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Mazurkiewicz J, Stanek E, Kolodziejczyk A, Karpiel M, Czamara K, Ferreira TH, Maximiano P, Simões PN, Reva I, Kalinowska-Tłuścik J, Kaczor A. Efficient delivery of carotenoids to adipocytes with albumin. Phys Chem Chem Phys 2024; 26:7865-7876. [PMID: 38376442 DOI: 10.1039/d3cp06075f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Carotenoids are very effectively delivered by albumin to adipocytes. The uptake of carotenoids to the cells occurs in the form of self-aggregates that localize in the vicinity of the adipocyte membrane, as shown by high spatial resolution Raman spectroscopy. The binding of carotenoids to albumin and the mechanism of their transport were elucidated with the help of chiroptical spectroscopies, in tandem with molecular docking and molecular dynamics simulations. In particular, apart from the recognized high affinity pocket of albumin that binds a carotenoid monomer in domain I, we have identified a hydrophobic periphery area in domain IIIB that loosely bounds the self-aggregated carotenoid in aqueous media and enables its easy detachment in hydrophobic environments. This explains the effectiveness of albumins as nanocarriers of carotenoids to adipocytes in vitro.
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Affiliation(s)
- Joanna Mazurkiewicz
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 11 Lojasiewicza Str., 30-348 Krakow, Poland
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Krakow, Poland.
| | - Ewa Stanek
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 11 Lojasiewicza Str., 30-348 Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego Str., 30-348 Krakow, Poland
| | - Aleksandra Kolodziejczyk
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 11 Lojasiewicza Str., 30-348 Krakow, Poland
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Krakow, Poland.
| | - Marta Karpiel
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 11 Lojasiewicza Str., 30-348 Krakow, Poland
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Krakow, Poland.
| | - Krzysztof Czamara
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego Str., 30-348 Krakow, Poland
| | - Tiago H Ferreira
- CERES, Department of Chemical Engineering, University of Coimbra, 3030-790 Coimbra, Portugal
| | - Pedro Maximiano
- CERES, Department of Chemical Engineering, University of Coimbra, 3030-790 Coimbra, Portugal
| | - Pedro N Simões
- CERES, Department of Chemical Engineering, University of Coimbra, 3030-790 Coimbra, Portugal
| | - Igor Reva
- CERES, Department of Chemical Engineering, University of Coimbra, 3030-790 Coimbra, Portugal
| | | | - Agnieszka Kaczor
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Krakow, Poland.
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2
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Wahhab BH, Oyewusi HA, Wahab RA, Mohammad Hood MH, Abdul Hamid AA, Al-Nimer MS, Edbeib MF, Kaya Y, Huyop F. Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey. J Biomol Struct Dyn 2024; 42:1429-1442. [PMID: 37038649 DOI: 10.1080/07391102.2023.2199870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 04/01/2023] [Indexed: 04/12/2023]
Abstract
This study presents the initial structural model of L-haloacid dehalogenase (DehLBHS1) from Bacillus megaterium BHS1, an alkalotolerant bacterium known for its ability to degrade halogenated environmental pollutants. The model provides insights into the structural features of DehLBHS1 and expands our understanding of the enzymatic mechanisms involved in the degradation of these hazardous pollutants. Key amino acid residues (Arg40, Phe59, Asn118, Asn176, and Trp178) in DehLBHS1 were identified to play critical roles in catalysis and molecular recognition of haloalkanoic acid, essential for efficient binding and transformation of haloalkanoic acid molecules. DehLBHS1 was modeled using I-TASSER, yielding a best TM-score of 0.986 and an RMSD of 0.53 Å. Validation of the model using PROCHECK revealed that 89.2% of the residues were located in the most favored region, providing confidence in its structural accuracy. Molecular docking simulations showed that the non-simulated DehLBHS1 preferred 2,2DCP over other substrates, forming one hydrogen bond with Arg40 and exhibiting a minimum energy of -2.5 kJ/mol. The simulated DehLBHS1 exhibited a minimum energy of -4.3 kJ/mol and formed four hydrogen bonds with Arg40, Asn176, Asp9, and Tyr11, further confirming the preference for 2,2DCP. Molecular dynamics simulations supported this preference, based on various metrics, including RMSD, RMSF, gyration, hydrogen bonding, and molecular distance. MM-PBSA calculations showed that the DehLBHS1-2,2-DCP complex had a markedly lower binding energy (-21.363 ± 1.26 kcal/mol) than the DehLBHS1-3CP complex (-14.327 ± 1.738 kcal/mol). This finding has important implications for the substrate specificity and catalytic function of DehLBHS1, particularly in the bioremediation of 2,2-DCP in contaminated alkaline environments. These results provide a detailed view of the molecular interactions between the enzyme and its substrate and may aid in the development of more efficient biocatalytic strategies for the degradation of halogenated compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Batool Hazim Wahhab
- Department of Microbiology, Faculty of Medicine, Al-Mustansiriyah University, Iraq
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Mohammad Hakim Mohammad Hood
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Marwan Salih Al-Nimer
- Department of Pharmacology, College of Medicine, University of Diyala, Baqubah, Iraq
| | - Mohamed Faraj Edbeib
- Department of Medical Laboratories, Faculty of Medical Technology, Bani Walid University, Libya
| | - Yilmaz Kaya
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
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Zahirul Kabir M, Tayyab H, Erkmen C, Kurbanoglu S, Mohamad SB, Uslu B. Characterization of Climbazole-Bovine serum albumin interaction by experimental and in silico approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 288:122197. [PMID: 36470090 DOI: 10.1016/j.saa.2022.122197] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Interactive association of an antifungal drug, climbazole (CBZ) with the carrier protein in bovine circulation, bovine serum albumin (BSA) was explored by fluorescence and absorption spectroscopy along with in silico techniques. The fluorescence and absorption spectral alterations of the protein upon addition of CBZ affirmed the complex foration between CBZ and BSA. The inverse temperature dependence behaviour of the KSV values as well as the hyperchromic result of the protein's absorption signals characterized CBZ-triggered quenching of BSA fluorescence as the static quenching. A weak binding affinity (Ka = 3.12-1.90-× 103 M-1) was reported towards the CBZ-BSA association process. Interpretation of thermodynamic data (entropy change = +14.68 J mol-1 K-1 and enthalpy change = -15.07 kJ mol-1) and in silico analyses anticipated that hydrophobic forces, van der Waals forces and hydrogen bonds were the key intermolecular forces in the complex stabilization. Inclusion of CBZ to BSA produced microenvironmental perturbations around Tyr and Trp residues, and also significantly defended temperature-induced destabilization of BSA. The binding locus of CBZ was detected in the proximity of Sudlow's sites I (subdomain IIA) and II (subdomain IIIA) of BSA, exhibiting greater preference towards site II, as revealed by competitive site-marker displacement investigations and in silico analysis. The stability of the CBZ-BSA complex was further validated by the molecular dynamics simulation assessments.
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Affiliation(s)
- Md Zahirul Kabir
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560, Ankara, Turkey
| | - Hafsa Tayyab
- Faculty of Science, Bioinformatics Programme, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Cem Erkmen
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560, Ankara, Turkey; Ankara University, The Graduate School of Health Sciences, 06110, Ankara, Turkey
| | - Sevinc Kurbanoglu
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560, Ankara, Turkey
| | - Saharuddin B Mohamad
- Faculty of Science, Bioinformatics Programme, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia; Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare, University of Malaya, Kuala Lumpur, Malaysia
| | - Bengi Uslu
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560, Ankara, Turkey.
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4
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Li H, Gong W. Study of Allosteric Transitions of Human P-Glycoprotein by Using the Two-State Anisotropic Network Model. Front Med (Lausanne) 2022; 9:815355. [PMID: 35223913 PMCID: PMC8863969 DOI: 10.3389/fmed.2022.815355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/04/2022] [Indexed: 11/25/2022] Open
Abstract
Human P-glycoprotein (P-gp) is a kind of ATP-binding cassette (ABC) transporters. Once human P-gp is overexpressed in tumor cells, which can lead to tumor multidrug resistance (MDR). However, the present experimental methods are difficult to obtain the large-scale conformational transition process of human P-gp. In this work, we explored the allosteric pathway of human P-gp from the inward-facing (IF) to the outward-facing (OF) state in the substrate transport process with the two-state anisotropic network model (tANM). These results suggest that the allosteric transitions proceed in a coupled way. The conformational changes of nucleotide-binding domains (NBDs) finally make the transmembrane domains (TMDs) to the OF state via the role of the allosteric propagation of the intracellular helices IH1 and IH2. Additionally, this allosteric pathway is advantageous in energy compared with other methods. This study reveals the conformational transition of P-gp, which contributes to an understanding of the allosteric mechanism of ABC exporters.
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Affiliation(s)
- Hongwu Li
- School of Mathematics and Statistics, Nanyang Normal University, Nanyang, China
| | - Weikang Gong
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
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5
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Mohammad A, Abubaker J, Al-Mulla F. Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Virus Res 2021; 303:198522. [PMID: 34314772 PMCID: PMC8310422 DOI: 10.1016/j.virusres.2021.198522] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 12/18/2022]
Abstract
The B.1.1.7 SARS-CoV-2 strain that has emerged in the UK in early December presents seven mutations and three deletions on S-protein structure that could lead to a more infective strain. The P681H mutation in the “PRRAR” furin cleavage site might affect the binding affinity to furin enzyme and hence its infectivity. Therefore, in this study, various structural bioinformatics approaches were used to model the S-protein structure with the B.1.1.7 variant amino acid substitutions and deletions. In addition to modelling the binding of furin to the cleavage site of the wild-type and the B.1.1.7 variant. Conclusively the B.1.1.7 variant resulted in dynamic stability, conformational changes and variations in binding energies in the S-protein structure, resulting in a more favourable binding of furin enzyme to the SARS-CoV-2 S-protein.
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Affiliation(s)
- Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait
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6
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Shmool TA, Martin LK, Bui-Le L, Moya-Ramirez I, Kotidis P, Matthews RP, Venter GA, Kontoravdi C, Polizzi KM, Hallett JP. An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid. Chem Sci 2021; 12:9528-9545. [PMID: 34349928 PMCID: PMC8278930 DOI: 10.1039/d1sc02520a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/26/2021] [Indexed: 12/26/2022] Open
Abstract
Understanding protein folding in different environmental conditions is fundamentally important for predicting protein structures and developing innovative antibody formulations. While the thermodynamics and kinetics of folding and unfolding have been extensively studied by computational methods, experimental methods for determining antibody conformational transition pathways are lacking. Motivated to fill this gap, we prepared a series of unique formulations containing a high concentration of a chimeric immunoglobin G4 (IgG4) antibody with different excipients in the presence and absence of the ionic liquid (IL) choline dihydrogen phosphate. We determined the effects of different excipients and IL on protein thermal and structural stability by performing variable temperature circular dichroism and bio-layer interferometry analyses. To further rationalise the observations of conformational changes with temperature, we carried out molecular dynamics simulations on a single antibody binding fragment from IgG4 in the different formulations, at low and high temperatures. We developed a methodology to study the conformational transitions and associated thermodynamics of biomolecules, and we showed IL-induced conformational transitions. We showed that the increased propensity for conformational change was driven by preferential binding of the dihydrogen phosphate anion to the antibody fragment. Finally, we found that a formulation containing IL with sugar, amino acids and surfactant is a promising candidate for stabilising proteins against conformational destabilisation and aggregation. We hope that ultimately, we can help in the quest to understand the molecular basis of the stability of antibodies and protein misfolding phenomena and offer new candidate formulations with the potential to revive lost therapeutic candidates.
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Affiliation(s)
- Talia A Shmool
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Laura K Martin
- Department of Engineering Science, University of Oxford Parks Road Oxford OX1 3PJ UK
| | - Liem Bui-Le
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Ignacio Moya-Ramirez
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Pavlos Kotidis
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Richard P Matthews
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Gerhard A Venter
- Scientific Computing Research Unit, Department of Chemistry, University of Cape Town Rondebosch Cape Town 7701 South Africa
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Karen M Polizzi
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Jason P Hallett
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
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Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci 2021; 7:607323. [PMID: 33614705 PMCID: PMC7886686 DOI: 10.3389/fmolb.2020.607323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022] Open
Abstract
Two new computational approaches are described to aid in the design of new peptide-based drugs by evaluating ensembles of protein structures from their dynamics and through the assessing of structures using empirical contact potential. These approaches build on the concept that conformational variability can aid in the binding process and, for disordered proteins, can even facilitate the binding of more diverse ligands. This latter consideration indicates that such a design process should be less restrictive so that multiple inhibitors might be effective. The example chosen here focuses on proteins/peptides that bind to hemagglutinin (HA) to block the large-scale conformational change for activation. Variability in the conformations is considered from sets of experimental structures, or as an alternative, from their simple computed dynamics; the set of designe peptides/small proteins from the David Baker lab designed to bind to hemagglutinin, is the large set considered and is assessed with the new empirical contact potentials.
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Affiliation(s)
- Robert L. Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Kannan Sankar
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Kejue Jia
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Eshel Faraggi
- Research and Information Systems, LLC, Indianapolis, IN, United States
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, IN, United States
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
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8
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Shahzadi Z, Abbas G, Azam SS. Relational dynamics obtained through simulation studies of thioredoxin reductase: From a multi-drug resistant Entamoeba histolytica. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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9
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Exploring Evolutionary Constraints in the Proteomes of Zika, Dengue, and Other Flaviviruses to Find Fitness-Critical Sites. J Mol Evol 2020; 88:399-414. [DOI: 10.1007/s00239-020-09941-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/24/2020] [Indexed: 12/16/2022]
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10
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Halder R, Jana B. Exploring and Engineering the Conformational Landscape of Calmodulin through Specific Interactions. J Phys Chem B 2019; 123:9321-9327. [DOI: 10.1021/acs.jpcb.9b06343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ritaban Halder
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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11
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Li D, Ji B. Protein conformational transitions coupling with ligand interactions: Simulations from molecules to medicine. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2019. [DOI: 10.1016/j.medntd.2019.100026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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12
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Pena CE, Costa MGS, Batista PR. Glycosylation effects on the structure and dynamics of a full-length Cel7A cellulase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140248. [PMID: 31279935 DOI: 10.1016/j.bbapap.2019.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 11/17/2022]
Abstract
Fungi cellulases are used to degrade cellulose-containing biomass for bioethanol production. Industrial cellulases such as Cel7A from Trichoderma reesei (TrCel7A) are critical in this process. Thus, the understanding of structure and dynamics is crucial for engineering variants with improved cellulolytic activity. This cellulase consists of two domains connected by a flexible and highly glycosylated linker. However, the linker flexibility has hindered the determination of Cel7A complete structure. Herein, based on atomic and sparse data, we applied integrative modelling to build a model of the complete enzyme structure. Next, through simulations, we studied the glycosylation effects on the structure and dynamics of a solubilized TrCel7A. Essential dynamics analysis showed that O-glycosylation in the linker led to the stabilization of protein overall dynamics. O-linked glycans seem to restrict protein dihedral angles distribution in this region, selecting more elongated conformations. Besides the reduced flexibility, functional interdomain motions occurred in a more concerted way in the glycosylated system. In contrast, in the absence of glycosylation, we observed vast conformational plasticity with the functional domains frequently collapsing. We report here evidence that targeting Cel7A linker flexibility by point mutations including modification of glycosylation sites could be a promising design strategy to improve cellulase activity.
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Affiliation(s)
- Carlos Eduardo Pena
- Fundação Oswaldo Cruz, Programa de Computação Científica, Rio de Janeiro 21040-900, Brazil; Instituto Oswaldo Cruz, Programa de Pós-graduação em Biologia Computacional e Sistemas, Rio de Janeiro 21040-900, Brazil
| | - Mauricio G S Costa
- Fundação Oswaldo Cruz, Programa de Computação Científica, Rio de Janeiro 21040-900, Brazil; Instituto Oswaldo Cruz, Programa de Pós-graduação em Biologia Computacional e Sistemas, Rio de Janeiro 21040-900, Brazil; École Normale Supérieure Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée, Cachan 94235, France
| | - Paulo Ricardo Batista
- Fundação Oswaldo Cruz, Programa de Computação Científica, Rio de Janeiro 21040-900, Brazil; Instituto Oswaldo Cruz, Programa de Pós-graduação em Biologia Computacional e Sistemas, Rio de Janeiro 21040-900, Brazil.
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13
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Land H, Campillo‐Brocal JC, Svedendahl Humble M, Berglund P. B-factor Guided Proline Substitutions in Chromobacterium violaceum Amine Transaminase: Evaluation of the Proline Rule as a Method for Enzyme Stabilization. Chembiochem 2019; 20:1297-1304. [PMID: 30637901 PMCID: PMC6593452 DOI: 10.1002/cbic.201800749] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/02/2022]
Abstract
Biocatalysis is attracting interest in the chemical industry as a sustainable alternative in large-scale chemical transformations. However, low operational stability of naturally evolved enzymes is a challenge and major efforts are required to engineer protein stability, usually by directed evolution. The development of methods for protein stabilization based on rational design is of great interest, as it would minimize the efforts needed to generate stable enzymes. Here we present a rational design strategy based on proline substitutions in flexible areas of the protein identified by analyzing B-factors. Several proline substitutions in the amine transaminase from Chromobacterium violaceum were shown to have a positive impact on stability with increased half-life at 60 °C by a factor of 2.7 (variant K69P/D218P/K304P/R432P) as well as increased melting temperature by 8.3 °C (variant K167P). Finally, the presented method utilizing B-factor analysis in combination with the proline rule was deemed successful at increasing the stability of this enzyme.
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Affiliation(s)
- Henrik Land
- KTH Royal Institute of TechnologySchool of Engineering Sciences in ChemistryBiotechnology and Health (CBH)Department of Industrial BiotechnologyAlbaNova University Center106 91StockholmSweden
- Uppsala UniversityDepartment of Chemistry–Ångström LaboratoryMolecular BiomimeticsBox 523751 20UppsalaSweden
| | - Jonatan C. Campillo‐Brocal
- KTH Royal Institute of TechnologySchool of Engineering Sciences in ChemistryBiotechnology and Health (CBH)Department of Industrial BiotechnologyAlbaNova University Center106 91StockholmSweden
| | | | - Per Berglund
- KTH Royal Institute of TechnologySchool of Engineering Sciences in ChemistryBiotechnology and Health (CBH)Department of Industrial BiotechnologyAlbaNova University Center106 91StockholmSweden
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14
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Substrate binding versus escape dynamics in a pH-affected fungal beta-glucosidase revealed by molecular dynamics simulations. Carbohydr Res 2019; 472:127-131. [PMID: 30579119 DOI: 10.1016/j.carres.2018.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 11/26/2018] [Accepted: 12/08/2018] [Indexed: 11/22/2022]
Abstract
The cellulolytic ability of fungal species is important to both natural and engineered biocycling of plant matter. One essential step is the conversion of cellobiose into glucose catalyzed by beta-glucosidases. Mutagenesis studies have implicated altering the substrate binding pocket to influence the pH-activity profile of this enzyme. However, structural understanding of the pH-affected substrate binding environment is lacking. Here we conducted molecular dynamics simulations of fully hydrated TrBgl2, a beta-glucosidase of Trichoderma reesei, equilibrated at its optimal pH (pH 6) and two unfavorable pHs (pH 5 and pH 7.5). We identified structural arrangement of specific residues that facilitated substrate escape from the catalytic site at pH 5 but locked the bound substrate in an unfavorable orientation at pH 7.5. For comparative analysis, we also performed simulations of a mutated TrBgl2 with previously demonstrated improved catalysis as a function of pH. We captured the responsible conformational changes in the engineered substrate binding pocket.
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15
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Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci 2018; 19:ijms19113496. [PMID: 30404229 PMCID: PMC6274762 DOI: 10.3390/ijms19113496] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022] Open
Abstract
Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this minireview, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions, and highly simplified structure-based elastic network models of protein flexibility. In contrast to classical all-atom molecular dynamics, the modeling strategies discussed here allow the quite accurate modeling of much larger systems and longer-time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.
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Insulin adsorption onto zinc oxide nanoparticle mediates conformational rearrangement into amyloid-prone structure with enhanced cytotoxic propensity. Biochim Biophys Acta Gen Subj 2018; 1863:153-166. [PMID: 30315849 DOI: 10.1016/j.bbagen.2018.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 09/02/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Injection localized amyloidosis is one of the most prevalent disorders in type II diabetes mellitus (TIIDM) patients relying on insulin injections. Previous studies have reported that nanoparticles can play a role in the amyloidogenic process of proteins. Hence, the present study deals with the effect of zinc oxide nanoparticles (ZnONP) on the amyloidogenicity and cytotoxicity of insulin. METHODS ZnONP is synthesised and characterized using XRD, Zeta Sizer, UV-Visible spectroscope and TEM. The characterization is followed by ZnONP interaction with insulin, which is studied employing fluorescence spectroscopes, isothermal titration calorimetry and molecular dynamics simulations. The interaction leads insulin conformational rearrangement into amyloid-like fibril, which is studied using thioflavin T dye binding assay, circular dichroism spectroscopy and TEM, followed by cytotoxicity propensity using Alamar Blue dye reduction assay. RESULTS Insulin has very weak interaction with ZnONP interface. Insulin at studied concentration forms amorphous aggregates at physiological pH, whereas in presence of ZnONP interface amyloid-like fibrils are formed. While the amyloid-like fibrils are cytotoxic to MIN6 and THP-1 cell lines, insulin and ZnONP individual solutions and their fresh mixtures enhance the cells proliferation. CONCLUSIONS The presence of ZnONP interface enhances insulin fibrillation at physiological pH by providing a favourable template for the nucleation and growth of insulin amyloids. GENERAL SIGNIFICANCE The studied protein-nanoparticle system from protein conformational dynamics point of view throws caution over nanoparticle use in biological applications, especially in vivo applications, considering the amyloidosis a very slow but non-curable degenerative disease.
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Yamasaki K, Nishi K, Anraku M, Taguchi K, Maruyama T, Otagiri M. Metal-catalyzed oxidation of human serum albumin does not alter the interactive binding to the two principal drug binding sites. Biochem Biophys Rep 2018; 14:155-160. [PMID: 29872747 PMCID: PMC5986994 DOI: 10.1016/j.bbrep.2018.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/12/2018] [Accepted: 05/06/2018] [Indexed: 12/20/2022] Open
Abstract
It is well known that various physiological factors such as pH, endogenous substances or post-translational modifications can affect the conformational state of human serum albumin (HSA). In a previous study, we reported that both pH- and long chain fatty acid-induced conformational changes can alter the interactive binding of ligands to the two principal binding sites of HSA, namely, site I and site II. In the present study, the effect of metal-catalyzed oxidation (MCO) caused by ascorbate/oxygen/trace metals on HSA structure and the interactive binding between dansyl-L-asparagine (DNSA; a site I ligand) and ibuprofen (a site II ligand) at pH 6.5 was investigated. MCO was accompanied by a time-dependent increase in carbonyl content in HSA, suggesting that the HSA was being oxidized. In addition, The MCO of HSA was accompanied by a change in net charge to a more negative charge and a decrease in thermal stability. SDS-PAGE patterns and α-helical contents of the oxidized HSAs were similar to those of native HSA, indicating that the HSA had not been extensively structurally modified by MCO. MCO also caused a selective decrease in ibuprofen binding. In spite of the changes in the HSA structure and ligand that bind to site II, no change in the interactive binding between DNSA and ibuprofen was observed. These data indicated that amino acid residues in site II are preferentially oxidized by MCO, whereas the spatial relationship between sites I and II (e.g. the distance between sites), the flexibility or space of each binding site are not altered. The present findings provide insights into the structural characteristics of oxidized HSA, and drug binding and drug-drug interactions on oxidized HSA.
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Affiliation(s)
- Keishi Yamasaki
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
- DDS Research Institute, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Koji Nishi
- Department of Clinical Medicine, Yokohama University of Pharmacy, 601 Matano-cho, Totsuka-ku, Yokohama 245-0066, Japan
| | - Makoto Anraku
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
- DDS Research Institute, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Kazuaki Taguchi
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Toru Maruyama
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5–1 Oe-honmachi, Kumamoto 862-0973, Japan
| | - Masaki Otagiri
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
- DDS Research Institute, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
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Fanning SW, Hodges-Gallagher L, Myles DC, Sun R, Fowler CE, Plant IN, Green BD, Harmon CL, Greene GL, Kushner PJ. Specific stereochemistry of OP-1074 disrupts estrogen receptor alpha helix 12 and confers pure antiestrogenic activity. Nat Commun 2018; 9:2368. [PMID: 29915250 PMCID: PMC6006285 DOI: 10.1038/s41467-018-04413-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 04/27/2018] [Indexed: 11/09/2022] Open
Abstract
Complex tissue-specific and cell-specific signaling by the estrogen receptor (ER) frequently leads to the development of resistance to endocrine therapy for breast cancer. Pure ER antagonists, which completely lack tissue-specific agonist activity, hold promise for preventing and treating endocrine resistance, however an absence of structural information hinders the development of novel candidates. Here we synthesize a small panel of benzopyrans with variable side chains to identify pure antiestrogens in a uterotrophic assay. We identify OP-1074 as a pure antiestrogen and a selective ER degrader (PA-SERD) that is efficacious in shrinking tumors in a tamoxifen-resistant xenograft model. Biochemical and crystal structure analyses reveal a structure activity relationship implicating the importance of a stereospecific methyl on the pyrrolidine side chain of OP-1074, particularly on helix 12. Estrogen receptor alpha (ERα) plays critical roles in the etiology and treatment of breast cancer. Here the authors synthesize benzopyrans with variable side chains to identify antiestrogenic compounds and characterize OP-1074, a compound that exhibits pure antiestrogenic activity by inducing the degradation of ERα and possesses greater potency than tamoxifen or fulvestrant in a xenograft model.
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Affiliation(s)
- S W Fanning
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA.
| | | | - D C Myles
- Olema Pharmaceuticals, San Francisco, CA, 94107, USA
| | - R Sun
- Olema Pharmaceuticals, San Francisco, CA, 94107, USA
| | - C E Fowler
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA
| | - I N Plant
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - B D Green
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA
| | - C L Harmon
- Olema Pharmaceuticals, San Francisco, CA, 94107, USA
| | - G L Greene
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA
| | - P J Kushner
- Olema Pharmaceuticals, San Francisco, CA, 94107, USA
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19
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Pandey B, Grover S, Goyal S, Kumari A, Singh A, Jamal S, Kaur J, Grover A. Alanine mutation of the catalytic sites of Pantothenate Synthetase causes distinct conformational changes in the ATP binding region. Sci Rep 2018; 8:903. [PMID: 29343701 PMCID: PMC5772511 DOI: 10.1038/s41598-017-19075-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/19/2017] [Indexed: 02/01/2023] Open
Abstract
The enzyme Pantothenate synthetase (PS) represents a potential drug target in Mycobacterium tuberculosis. Its X-ray crystallographic structure has demonstrated the significance and importance of conserved active site residues including His44, His47, Asn69, Gln72, Lys160 and Gln164 in substrate binding and formation of pantoyl adenylate intermediate. In the current study, molecular mechanism of decreased affinity of the enzyme for ATP caused by alanine mutations was investigated using molecular dynamics (MD) simulations and free energy calculations. A total of seven systems including wild-type + ATP, H44A + ATP, H47A + ATP, N69A + ATP, Q72A + ATP, K160A + ATP and Q164A + ATP were subjected to 50 ns MD simulations. Docking score, MM-GBSA and interaction profile analysis showed weak interactions between ATP (substrate) and PS (enzyme) in H47A and H160A mutants as compared to wild-type, leading to reduced protein catalytic activity. However, principal component analysis (PCA) and free energy landscape (FEL) analysis revealed that ATP was strongly bound to the catalytic core of the wild-type, limiting its movement to form a stable complex as compared to mutants. The study will give insight about ATP binding to the PS at the atomic level and will facilitate in designing of non-reactive analogue of pantoyl adenylate which will act as a specific inhibitor for PS.
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Affiliation(s)
- Bharati Pandey
- Department of Biotechnology, Panjab University, Chandigarh, 160014, India
| | - Sonam Grover
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, 304022, India
| | - Anchala Kumari
- Department of Biotechnology, TERI University, VasantKunj, New Delhi, 110070, India
| | - Aditi Singh
- Department of Biotechnology, TERI University, VasantKunj, New Delhi, 110070, India
| | - Salma Jamal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, 304022, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, 160014, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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Kist R, Timmers LFSM, Caceres RA. Searching for potential mTOR inhibitors: Ligand-based drug design, docking and molecular dynamics studies of rapamycin binding site. J Mol Graph Model 2017; 80:251-263. [PMID: 29414044 DOI: 10.1016/j.jmgm.2017.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/19/2017] [Accepted: 12/21/2017] [Indexed: 12/17/2022]
Abstract
The PI3K/Akt/mTOR pathway is an important intracellular signaling pathway in cell cycle regulation and its dysregulation is associated with various types of diseases. mTOR (mechanistic or mammalian target of rapamycin) is the main enzyme that performs intermediate control of the signaling pathway through a phosphotransfer process. The classical inhibition of the mTOR pathway is effected by rapamycin and its analogous blocking allosterically the catalytic phosphorylation site, avoiding the deleterious side effects induced by ATP-competitive inhibitors. We employed ligand-based drug design strategies such as pharmacophore searching and analysis, molecular docking, absorption, distribution, metabolism, excretion and toxicity (ADMETox) properties filtering, and molecular dynamics to select potential molecules to become non-ATP competitive inhibitors of the mTOR complex. According to our findings, we propose eight novel potential mTOR inhibitors with similar or better properties than the classic inhibitor complex, rapamycin.
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Affiliation(s)
- Roger Kist
- Graduate Program in Health Sciences of Federal University of Health Sciences of Porto Alegre-UFCSPA, Porto Alegre City, Brazil
| | - Luis Fernando Saraiva Macedo Timmers
- Laboratory for Bioinformatics, Modelling and Simulation of Biosystems-LABIO, Pontifical Catholic University of Rio Grande do Sul-PUCRS, Porto Alegre City, Brazil; Graduate Program in Cellular and Molecular Biology (PPGBCM), PUCRS, Porto Alegre, RS, Brazil
| | - Rafael Andrade Caceres
- Graduate Program in Health Sciences of Federal University of Health Sciences of Porto Alegre-UFCSPA, Porto Alegre City, Brazil; Pharmacosciences Department of Federal University of Health Sciences of Porto Alegre-UFCSPA, Porto Alegre City, Brazil.
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21
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Dong Z, Zhou H, Tao P. Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily. Protein Sci 2017; 27:421-430. [PMID: 29052279 DOI: 10.1002/pro.3329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/10/2017] [Accepted: 10/15/2017] [Indexed: 11/11/2022]
Abstract
PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics.
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Affiliation(s)
- Zheng Dong
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, Texas, 75275
| | - Hongyu Zhou
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, Texas, 75275
| | - Peng Tao
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, Texas, 75275
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22
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Abstract
We present a new conceptually simple and computationally efficient method for nonlinear normal-mode analysis called NOLB. It relies on the rotations-translations of blocks (RTB) theoretical basis developed by Y.-H. Sanejouand and colleagues [ Durand et al. Biopolymers 1994 , 34 , 759 - 771 . Tama et al. Proteins: Struct., Funct., Bioinf . 2000 , 41 , 1 - 7 ]. We demonstrate how to physically interpret the eigenvalues computed in the RTB basis in terms of angular and linear velocities applied to the rigid blocks and how to construct a nonlinear extrapolation of motion out of these velocities. The key observation of our method is that the angular velocity of a rigid block can be interpreted as the result of an implicit force, such that the motion of the rigid block can be considered as a pure rotation about a certain center. We demonstrate the motions produced with the NOLB method on three different molecular systems and show that some of the lowest frequency normal modes correspond to the biologically relevant motions. For example, NOLB detects the spiral sliding motion of the TALE protein, which is capable of rapid diffusion along its target DNA. Overall, our method produces better structures compared to the standard approach, especially at large deformation amplitudes, as we demonstrate by visual inspection, energy, and topology analyses and also by the MolProbity service validation. Finally, our method is scalable and can be applied to very large molecular systems, such as ribosomes. Standalone executables of the NOLB normal-mode analysis method are available at https://team.inria.fr/nano-d/software/nolb-normal-modes/ . A graphical user interface created for the SAMSON software platform will be made available at https://www.samson-connect.net .
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Knowledge-based entropies improve the identification of native protein structures. Proc Natl Acad Sci U S A 2017; 114:2928-2933. [PMID: 28265078 DOI: 10.1073/pnas.1613331114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Evaluating protein structures requires reliable free energies with good estimates of both potential energies and entropies. Although there are many demonstrated successes from using knowledge-based potential energies, computing entropies of proteins has lagged far behind. Here we take an entirely different approach and evaluate knowledge-based conformational entropies of proteins based on the observed frequencies of contact changes between amino acids in a set of 167 diverse proteins, each of which has two alternative structures. The results show that charged and polar interactions break more often than hydrophobic pairs. This pattern correlates strongly with the average solvent exposure of amino acids in globular proteins, as well as with polarity indices and the sizes of the amino acids. Knowledge-based entropies are derived by using the inverse Boltzmann relationship, in a manner analogous to the way that knowledge-based potentials have been extracted. Including these new knowledge-based entropies almost doubles the performance of knowledge-based potentials in selecting the native protein structures from decoy sets. Beyond the overall energy-entropy compensation, a similar compensation is seen for individual pairs of interacting amino acids. The entropies in this report have immediate applications for 3D structure prediction, protein model assessment, and protein engineering and design.
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24
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Kist R, Caceres RA. New potential inhibitors of mTOR: a computational investigation integrating molecular docking, virtual screening and molecular dynamics simulation. J Biomol Struct Dyn 2016; 35:3555-3568. [PMID: 27860549 DOI: 10.1080/07391102.2016.1262279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The mTOR (mammalian or mechanistic Target Of Rapamycin), a complex metabolic pathway that involves multiple steps and regulators, is a major human metabolic pathway responsible for cell growth control in response to multiple factors and that is dysregulated in various types of cancer. The classical inhibition of the mTOR pathway is performed by rapamycin and its analogs (rapalogs). Considering that rapamycin binds to an allosteric site and performs a crucial role in the inhibition of the mTOR complex without causing the deleterious side effects common to ATP-competitive inhibitors, we employ ligand-based drug design strategies, such as virtual screening methodology, computational determination of ADME/Tox properties of selected molecules, and molecular dynamics in order to select molecules with the potential to become non-ATP-competitive inhibitors of the mTOR enzymatic complex. Our findings suggest five novel potential mTOR inhibitors, with similar or better properties than the classic inhibitor complex, rapamycin.
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Affiliation(s)
- Roger Kist
- a Health Sciences Postgraduate Program of Federal University of Health Sciences of Porto Alegre - UFCSPA , Porto Alegre City , Brazil
| | - Rafael Andrade Caceres
- a Health Sciences Postgraduate Program of Federal University of Health Sciences of Porto Alegre - UFCSPA , Porto Alegre City , Brazil.,b Pharmacosciences Department of Federal University of Health Sciences of Porto Alegre - UFCSPA , Porto Alegre City , Brazil
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25
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Saravanan KM, Senthil R. PreFRP: Prediction and visualization of fluctuation residues in proteins. J Nat Sci Biol Med 2016; 7:124-6. [PMID: 27433060 PMCID: PMC4934099 DOI: 10.4103/0976-9668.184696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aim: The PreFRP web server extracts sequence and basic information of a protein structure and groups amino acid residues in a protein into three important types such as high, moderate, and weak fluctuating residues. Materials and Methods: The server takes a protein data bank file or an amino acid sequence as input and prints the probability of amino acid residues to fluctuate. The server also provides a link to Jmol, a molecular visualization program to visualize the high, moderate, and weak fluctuating residues in three different colors. Results: Prediction and visualization of fluctuating amino acid residues in proteins may help to understand the complex three-dimensional structure of proteins and may further help in docking and mutation experiments. Availability: The web server is freely accessible through the web page of the author's institution http://www.mpi.edu.in/prefrp/link.html.
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Affiliation(s)
- Konda Mani Saravanan
- Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Renganathan Senthil
- Department of Bioinformatics, School of Biosciences, The Marudupandiyar Institutions (Affiliated to Bharathidasan University), Thanjavur, Tamil Nadu, India
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26
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Ruvinsky AM, Vakser IA, Rivera M. Local packing modulates diversity of iron pathways and cooperative behavior in eukaryotic and prokaryotic ferritins. J Chem Phys 2014; 140:115104. [PMID: 24655206 DOI: 10.1063/1.4868229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ferritin-like molecules show a remarkable combination of the evolutionary conserved activity of iron uptake and release that engage different pores in the conserved ferritin shell. It was hypothesized that pore selection and iron traffic depend on dynamic allostery with no conformational changes in the backbone. In this study, we detect the allosteric networks in Pseudomonas aeruginosa bacterioferritin (BfrB), bacterial ferritin (FtnA), and bullfrog M and L ferritins (Ftns) by a network-weaving algorithm (NWA) that passes threads of an allosteric network through highly correlated residues using hierarchical clustering. The residue-residue correlations are calculated in the packing-on elastic network model that introduces atom packing into the common packing-off model. Applying NWA revealed that each of the molecules has an extended allosteric network mostly buried inside the ferritin shell. The structure of the networks is consistent with experimental observations of iron transport: The allosteric networks in BfrB and FtnA connect the ferroxidase center with the 4-fold pores and B-pores, leaving the 3-fold pores unengaged. In contrast, the allosteric network directly links the 3-fold pores with the 4-fold pores in M and L Ftns. The majority of the network residues are either on the inner surface or buried inside the subunit fold or at the subunit interfaces. We hypothesize that the ferritin structures evolved in a way to limit the influence of functionally unrelated events in the cytoplasm on the allosteric network to maintain stability of the translocation mechanisms. We showed that the residue-residue correlations and the resultant long-range cooperativity depend on the ferritin shell packing, which, in turn, depends on protein sequence composition. Switching from the packing-on to the packing-off model reduces correlations by 35%-38% so that no allosteric network can be found. The influence of the side-chain packing on the allosteric networks explains the diversity in mechanisms of iron traffic suggested by experimental approaches.
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Affiliation(s)
- Anatoly M Ruvinsky
- Infection Innovative Medicine, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Ilya A Vakser
- Center for Bioinformatics, The University of Kansas, Lawrence, Kansas 66047, USA
| | - Mario Rivera
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
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Balendiran GK, Pandian JR, Drake E, Vinayak A, Verma M, Cascio D. B-factor Analysis and Conformational Rearrangement of Aldose Reductase. CURR PROTEOMICS 2014; 11:151-160. [PMID: 25364319 DOI: 10.2174/157016461103140922163444] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The NADPH-dependent reduction of glucose reaction that is catalyzed by Aldose Reductase (AR) follows a sequential ordered kinetic mechanism in which the co-factor NADPH binds to the enzyme prior to the aldehyde substrate. The kinetic/structural experiments have found a conformational change involving a hinge-like movement of a surface loop (residues 213-224) which is anticipated to take place upon the binding of the diphosphate moiety of NADPH. The reorientation of this loop, expected to permit the release of NADP+, represents the rate-limiting step of the catalytic mechanism. This study reveals: 1) The Translation/Libration/Screw (TLS) analysis of absolute B-factors of apo AR crystal structures indicates that the 212-224 loop might move as a rigid group. 2) Residues that make the flexible loop slide in the AR binary and ternary complexes. 3) The normalized B-factors separate this segment into three different clusters with fewer residues.
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Affiliation(s)
- Ganesaratnam K Balendiran
- Department of Chemistry, WBSH 6017, Youngstown State University, One University Plaza, Youngstown, OH 44555
| | - J Rajendran Pandian
- Department of Business Administration, College of Business Administration, Gulf University for Science and Technology, Mubarak Al-Abdullah Area/West Mishref, Kuwait
| | - Evin Drake
- Department of Chemistry, WBSH 6017, Youngstown State University, One University Plaza, Youngstown, OH 44555
| | - Anubhav Vinayak
- Department of Chemistry, WBSH 6017, Youngstown State University, One University Plaza, Youngstown, OH 44555
| | - Malkhey Verma
- Manchester Institute of Biotechnology, 131 Princess Street, The University of Manchester, Manchester, M1 7DN, UK
| | - Duilio Cascio
- UCLA-DOE, 611 Charles E. Young Drive East, 220 Boyer Hall, Los Angeles, CA 90095, USA
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28
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Gaspar ME, Csermely P. Rigidity and flexibility of biological networks. Brief Funct Genomics 2012; 11:443-56. [DOI: 10.1093/bfgp/els023] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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