure of the complex is challenging, primarily due to the heterogeneity of their binding energy landscape and the greater flexibility of ssDNA or ssRNA compared with double-stranded nucleic acids. Consequently, considerably fewer computational studies have explored interactions between proteins and single-stranded nucleic acids compared with protein interactions with double-stranded nucleic acids. Here, we report a newly developed energy-based coarse-grained model to predict the structure of ssDNA–ssDBP and ssRNA–ssRBP complexes and to assess their sequence-specific interactions and stabilities. We tuned two factors that can modulate specific recognition: base–aromatic stacking strength and the flexibility of the single-stranded nucleic acid. The model was successfully applied to predict the binding conformations of 12 distinct ssDBP and ssRBP structures with their cognate ssDNA and ssRNA partners having various sequences. Estimated binding energies agreed well with the corresponding experimental binding affinities. Bound conformations from the simulation showed a funnel-shaped binding energy distribution where the native-like conformations corresponded to the energy minima. The various ssDNA–protein and ssRNA–protein complexes differed in the balance of electrostatic and aromatic energies. The lower affinity of the ssRNA–ssRBP complexes compared with the ssDNA–ssDBP complexes stems from lower flexibility of ssRNA compared to ssDNA, which results in higher rate constants for the dissociation of the complex (koff) for complexes involving the former. Quantifying bimolecular self-assembly is pivotal to understanding cellular function. In recent years, a large progress has been made in understanding the structure and biophysics of protein-protein interactions. Particularly, various computational tools are available for predicting these structures and to estimate their stability and the driving forces of their formation. The understating of the interactions between proteins and nucleic acids, however, is still limited, presumably due to the involvement of non-specific interactions as well as the high conformational plasticity that may demand an induced-fit mechanism. In particular, the interactions between proteins and single-stranded nucleic acids (i.e., single-stranded DNA and RNA) is very challenging due to their high flexibility. Furthermore, the interface between proteins and single-stranded nucleic acids is often chemically more heterogeneous than the interface between proteins and double-stranded DNA. In this study, we developed a coarse-grained computational model to predict the structure of complexes between proteins and single-stranded nucleic acids. The model was applied to estimate binding affinities and the estimated binding energies agreed well with the corresponding experimental binding affinities. The kinetics of association as well as the specificity of the complexes between proteins and ssDNA are different than those with ssRNA, mostly due to differences in their conformational flexibility.
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Affiliation(s)
- Arumay Pal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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19
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Rubio AM, Rey A. Design of a structure-based model for protein folding from flexible conformations. Phys Chem Chem Phys 2019; 21:6544-6552. [DOI: 10.1039/c9cp00168a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We introduce a coarse-grained, structure-based model for protein folding that considers the flexibility of the native state in the definition of the model interactions.
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Affiliation(s)
- Ana M. Rubio
- Departamento de Química Física
- Facultad de Ciencias Químicas
- Universidad Complutense de Madrid
- E-28040 Madrid
- Spain
| | - Antonio Rey
- Departamento de Química Física
- Facultad de Ciencias Químicas
- Universidad Complutense de Madrid
- E-28040 Madrid
- Spain
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20
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Verkhivker GM. Biophysical simulations and structure-based modeling of residue interaction networks in the tumor suppressor proteins reveal functional role of cancer mutation hotspots in molecular communication. Biochim Biophys Acta Gen Subj 2018; 1863:210-225. [PMID: 30339916 DOI: 10.1016/j.bbagen.2018.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/06/2018] [Accepted: 10/13/2018] [Indexed: 12/19/2022]
Abstract
In the current study, we have combined molecular simulations and energetic analysis with dynamics-based network modeling and perturbation response scanning to determine molecular signatures of mutational hotspot residues in the p53, PTEN, and SMAD4 tumor suppressor proteins. By examining structure, energetics and dynamics of these proteins, we have shown that inactivating mutations preferentially target a group of structurally stable residues that play a fundamental role in global propagation of dynamic fluctuations and mediating allosteric interaction networks. Through integration of long-range perturbation dynamics and network-based approaches, we have quantified allosteric potential of residues in the studied proteins. The results have revealed that mutational hotspot sites often correspond to high centrality mediating centers of the residue interaction networks that are responsible for coordination of global dynamic changes and allosteric signaling. Our findings have also suggested that structurally stable mutational hotpots can act as major effectors of allosteric interactions and mutations in these positions are typically associated with severe phenotype. Modeling of shortest inter-residue pathways has shown that mutational hotspot sites can also serve as key mediating bridges of allosteric communication in the p53 and PTEN protein structures. Multiple regression models have indicated that functional significance of mutational hotspots can be strongly associated with the network signatures serving as robust predictors of critical regulatory positions responsible for loss-of-function phenotype. The results of this computational investigation are compared with the experimental studies and reveal molecular signatures of mutational hotspots, providing a plausible rationale for explaining and localizing disease-causing mutations in tumor suppressor genes.
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Affiliation(s)
- Gennady M Verkhivker
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States; Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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21
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Stetz G, Tse A, Verkhivker GM. Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones. Sci Rep 2018; 8:6899. [PMID: 29720613 PMCID: PMC5932063 DOI: 10.1038/s41598-018-25329-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/19/2018] [Indexed: 01/19/2023] Open
Abstract
Post-translational modifications (PTMs) represent an important regulatory instrument that modulates structure, dynamics and function of proteins. The large number of PTM sites in the Hsp90 proteins that are scattered throughout different domains indicated that synchronization of multiple PTMs through a combinatorial code can be invoked as an important mechanism to orchestrate diverse chaperone functions and recognize multiple client proteins. In this study, we have combined structural and coevolutionary analysis with molecular simulations and perturbation response scanning analysis of the Hsp90 structures to characterize functional role of PTM sites in allosteric regulation. The results reveal a small group of conserved PTMs that act as global mediators of collective dynamics and allosteric communications in the Hsp90 structures, while the majority of flexible PTM sites serve as sensors and carriers of the allosteric structural changes. This study provides a comprehensive structural, dynamic and network analysis of PTM sites across Hsp90 proteins, identifying specific role of regulatory PTM hotspots in the allosteric mechanism of the Hsp90 cycle. We argue that plasticity of a combinatorial PTM code in the Hsp90 may be enacted through allosteric coupling between effector and sensor PTM residues, which would allow for timely response to structural requirements of multiple modified enzymes.
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Affiliation(s)
- Gabrielle Stetz
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Amanda Tse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America.
- Chapman University School of Pharmacy, Irvine, California, United States of America.
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22
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Stetz G, Tse A, Verkhivker GM. Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone. PLoS One 2017; 12:e0186089. [PMID: 29095844 PMCID: PMC5667858 DOI: 10.1371/journal.pone.0186089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK family are of particular interest as functional diversification among these kinases may be related to variations in chaperone dependencies and can be exploited in drug discovery of personalized therapeutic agents. In this work, we report the results of a computational investigation of several members of CDK family (CDK5, CDK6, CDK9) that represented a broad repertoire of chaperone dependencies—from nonclient CDK5, to weak client CDK6, and strong client CDK9. By using molecular simulations of multiple crystal structures we characterized conformational ensembles and collective dynamics of CDK proteins. We found that the elevated dynamics of CDK9 can trigger imbalances in cooperative collective motions and reduce stability of the active fold, thus creating a cascade of favorable conditions for chaperone intervention. The ensemble-based modeling of residue interaction networks and community analysis determined how differences in modularity of allosteric networks and topography of communication pathways can be linked with the client status of CDK proteins. This analysis unveiled depleted modularity of the allosteric network in CDK9 that alters distribution of communication pathways and leads to impaired signaling in the client kinase. According to our results, these network features may uniquely define chaperone dependencies of CDK clients. The perturbation response scanning and rigidity decomposition approaches identified regulatory hotspots that mediate differences in stability and cooperativity of allosteric interaction networks in the CDK structures. By combining these synergistic approaches, our study revealed dynamic and network signatures that can differentiate kinase clients and rationalize subtle divergences in the activation mechanisms of CDK family members. The therapeutic implications of these results are illustrated by identifying structural hotspots of pathogenic mutations that preferentially target regions of the increased flexibility to enable modulation of activation changes. Our study offers a network-based perspective on dynamic kinase mechanisms and drug design by unravelling relationships between protein kinase dynamics, allosteric communications and chaperone dependencies.
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Affiliation(s)
- Gabrielle Stetz
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Amanda Tse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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23
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Emperador A, Orozco M. Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins. J Chem Theory Comput 2017; 13:1454-1461. [PMID: 28157327 DOI: 10.1021/acs.jctc.6b01153] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.
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Affiliation(s)
- Agustí Emperador
- Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Parc Científic de Barcelona , Josep Samitier 1-5, Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Parc Científic de Barcelona , Josep Samitier 1-5, Barcelona 08028, Spain.,Joint IRB-BSC Program on Computational Biology , Barcelona 08028, Spain.,Departament de Bioquímica i Biomedicina, Facultat de Biología, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain
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24
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Hospital A, Candotti M, Gelpí JL, Orozco M. The Multiple Roles of Waters in Protein Solvation. J Phys Chem B 2017; 121:3636-3643. [DOI: 10.1021/acs.jpcb.6b09676] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adam Hospital
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Joint
BSC-IRB Research Program in Computational Biology, The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
| | - Michela Candotti
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Joint
BSC-IRB Research Program in Computational Biology, The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
| | - Josep Lluís Gelpí
- Joint
BSC-IRB Research Program in Computational Biology, The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Department
of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, 08028, Spain
- Barcelona Supercomputing Center (BSC), Jordi Girona 29, Barcelona, 08034, Spain
| | - Modesto Orozco
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Joint
BSC-IRB Research Program in Computational Biology, The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Department
of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, 08028, Spain
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25
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Swanson J, Audie J. An unexpected way forward: towards a more accurate and rigorous protein-protein binding affinity scoring function by eliminating terms from an already simple scoring function. J Biomol Struct Dyn 2016; 36:83-97. [PMID: 27989231 DOI: 10.1080/07391102.2016.1268974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A fundamental and unsolved problem in biophysical chemistry is the development of a computationally simple, physically intuitive, and generally applicable method for accurately predicting and physically explaining protein-protein binding affinities from protein-protein interaction (PPI) complex coordinates. Here, we propose that the simplification of a previously described six-term PPI scoring function to a four term function results in a simple expression of all physically and statistically meaningful terms that can be used to accurately predict and explain binding affinities for a well-defined subset of PPIs that are characterized by (1) crystallographic coordinates, (2) rigid-body association, (3) normal interface size, and hydrophobicity and hydrophilicity, and (4) high quality experimental binding affinity measurements. We further propose that the four-term scoring function could be regarded as a core expression for future development into a more general PPI scoring function. Our work has clear implications for PPI modeling and structure-based drug design.
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Affiliation(s)
- Jon Swanson
- a ChemModeling LLC , Suite 101, 500 Huber Park Ct, Weldon Spring , MO 63304 , USA
| | - Joseph Audie
- b CMD Bioscience , 5 Science Park , New Haven , CT 06511 , USA.,c Department of Chemistry , Sacred Heart University , 5151 Park Ave, Fairfield , CT 06825 , USA
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26
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Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations. Nat Commun 2016; 7:12575. [PMID: 27578633 PMCID: PMC5013691 DOI: 10.1038/ncomms12575] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 07/13/2016] [Indexed: 12/28/2022] Open
Abstract
Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general. Protein conformational changes are key to a wide range of cellular functions but remain difficult to access experimentally. Here the authors describe eBDIMS, a novel approach to predict intermediates observed in structural transition pathways from experimental ensembles.
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27
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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28
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Boer DR, Ruiz-Masó JA, Rueda M, Petoukhov MV, Machón C, Svergun DI, Orozco M, del Solar G, Coll M. Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158. Sci Rep 2016; 6:20915. [PMID: 26875695 PMCID: PMC4753449 DOI: 10.1038/srep20915] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 01/13/2016] [Indexed: 11/16/2022] Open
Abstract
DNA replication initiation is a vital and tightly regulated step in all replicons and requires an initiator factor that specifically recognizes the DNA replication origin and starts replication. RepB from the promiscuous streptococcal plasmid pMV158 is a hexameric ring protein evolutionary related to viral initiators. Here we explore the conformational plasticity of the RepB hexamer by i) SAXS, ii) sedimentation experiments, iii) molecular simulations and iv) X-ray crystallography. Combining these techniques, we derive an estimate of the conformational ensemble in solution showing that the C-terminal oligomerisation domains of the protein form a rigid cylindrical scaffold to which the N-terminal DNA-binding/catalytic domains are attached as highly flexible appendages, featuring multiple orientations. In addition, we show that the hinge region connecting both domains plays a pivotal role in the observed plasticity. Sequence comparisons and a literature survey show that this hinge region could exists in other initiators, suggesting that it is a common, crucial structural element for DNA binding and manipulation.
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Affiliation(s)
- D Roeland Boer
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Barcelona, 08028, Spain
| | - José Angel Ruiz-Masó
- Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas), Madrid, 28040, Spain
| | - Manuel Rueda
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
| | - Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, 22607, Germany
| | - Cristina Machón
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Barcelona, 08028, Spain
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, 22607, Germany
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Departament de Bioquímica, Facultat de Biologia, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Gloria del Solar
- Centro de Investigaciones Biológicas (Consejo Superior de Investigaciones Científicas), Madrid, 28040, Spain
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.,Institut de Biologia Molecular de Barcelona (Consejo Superior de Investigaciones Científicas), Barcelona, 08028, Spain
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29
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Sfriso P, Duran-Frigola M, Mosca R, Emperador A, Aloy P, Orozco M. Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins. Structure 2016; 24:116-126. [DOI: 10.1016/j.str.2015.10.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/13/2015] [Accepted: 10/17/2015] [Indexed: 12/12/2022]
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30
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Orellana L, Rueda M, Ferrer-Costa C, Lopez-Blanco JR, Chacón P, Orozco M. Approaching Elastic Network Models to Molecular Dynamics Flexibility. J Chem Theory Comput 2015; 6:2910-23. [PMID: 26616090 DOI: 10.1021/ct100208e] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Elastic network models (ENMs) are coarse-grained descriptions of proteins as networks of coupled harmonic oscillators. However, despite their widespread application to study collective movements, there is still no consensus parametrization for the ENMs. When compared to molecular dynamics (MD) flexibility in solution, the ENMs tend to disperse the important motions into multiple modes. We present here a new ENM, trained against a database of atomistic MD trajectories. The role of residue connectivity, the analytical form of the force constants, and the threshold for interactions were systematically explored. We found that contacts between the three nearest sequence neighbors are crucial determinants of the fundamental motions. We developed a new general potential function including both the sequential and spatial relationships between interacting residue pairs which is robust against size and fold variations. The proposed model provides a systematic improvement compared to standard ENMs: Not only do its results match the MD results-even for long time scales-but also the model is able to capture large X-ray conformational transitions as well as NMR ensemble diversity.
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Affiliation(s)
- Laura Orellana
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| | - Manuel Rueda
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| | - Carles Ferrer-Costa
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| | - José Ramón Lopez-Blanco
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| | - Pablo Chacón
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
| | - Modesto Orozco
- Joint Research Program in Computational Biology from the Institute for Research in Biomedicine Barcelona (IRBB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain, Chemical and Physical Biology, Centro de Investigaciones Biológicas, Madrid, Spain, Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain, and Skaggs School of Pharmacy, University of California-San Diego, La Jolla, California 92093
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31
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Mukherjee A. Computational analysis of a cys-loop ligand gated ion channel from the green alga Chlamydomonas reinhardtii. Mol Biol 2015. [DOI: 10.1134/s002689331505012x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Abstract
The hydrodynamic parameters measured in an AUC experiment, s(20,w) and D(t)(20,w)(0), can be used to gain information on the solution structure of (bio)macromolecules and their assemblies. This entails comparing the measured parameters with those that can be computed from usually "dry" structures by "hydrodynamic modeling." In this chapter, we will first briefly put hydrodynamic modeling in perspective and present the basic physics behind it as implemented in the most commonly used methods. The important "hydration" issue is also touched upon, and the distinction between rigid bodies versus those for which flexibility must be considered in the modeling process is then made. The available hydrodynamic modeling/computation programs, HYDROPRO, BEST, SoMo, AtoB, and Zeno, the latter four all implemented within the US-SOMO suite, are described and their performance evaluated. Finally, some literature examples are presented to illustrate the potential applications of hydrodynamics in the expanding field of multiresolution modeling.
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Affiliation(s)
- Mattia Rocco
- Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy.
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, United Kingdom.
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33
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Barbany M, Meyer T, Hospital A, Faustino I, D'Abramo M, Morata J, Orozco M, de la Cruz X. Molecular dynamics study of naturally existing cavity couplings in proteins. PLoS One 2015; 10:e0119978. [PMID: 25816327 PMCID: PMC4376744 DOI: 10.1371/journal.pone.0119978] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 01/26/2015] [Indexed: 11/18/2022] Open
Abstract
Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100 ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.
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Affiliation(s)
- Montserrat Barbany
- Translational Bioinformatics in Neurosciences, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Tim Meyer
- Theoretische und computergestützte Biophysik, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
| | - Adam Hospital
- Joint IRB (Institute for Research in Biomedicine)—BSC (Barcelona Supercomputing Center) Program on Computational Biology, Barcelona, Spain
| | - Ignacio Faustino
- Joint IRB (Institute for Research in Biomedicine)—BSC (Barcelona Supercomputing Center) Program on Computational Biology, Barcelona, Spain
| | - Marco D'Abramo
- Department of Chemistry, Università degli Studi di Roma "La Sapienza", Roma, Italy
| | - Jordi Morata
- Centre for Research in Agricultural Genomics (CRAG), Barcelona, Spain
| | - Modesto Orozco
- Joint IRB (Institute for Research in Biomedicine)—BSC (Barcelona Supercomputing Center) Program on Computational Biology, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Xavier de la Cruz
- Translational Bioinformatics in Neurosciences, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- * E-mail:
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34
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Two-step mechanism involving active-site conformational changes regulates human telomerase DNA binding. Biochem J 2015; 465:347-57. [PMID: 25365545 DOI: 10.1042/bj20140922] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ribonucleoprotein enzyme telomerase maintains telomeres and is essential for cellular immortality in most cancers. Insight into the telomerase mechanism can be gained from syndromes such as dyskeratosis congenita, in which mutation of telomerase components manifests in telomere dysfunction. We carried out detailed kinetic and thermodynamic analyses of wild-type telomerase and two disease-associated mutations in the reverse transcriptase domain. Differences in dissociation rates between primers with different 3' ends were independent of DNA affinities, revealing that initial binding of telomerase to telomeric DNA occurs through a previously undescribed two-step mechanism involving enzyme conformational changes. Both mutations affected DNA binding, but through different mechanisms: P704S specifically affected protein conformational changes during DNA binding, whereas R865H showed defects in binding to the 3' region of the DNA. To gain further insight at the structural level, we generated the first homology model of the human telomerase reverse transcriptase domain; the positions of P704S and R865H corroborate their observed mechanistic defects, providing validation for the structural model. Our data reveal the importance of protein interactions with the 3' end of telomeric DNA and the role of protein conformational change in telomerase DNA binding, and highlight naturally occurring disease mutations as a rich source of mechanistic insight.
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35
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Yu H, Zhao Y, Guo C, Gan Y, Huang H. The role of proline substitutions within flexible regions on thermostability of luciferase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:65-72. [PMID: 25448017 DOI: 10.1016/j.bbapap.2014.10.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/19/2014] [Accepted: 10/21/2014] [Indexed: 11/18/2022]
Abstract
Improving the stability of firefly luciferase has been a critical issue for its wider industrial applications. Studies about hyperthermophile proteins show that flexibility could be an effective indicator to find out weak spots to engineering thermostability of proteins. However, the relationship among flexibility, activity and stability in most of proteins is unclear. Proline is the most rigid residue and can be introduced to rigidify flexible regions to enhance thermostability of proteins. We firstly apply three different methods, molecular dynamics (MD) simulation, B-FITTER and framework rigidity optimized dynamics algorithm (FRODA) to determine the flexible regions of Photinus pyralis luciferase: Fragment 197-207; Fragment 471-481 and Fragment 487-495. Then, introduction of proline is used to rigidify these flexible regions. Two mutants D476P and H489P within most flexible regions are finally designed. In the results, H489P mutant shows improved thermostability while maintaining its catalytic efficiency compared to that of wild type luciferase. Flexibility analysis confirms that the overall rigidity and local rigidity of H489P mutant are greatly strengthened. D476P mutant shows decreased thermosatbility and the reason for this is elucidated at the molecular level. S307P mutation is randomly chosen outside the flexible regions as a control. Thermostability analysis shows that S307P mutation has decreased kinetic stability and enhanced thermodynamic stability.
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Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China
| | - Yang Zhao
- National Institutes for Food and Drug Control (NIFDC), Beijing 100050, PR China
| | - Chao Guo
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China
| | - Yiru Gan
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China.
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36
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Fenollosa C, Otón M, Andrio P, Cortés J, Orozco M, Goñi JR. SEABED: Small molEcule activity scanner weB servicE baseD. ACTA ACUST UNITED AC 2014; 31:773-5. [PMID: 25348211 PMCID: PMC7297214 DOI: 10.1093/bioinformatics/btu709] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Motivation: The SEABED web server integrates a variety of docking and QSAR techniques in a user-friendly environment. SEABED goes beyond the basic docking and QSAR web tools and implements extended functionalities like receptor preparation, library editing, flexible ensemble docking, hybrid docking/QSAR experiments or virtual screening on protein mutants. SEABED is not a monolithic workflow tool but Software as a Service platform. Availability and implementation: SEABED is a free web server available athttp://www.bsc.es/SEABED. No registration is required. Contact:ramon.goni@bsc.es Supplementary information:Supplementary data are available atBioinformatics online.
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Affiliation(s)
- Carlos Fenollosa
- Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain
| | - Marcel Otón
- Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain
| | - Pau Andrio
- Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain
| | - Jorge Cortés
- Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain
| | - Modesto Orozco
- Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molec
| | - J Ramon Goñi
- Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain
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Touw WG, Vriend G. BDB: Databank of PDB files with consistent B-factors. Protein Eng Des Sel 2014; 27:457-62. [DOI: 10.1093/protein/gzu044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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López-Blanco JR, Aliaga JI, Quintana-Ortí ES, Chacón P. iMODS: internal coordinates normal mode analysis server. Nucleic Acids Res 2014; 42:W271-6. [PMID: 24771341 PMCID: PMC4086069 DOI: 10.1093/nar/gku339] [Citation(s) in RCA: 361] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. The server is free and open to all users with no login requirement at http://imods.chaconlab.org.
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Affiliation(s)
- José Ramón López-Blanco
- Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C., Serrano 119, 28006 Madrid, Spain
| | - José I Aliaga
- Department of Computer Science and Engineering, University Jaume I, 12071 Castellón, Spain
| | | | - Pablo Chacón
- Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C., Serrano 119, 28006 Madrid, Spain
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39
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Bastolla U. Computing protein dynamics from protein structure with elastic network models. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1186] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ugo Bastolla
- Centro de Biologa Molecular Severo Ochoa (CSIC‐UAM)Universidad Autónoma de MadridMadridSpain
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40
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Abstract
Proteins are fascinating supramolecular structures, which are able to recognize ligands transforming binding information into chemical signals. They can transfer information across the cell, can catalyse complex chemical reactions, and are able to transform energy into work with much more efficiency than any human engine. The unique abilities of proteins are tightly coupled with their dynamic properties, which are coded in a complex way in the sequence and carefully refined by evolution. Despite its importance, our experimental knowledge of protein dynamics is still rather limited, and mostly derived from theoretical calculations. I will review here, in a systematic way, the current state-of-the-art theoretical approaches to the study of protein dynamics, emphasizing the most recent advances, examples of use and the expected lines of development in the near future.
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Affiliation(s)
- Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri i Reixac 8, Barcelona 08028, Spain.
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41
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Blacklock K, Verkhivker GM. Allosteric regulation of the Hsp90 dynamics and stability by client recruiter cochaperones: protein structure network modeling. PLoS One 2014; 9:e86547. [PMID: 24466147 PMCID: PMC3896489 DOI: 10.1371/journal.pone.0086547] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 12/06/2013] [Indexed: 12/29/2022] Open
Abstract
The fundamental role of the Hsp90 chaperone in supporting functional activity of diverse protein clients is anchored by specific cochaperones. A family of immune sensing client proteins is delivered to the Hsp90 system with the aid of cochaperones Sgt1 and Rar1 that act cooperatively with Hsp90 to form allosterically regulated dynamic complexes. In this work, functional dynamics and protein structure network modeling are combined to dissect molecular mechanisms of Hsp90 regulation by the client recruiter cochaperones. Dynamic signatures of the Hsp90-cochaperone complexes are manifested in differential modulation of the conformational mobility in the Hsp90 lid motif. Consistent with the experiments, we have determined that targeted reorganization of the lid dynamics is a unifying characteristic of the client recruiter cochaperones. Protein network analysis of the essential conformational space of the Hsp90-cochaperone motions has identified structurally stable interaction communities, interfacial hubs and key mediating residues of allosteric communication pathways that act concertedly with the shifts in conformational equilibrium. The results have shown that client recruiter cochaperones can orchestrate global changes in the dynamics and stability of the interaction networks that could enhance the ATPase activity and assist in the client recruitment. The network analysis has recapitulated a broad range of structural and mutagenesis experiments, particularly clarifying the elusive role of Rar1 as a regulator of the Hsp90 interactions and a stability enhancer of the Hsp90-cochaperone complexes. Small-world organization of the interaction networks in the Hsp90 regulatory complexes gives rise to a strong correspondence between highly connected local interfacial hubs, global mediator residues of allosteric interactions and key functional hot spots of the Hsp90 activity. We have found that cochaperone-induced conformational changes in Hsp90 may be determined by specific interaction networks that can inhibit or promote progression of the ATPase cycle and thus control the recruitment of client proteins.
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Affiliation(s)
- Kristin Blacklock
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Pharmacology, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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42
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Rueda M, Orozco M, Totrov M, Abagyan R. BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry. BMC STRUCTURAL BIOLOGY 2013; 13:32. [PMID: 24330655 PMCID: PMC3924234 DOI: 10.1186/1472-6807-13-32] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 12/03/2013] [Indexed: 12/02/2022]
Abstract
Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser. Results BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin. Conclusions BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper.
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Affiliation(s)
| | | | | | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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43
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Yu H, Huang H. Engineering proteins for thermostability through rigidifying flexible sites. Biotechnol Adv 2013; 32:308-15. [PMID: 24211474 DOI: 10.1016/j.biotechadv.2013.10.012] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 09/04/2013] [Accepted: 10/29/2013] [Indexed: 01/06/2023]
Abstract
Engineering proteins for thermostability is an exciting and challenging field since it is critical for broadening the industrial use of recombinant proteins. Thermostability of proteins arises from the simultaneous effect of several forces such as hydrophobic interactions, disulfide bonds, salt bridges and hydrogen bonds. All of these interactions lead to decreased flexibility of polypeptide chain. Structural studies of mesophilic and thermophilic proteins showed that the latter need more rigid structures to compensate for increased thermal fluctuations. Hence flexibility can be an indicator to pinpoint weak spots for enhancing thermostability of enzymes. A strategy has been proven effective in enhancing proteins' thermostability with two steps: predict flexible sites of proteins firstly and then rigidify these sites. We refer to this approach as rigidify flexible sites (RFS) and give an overview of such a method through summarizing the methods to predict flexibility of a protein, the methods to rigidify residues with high flexibility and successful cases regarding enhancing thermostability of proteins using RFS.
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Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
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Hobbs GA, Gunawardena HP, Baker R, Campbell SL. Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function. Small GTPases 2013; 4:186-92. [PMID: 24030601 DOI: 10.4161/sgtp.26270] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
KRas has recently been shown to be activated by monoubiquitination (mUb). Similar to oncogenic mutations, mUb of Ras at position 147 activates Ras by causing a defect in GTPase activating protein (GAP) function. To characterize the mechanism by which mUb impairs GAP-mediated downregulation of Ras, we made various modifications at position 147 of Ras and examined the impact on Ras sensitivity to GAP function. Whereas small modifications (iodoacetamide and glutathione) at position 147 of Ras do not affect GAP-mediated hydrolysis, ligation of Ras to Ub(G76C) (native linker), Ub(X77C) (one residue longer), and PDZ2 (with a native ubiquitin linker) was defective in GAP-mediated GTP hydrolysis. However, restoration of GAP activity was observed for Ras modified with the PDZ2 domain containing a shorter and stiffer linker region than ubiquitin. Therefore, the properties of the linker region dictate whether modification affects GAP-mediated hydrolysis, and our data indicate that the GAP defect requires a minimum linker length of 7 to 8 residues.
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Affiliation(s)
- G Aaron Hobbs
- Department of Biochemistry and Biophysics; University of North Carolina; Chapel Hill, NC USA
| | - Harsha P Gunawardena
- Department of Biochemistry and Biophysics; University of North Carolina; Chapel Hill, NC USA
| | - Rachael Baker
- Department of Biochemistry and Biophysics; University of North Carolina; Chapel Hill, NC USA
| | - Sharon L Campbell
- Department of Biochemistry and Biophysics; University of North Carolina; Chapel Hill, NC USA; Lineberger Comprehensive Cancer Center; University of North Carolina; Chapel Hill, NC USA
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Rodgers TL, Burnell D, Townsend PD, Pohl E, Cann MJ, Wilson MR, McLeish TCB. ΔΔPT: a comprehensive toolbox for the analysis of protein motion. BMC Bioinformatics 2013; 14:183. [PMID: 23758746 PMCID: PMC3689072 DOI: 10.1186/1471-2105-14-183] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 05/24/2013] [Indexed: 11/30/2022] Open
Abstract
Background Normal Mode Analysis is one of the most successful techniques for studying motions in proteins and macromolecules. It can provide information on the mechanism of protein functions, used to aid crystallography and NMR data reconstruction, and calculate protein free energies. Results ΔΔPT is a toolbox allowing calculation of elastic network models and principle component analysis. It allows the analysis of pdb files or trajectories taken from; Gromacs, Amber, and DL_POLY. As well as calculation of the normal modes it also allows comparison of the modes with experimental protein motion, variation of modes with mutation or ligand binding, and calculation of molecular dynamic entropies. Conclusions This toolbox makes the respective tools available to a wide community of potential NMA users, and allows them unrivalled ability to analyse normal modes using a variety of techniques and current software.
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46
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Hospital A, Faustino I, Collepardo-Guevara R, González C, Gelpí JL, Orozco M. NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res 2013; 41:W47-55. [PMID: 23685436 PMCID: PMC3692121 DOI: 10.1093/nar/gkt378] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server allows the user to incorporate structures from protein data banks, completing gaps and removing structural inconsistencies. It is also possible to define canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal libraries, as well to create specific nucleic acid conformations from the sequence. The server offers a variety of methods to explore nucleic acid flexibility, such as a colorless wormlike-chain model, a base-pair resolution mesoscopic model and atomistic molecular dynamics simulations with a wide variety of protocols and force fields. The trajectories obtained by simulations, or imported externally, can be visualized and analyzed using a large number of tools, including standard Cartesian analysis, essential dynamics, helical analysis, local and global stiffness, energy decomposition, principal components and in silico NMR spectra. The server is accessible free of charge from the mmb.irbbarcelona.org/NAFlex webpage.
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Affiliation(s)
- Adam Hospital
- Institute for Research in Biomedicine, Molecular Modelling and Bioinformatics Department, 08028, Barcelona, Spain
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47
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Hospital A, Gelpi JL. High-throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1142] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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48
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Cheng J, Karri S, Grauffel C, Wang F, Reuter N, Roberts MF, Wintrode PL, Gershenson A. Does changing the predicted dynamics of a phospholipase C alter activity and membrane binding? Biophys J 2013; 104:185-95. [PMID: 23332071 DOI: 10.1016/j.bpj.2012.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 11/02/2012] [Accepted: 11/19/2012] [Indexed: 12/11/2022] Open
Abstract
The enzymatic activity of secreted phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes is associated with bacterial virulence. Although the PI-PLC active site has no obvious lid, molecular-dynamics simulations suggest that correlated loop motions may limit access to the active site, and two Pro residues, Pro(245) and Pro(254), are associated with these correlated motions. Whereas the region containing both Pro residues is quite variable among PI-PLCs, it shows high conservation in virulence-associated, secreted PI-PLCs that bind to the surface of cells. These regions of the protein are also associated with phosphatidylcholine binding, which enhances PI-PLC activity. In silico mutagenesis of Pro(245) disrupts correlated motions between the two halves of Bacillus thuringiensis PI-PLC, and Pro(245) variants show significantly reduced enzymatic activity in all assay systems. PC still enhanced activity, but not to the level of wild-type enzyme. Mutagenesis of Pro(254) appears to stiffen the PI-PLC structure, but experimental mutations had minor effects on activity and membrane binding. With the exception of P245Y, reduced activity was not associated with reduced membrane affinity. This combination of simulations and experiments suggests that correlated motions between the two halves of PI-PLC may be more important for enzymatic activity than for vesicle binding.
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Affiliation(s)
- Jiongjia Cheng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
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49
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Micheletti C. Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments. Phys Life Rev 2012. [PMID: 23199577 DOI: 10.1016/j.plrev.2012.10.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an account of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure-function relationship.
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Affiliation(s)
- Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste, Italy.
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50
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Verma R, Schwaneberg U, Roccatano D. Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering. Comput Struct Biotechnol J 2012; 2:e201209008. [PMID: 24688649 PMCID: PMC3962222 DOI: 10.5936/csbj.201209008] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/07/2012] [Accepted: 10/12/2012] [Indexed: 12/01/2022] Open
Abstract
The combination of computational and directed evolution methods has proven a winning strategy for protein engineering. We refer to this approach as computer-aided protein directed evolution (CAPDE) and the review summarizes the recent developments in this rapidly growing field. We will restrict ourselves to overview the availability, usability and limitations of web servers, databases and other computational tools proposed in the last five years. The goal of this review is to provide concise information about currently available computational resources to assist the design of directed evolution based protein engineering experiment.
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Affiliation(s)
- Rajni Verma
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany ; Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Department of Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | - Danilo Roccatano
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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