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Oduro-Kwateng E, Ali M, Kehinde IO, Zhang Z, Soliman MES. De Novo Rational Design of Peptide-Based Protein-Protein Inhibitors (Pep-PPIs) Approach by Mapping the Interaction Motifs of the PP Interface and Physicochemical Filtration: A Case on p25-Cdk5-Mediated Neurodegenerative Diseases. J Cell Biochem 2024:e30633. [PMID: 39148280 DOI: 10.1002/jcb.30633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/10/2024] [Accepted: 07/18/2024] [Indexed: 08/17/2024]
Abstract
Protein-protein interactions, or PPIs, are a part of every biological activity and have been linked to a number of diseases, including cancer, infectious diseases, and neurological disorders. As such, targeting PPIs is considered a strategic and vital approach in the development of new medications. Nonetheless, the wide and flat contact interface makes it difficult to find small-molecule PP inhibitors. An alternative strategy would be to use the PPI interaction motifs as building blocks for the design of peptide-based inhibitors. Herein, we designed 12-mer peptide inhibitors to target p25-inducing-cyclin-dependent kinase (Cdk5) hyperregulation, a PPI that has been shown to perpetuate neuroinflammation, which is one of the major causal implications of neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and frontotemporal dementia. We generated a library of 5 062 500 peptide combination sequences (PCS) derived from the interaction motif of Cdk5/p25 PP interface. The 20 amino acids were differentiated into six groups, namely, hydrophobic (aliphatic), aromatic, basic, acidic, unique, and polar uncharged, on the basis of their physiochemical properties. To preserve the interaction motif necessary for ideal binding, de novo modeling of all possible peptide sequence substitutions was considered. A set of filters, backed by the Support Vector Machine (SVM) algorithm, was then used to create a shortlisted custom peptide library that met specific bioavailability, toxicity, and therapeutic relevance, leading to a refined library of 15 PCS. A greedy algorithm and coarse-grained force field were used to predict peptide structure and folding before subsequent modeling studies. Molecular docking was performed to estimate the relative binding affinities, and out of the top hits, Pep15 was subjected to molecular dynamics simulations and binding free-energy calculations in comparison to a known peptide inhibitor with experimental data (template peptide). Interestingly, the identified peptide through our protocol, Pep15, was found to show a significantly higher binding affinity than the reference template peptide (-48.10 ± 0.23 kcal/mol and -17.53 ± 0.27 kcal/mol, respectively). In comparison to the template peptide, Pep15 was found to possess a more compact and buried surface area, tighter binding landscape, and reduced conformational variability, leading to enhanced structural and kinetic stability of the Cdk5/p25 complex. Notably, both peptide inhibitors were found to have a minimal impact on the architectural integrity of the Cdk5/p25 secondary structure. Herein, we propose Pep15 as a novel and potentially disruptive peptide drug for Cdk5/p25-mediated neurodegenerative phenotypes that require further clinical investigation. The systematic protocol and findings of this report would serve as a valuable tool in the identification of critical PPI interface reactive residues, designing of analogs, and identification of more potent peptide-based PPI inhibitors.
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Affiliation(s)
- Ernest Oduro-Kwateng
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Westville Campus, Durban, South Africa
| | - Musab Ali
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Westville Campus, Durban, South Africa
| | - Ibrahim Oluwatobi Kehinde
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Westville Campus, Durban, South Africa
| | - Zhichao Zhang
- School of Chemistry, Dalian University of Technology, Dalian, Liaoning, China
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Westville Campus, Durban, South Africa
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Kashif M, Waseem M, Subbarao N. In silico prediction of CD8 + and CD4 + T cell epitopes in Leishmania major proteome: Using immunoinformatics. J Mol Graph Model 2024; 129:108759. [PMID: 38492406 DOI: 10.1016/j.jmgm.2024.108759] [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: 10/05/2023] [Revised: 02/12/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
The leishmaniases are NDTs (neglected tropical diseases) that affect people all over the world. They are brought on by protozoans from the genus Leishmania and disseminated by phlebotomine flies that are afflicted with the disease. The best option to manage and lower the incidence of these diseases has been thought by the creation of a safe and effective vaccination. This research used an in silico based mining approach to look for high potential epitopes that might bind to MHC Class I and MHC Class II molecules (mainly; HLA-A*02:01 & HLA-DRB1*03:01) from human population in order to promote vaccine development. Based on the presence of signal peptides, GPI anchors, antigenicity predictions, and a subtractive proteomic technique, we have screened 17 putative antigenic proteins from the 8083 total proteins of L. major. After that thorough immunogenic epitope prediction were done using IEDB-AR tools. We isolated five immunogenic epitopes (three 9-mer & two 15-mer) from five antigenic proteins through docking and MD simulation analysis. Finally, these five anticipated epitopes, viz., TLPEIPVNV, ELMAPVFGL, TLAAAVALL, NSINIRLDGVTSAGF and NVPLVVDASSLFRVA have considerably stronger binding potential with their respective alleles and may trigger immunological responses. The goal of this work was to identify MHC restricted epitopes for CD8+ and CD4+ T cells activation using immunoinformatics in order to identify potential vaccine candidates against L. major parasites.
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Affiliation(s)
- Mohammad Kashif
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Mohd Waseem
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Ghafoor D, Zeb A, Ali SS, Ali M, Akbar F, Ud Din Z, Ur Rehman S, Suleman M, Khan W. Immunoinformatic based designing of potential immunogenic novel mRNA and peptide-based prophylactic vaccines against H5N1 and H7N9 avian influenza viruses. J Biomol Struct Dyn 2024; 42:3641-3658. [PMID: 37222664 DOI: 10.1080/07391102.2023.2214228] [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: 10/31/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
Influenza viruses are the most common cause of serious respiratory illnesses worldwide and are responsible for a significant number of annual fatalities. Therefore, it is crucial to look for new immunogenic sites that might trigger an effective immune response. In the present study, bioinformatics tools were used to design mRNA and multiepitope-based vaccines against H5N1 and H7N9 subtypes of avian influenza viruses. Several Immunoinformatic tools were employed to extrapolate T and B lymphocyte epitopes of HA and NA proteins of both subtypes. The molecular docking approach was used to dock the selected HTL and CTL epitopes with the corresponding MHC molecules. Eight (8) CTL, four (4) HTL, and Six (6) linear B cell epitopes were chosen for the structural arrangement of mRNA and of peptide-based prophylactic vaccine designs. Different physicochemical characteristics of the selected epitopes fitted with suitable linkers were analyzed. High antigenic, non-toxic, and non-allergenic features of the designed vaccines were noted at a neutral physiological pH. Codon optimization tool was used to check the GC content and CAI value of constructed MEVC-Flu vaccine, which were recorded to be 50.42% and 0.97 respectively. the GC content and CAI value verify the stable expression of vaccine in pET28a + vector. In-silico immunological simulation the MEVC-Flu vaccine construct revealed a high level of immune responses. The molecular dynamics simulation and docking results confirmed the stable interaction of TLR-8 and MEVC-Flu vaccine. Based on these parameters, vaccine constructs can be regarded as an optimistic choice against H5N1 and H7N9 strains of the influenza virus. Further experimental testing of these prophylactic vaccine designs against pathogenic avian influenza strains may clarify their safety and efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dawood Ghafoor
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Wuhan, Hubei, China
| | - Adnan Zeb
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fazal Akbar
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ud Din
- Center for Advanced Studies in Vaccinology and Biotechnology, University of Balochistan Quetta, Quetta, Pakistan
| | - Shoaib Ur Rehman
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Wajid Khan
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
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Muhammad AM, Salum GM, Meguid MAE, Fotouh BE, Dawood RM. Bioinformatics analysis of multi-epitope peptide vaccines against Hepatitis C virus: a molecular docking study. J Genet Eng Biotechnol 2023; 21:117. [PMID: 37962693 PMCID: PMC10646107 DOI: 10.1186/s43141-023-00583-w] [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: 01/16/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Hepatitis C Virus (HCV) infection is one of the causal agents of liver disease burden. Six multiple antigenic peptides were synthesized including (P315, P412, and P517) plus (P1771, P2121, and P2941) to induce humoral and cellular responses, respectively against HCV infection. AIM This paper aimed to employ computational tools to evaluate the efficacy of each peptide individually and to determine the most effective one for better vaccine development and/or immunotherapy. METHODS VaxiJen web and AllerTOP servers were used for antigenicity and allergenicity prediction, respectively. The ToxinPred web server was used to investigate the peptide toxicity. Each peptide was docked with its corresponding receptors. RESULTS No peptides were expected to be toxic. P315 and P2941 are predicted to have robust antigenic properties, lowest allergenicity, and minimal sOPEP energies. In turn, P315 (derived from gpE1) formed the highest hydrophobic bonds with the BCR and CD81 receptors that will elicit B cell function. P2941 (derived from NS5B) was shown to strongly bind to both CD4 and CD8 receptors that will elicit T cell function. CONCLUSION P315 successfully bound to B cell (BCR and CD81) receptors. Also, P2941 is strongly bound to T cell (CD4 and CD8) receptors.
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Affiliation(s)
- Ashraf M Muhammad
- Applied Biotechnology Program, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt
| | - Ghada M Salum
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt.
| | - Mai Abd El Meguid
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
| | - Basma E Fotouh
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
| | - Reham M Dawood
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
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Völkle Nee Evgrafov E, Schulz F, Kanold JM, Michaelis M, Wissel K, Brümmer F, Schenk AS, Ludwigs S, Bill J, Rothenstein D. Functional mimicry of sea urchin biomineralization proteins with CaCO 3-binding peptides selected by phage display. J Mater Chem B 2023; 11:10174-10188. [PMID: 37850271 DOI: 10.1039/d3tb01584j] [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: 10/19/2023]
Abstract
The intricate process of biomineralization, e.g. in sea urchins, involves the precise interplay of highly regulated mineralization proteins and the spatiotemporal coordination achieved through compartmentalization. However, the investigation of biomineralization effector molecules, e.g. proteins, is challenging, due to their very low abundance. Therefore, we investigate the functional mimicry in the bioinspired precipitation of calcium carbonate (CaCO3) with artificial peptides selected from a peptide library by phage display based on peptide-binding to calcite and aragonite, respectively. The structure-directing effects of the identified peptides were compared to those of natural protein mixes isolated from skeletal (test) structures of two sea urchin species (Arbacia lixula and Paracentrotus lividus). The calcium carbonate samples deposited in the absence or presence of peptides were analyzed with a set of complementary techniques with regard to morphology, polymorph, and nanostructural motifs. Remarkably, some of the CaCO3-binding peptides induced morphological features in calcite that appeared similar to those obtained in the presence of the natural protein mixes. Many of the peptides identified as most effective in exerting a structure-directing effect on calcium carbonate crystallization were rich in basic amino acid residues. Hence, our in vitro mineralization study further highlights the important, but often neglected, role of positively charged soluble organic matrices associated with biological and bioinspired CaCO3 deposition.
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Affiliation(s)
- Elke Völkle Nee Evgrafov
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
| | - Fabian Schulz
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
| | - Julia Maxi Kanold
- Institute for Biomaterials and Biomolecular Systems & Scientific Diving Group (WiTUS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Monika Michaelis
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Kerstin Wissel
- Dept. Chemical Materials Synthesis, Institute for Materials Science, University of Stuttgart, Heisenbergstraβe 3, 70569 Stuttgart, Germany
| | - Franz Brümmer
- Institute for Biomaterials and Biomolecular Systems & Scientific Diving Group (WiTUS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Anna S Schenk
- Physical Chemistry IV, Department of Chemistry, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Sabine Ludwigs
- IPOC - Functional Polymers, Institute of Polymer Chemistry (IPOC), University of Stuttgart, Stuttgart 70569, Germany
| | - Joachim Bill
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
| | - Dirk Rothenstein
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
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Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. J Chem Theory Comput 2023; 19:7112-7135. [PMID: 37788237 DOI: 10.1021/acs.jctc.3c00733] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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Affiliation(s)
- Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Ilias Patmanidis
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Akhil P Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Lucianna H S Santos
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Inserm, CNRS, 06560 Valbonne, France
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita, Okayama 700-8530, Japan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
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Fagerberg E, Skepö M. Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining. J Chem Inf Model 2023. [PMID: 37339604 DOI: 10.1021/acs.jcim.3c00113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Coarse-graining is commonly used to decrease the computational cost of simulations. However, coarse-grained models are also considered to have lower transferability, with lower accuracy for systems outside the original scope of parametrization. Here, we benchmark a bead-necklace model and a modified Martini 2 model, both coarse-grained models, for a set of intrinsically disordered proteins, with the different models having different degrees of coarse-graining. The SOP-IDP model has earlier been used for this set of proteins; thus, those results are included in this study to compare how models with different levels of coarse-graining compare. The sometimes naive expectation of the least coarse-grained model performing best does not hold true for the experimental pool of proteins used here. Instead, it showed the least good agreement, indicating that one should not necessarily trust the otherwise intuitive notion of a more advanced model inherently being better in model choice.
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Affiliation(s)
- Eric Fagerberg
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
| | - Marie Skepö
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
- LINXS - Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden
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8
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Marriam S, Afghan MS, Nadeem M, Sajid M, Ahsan M, Basit A, Wajid M, Sabri S, Sajid M, Zafar I, Rashid S, Sehgal SA, Alkhalifah DHM, Hozzein WN, Chen KT, Sharma R. Elucidation of novel compounds and epitope-based peptide vaccine design against C30 endopeptidase regions of SARS-CoV-2 using immunoinformatics approaches. Front Cell Infect Microbiol 2023; 13:1134802. [PMID: 37293206 PMCID: PMC10244718 DOI: 10.3389/fcimb.2023.1134802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/29/2023] [Indexed: 06/10/2023] Open
Abstract
There has been progressive improvement in immunoinformatics approaches for epitope-based peptide design. Computational-based immune-informatics approaches were applied to identify the epitopes of SARS-CoV-2 to develop vaccines. The accessibility of the SARS-CoV-2 protein surface was analyzed, and hexa-peptide sequences (KTPKYK) were observed having a maximum score of 8.254, located between amino acids 97 and 102, whereas the FSVLAC at amino acids 112 to 117 showed the lowest score of 0.114. The surface flexibility of the target protein ranged from 0.864 to 1.099 having amino acid ranges of 159 to 165 and 118 to 124, respectively, harboring the FCYMHHM and YNGSPSG hepta-peptide sequences. The surface flexibility was predicted, and a 0.864 score was observed from amino acids 159 to 165 with the hepta-peptide (FCYMHHM) sequence. Moreover, the highest score of 1.099 was observed between amino acids 118 and 124 against YNGSPSG. B-cell epitopes and cytotoxic T-lymphocyte (CTL) epitopes were also identified against SARS-CoV-2. In molecular docking analyses, -0.54 to -26.21 kcal/mol global energy was observed against the selected CTL epitopes, exhibiting binding solid energies of -3.33 to -26.36 kcal/mol. Based on optimization, eight epitopes (SEDMLNPNY, GSVGFNIDY, LLEDEFTPF, DYDCVSFCY, GTDLEGNFY, QTFSVLACY, TVNVLAWLY, and TANPKTPKY) showed reliable findings. The study calculated the associated HLA alleles with MHC-I and MHC-II and found that MHC-I epitopes had higher population coverage (0.9019% and 0.5639%) than MHC-II epitopes, which ranged from 58.49% to 34.71% in Italy and China, respectively. The CTL epitopes were docked with antigenic sites and analyzed with MHC-I HLA protein. In addition, virtual screening was conducted using the ZINC database library, which contained 3,447 compounds. The 10 top-ranked scrutinized molecules (ZINC222731806, ZINC077293241, ZINC014880001, ZINC003830427, ZINC030731133, ZINC003932831, ZINC003816514, ZINC004245650, ZINC000057255, and ZINC011592639) exhibited the least binding energy (-8.8 to -7.5 kcal/mol). The molecular dynamics (MD) and immune simulation data suggest that these epitopes could be used to design an effective SARS-CoV-2 vaccine in the form of a peptide-based vaccine. Our identified CTL epitopes have the potential to inhibit SARS-CoV-2 replication.
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Affiliation(s)
- Saigha Marriam
- Department of Microbiology and Molecular Genetics, Faculty of Life Sciences, University of Okara, Okara, Pakistan
| | - Muhammad Sher Afghan
- Department of Ear, Nose, and Throat (ENT), District Headquarter (DHQ) Teaching Hospital Faisalabad, Faisalabad, Punjab, Pakistan
| | - Mazhar Nadeem
- Department of Ear, Nose, and Throat (ENT), District Headquarter (DHQ) Teaching Hospital Faisalabad, Faisalabad, Punjab, Pakistan
| | - Muhammad Sajid
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, Pakistan
| | - Muhammad Ahsan
- Institute of Environmental and Agricultural Sciences, University of Okara, Okara, Pakistan
| | - Abdul Basit
- Department of Microbiology, University of Jhang, Jhang, Pakistan
| | - Muhammad Wajid
- Department of Zoology, Faculty of Life Sciences, University of Okara, Okara, Pakistan
| | - Sabeen Sabri
- Department of Microbiology and Molecular Genetics, Faculty of Life Sciences, University of Okara, Okara, Pakistan
| | - Muhammad Sajid
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, Pakistan
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University, Punjab, Pakistan
| | - Summya Rashid
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics, Faculty of Life Sciences, University of Okara, Okara, Pakistan
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Dalal Hussien M Alkhalifah
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Wael N Hozzein
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Kow-Tong Chen
- Department of Occupational Medicine, Tainan Municipal Hospital (managed by ShowChwan Medical Care Corporation), Tainan, Taiwan
- Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Pradhan S, Rath R, Biswas M. GB1 Dimerization in Crowders: A Multiple Resolution Approach. J Chem Inf Model 2023; 63:1570-1577. [PMID: 36858485 DOI: 10.1021/acs.jcim.3c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
In-cell protein-protein association, which is crucial in enzyme catalysis and polymerization, occurs in an environment that is highly heterogeneous and crowded. The crowder molecules exclude the reactant molecules from occupying certain regions of the cell, resulting in changes in the reaction thermodynamics and kinetics. Recent studies, both experiment and simulations, revealed that the nature of the interaction between crowder and protein species, in particular the soft interactions, plays an important role in crowder induced effects on protein association. To this end, from a simulation perspective, it is important to decipher the level of structural resolution in a protein-crowder model that can faithfully capture the influence of crowding on protein association. Here, we investigate the dimerization of model system GB1 in the presence of lysozyme crowders at two structural resolutions. The lower resolution model assumes both protein and crowder species as spherical beads, similar to the analytical scaled particle theory model, whereas the higher resolution model retains residue specific structural details for protein and crowder species. From the higher resolution model, it is found that GB1 dimer formation is destabilized in the presence of lysozyme crowders, and the destabilization is more for the side-by-side dimer compared to the domain-swapped dimer, in qualitative agreement with experimental findings. However, the low resolution CG model predicts stabilization of the dimers in the presence of the lysozyme crowder, similar to the SPT model. Our results indicate a nontrivial role of the choice of model resolution in computer simulation studies investigating crowder induced effects.
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Affiliation(s)
- Sweta Pradhan
- National Institute of Technology Rourkela, Rourkela 769008, India
| | - Rajendra Rath
- National Institute of Technology Rourkela, Rourkela 769008, India
| | - Mithun Biswas
- National Institute of Technology Rourkela, Rourkela 769008, India
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Chitosan and HPMCAS double-coating as protective systems for alginate microparticles loaded with Ctx(Ile 21)-Ha antimicrobial peptide to prevent intestinal infections. Biomaterials 2023; 293:121978. [PMID: 36580719 DOI: 10.1016/j.biomaterials.2022.121978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 11/03/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
The incorrect use of conventional drugs for both prevention and control of intestinal infections has contributed to a significant spread of bacterial resistance. In this way, studies that promote their replacement are a priority. In the last decade, the use of antimicrobial peptides (AMP), especially Ctx(Ile21)-Ha AMP, has gained strength, demonstrating efficient antimicrobial activity (AA) against pathogens, including multidrug-resistant bacteria. However, gastrointestinal degradation does not allow its direct oral application. In this research, double-coating systems using alginate microparticles loaded with Ctx(Ile21)-Ha peptide were designed, and in vitro release assays simulating the gastrointestinal tract were evaluated. Also, the AA against Salmonella spp. and Escherichia coli was examined. The results showed the physicochemical stability of Ctx(Ile21)-Ha peptide in the system and its potent antimicrobial activity. In addition, the combination of HPMCAS and chitosan as a gastric protection system can be promising for peptide carriers or other low pH-sensitive molecules, adequately released in the intestine. In conclusion, the coated systems employed in this study can improve the formulation of new foods or biopharmaceutical products for specific application against intestinal pathogens in animal production or, possibly, in the near future, in human health.
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11
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Tufféry P, Derreumaux P. A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution. FRONTIERS IN BIOINFORMATICS 2023; 3:1113928. [PMID: 36727106 PMCID: PMC9885153 DOI: 10.3389/fbinf.2023.1113928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/06/2023] [Indexed: 01/17/2023] Open
Abstract
Introduction: Peptides carry out diverse biological functions and the knowledge of the conformational ensemble of polypeptides in various experimental conditions is important for biological applications. All fast dedicated softwares perform well in aqueous solution at neutral pH. Methods: In this study, we go one step beyond by combining the Debye-Hückel formalism for charged-charged amino acid interactions and a coarse-grained potential of the amino acids to treat pH and salt variations. Results: Using the PEP-FOLD framework, we show that our approach performs as well as the machine-leaning AlphaFold2 and TrRosetta methods for 15 well-structured sequences, but shows significant improvement in structure prediction of six poly-charged amino acids and two sequences that have no homologous in the Protein Data Bank, expanding the range of possibilities for the understanding of peptide biological roles and the design of candidate therapeutic peptides.
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Affiliation(s)
- Pierre Tufféry
- Université Paris Cité, CNRS UMR 8251, INSERM U1133, Paris, France,*Correspondence: Pierre Tufféry,
| | - Philippe Derreumaux
- Université Paris Cité, CNRSUPR9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France,Institut Universitaire de France (IUF), Paris, France
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12
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Kashif M, Hira SK, Manna PP. Immunoinformatics based design and prediction of proteome-wide killer cell epitopes of Leishmania donovani: Potential application in vaccine development. J Biomol Struct Dyn 2022; 40:10578-10591. [PMID: 34219625 DOI: 10.1080/07391102.2021.1945495] [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] [Indexed: 10/20/2022]
Abstract
Despite several extensive and exhaustive efforts, search for potential therapy against leishmaniasis has not made much progress. In the present work, we have employed mining strategy to screen Leishmania donovani proteome for identification of promising vaccine candidate. We have screened 21 potential antigenic proteins from 7960 total protein of L. donovani, based on the presence of signal peptide, GPI anchor, antigenicity prediction and substractive proteomic approach. Secondly, we have also performed comprehensive immunogenic epitope prediction from the screened 21 proteins, using IEDB-AR tools. Out of the 21 antigenic proteins, we obtained 11 immunogenic epitopes from 9 proteins. The final results revealed that four predicted epitopes namely; YPAFAALVF, VAVAATVAY, AAAPTEAAL and MYPLVAVVF, have significantly better binding potential with respective alleles and could elicits immune responses. Docking analysis using PATCHDOCK server and molecular dynamic simulation using GROMACS revealed the potential of the sequences as immunogenic epitopes. In silico studies also suggested that the epitopes occupied almost same binding cleft with the respective alleles, when compared with the reference peptides. It is also suggested from the molecular dynamic simulation data that the peptides were intact in the pocket for longer periods of time. Our study was designed to select MHC class I restricted epitopes for the activation of CD8 T cells using immunoinformatics for the prediction of probable vaccine candidate against L. donovani parasites. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Kashif
- Immunobiology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Sumit Kumar Hira
- Cellular Immunology Laboratory, Department of Zoology, The University of Burdwan, Purba Bardhhaman, India
| | - Partha Pratim Manna
- Immunobiology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, India
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13
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Toxicological and Safety Pharmacological Profiling of the Anti-Infective and Anti-Inflammatory Peptide Pep19-2.5. Microorganisms 2022; 10:microorganisms10122412. [PMID: 36557665 PMCID: PMC9782211 DOI: 10.3390/microorganisms10122412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Aspidasept (Pep19-2.5) and its derivative Pep19-4LF ("Aspidasept II") are anti-infective and anti-inflammatory synthetic polypeptides currently in development for application against a variety of moderate to severe bacterial infections that could lead to systemic inflammation, as in the case of severe sepsis and septic shock, as well as application to non-systemic diseases in the case of skin and soft tissue infections (SSTI). In the present study, Aspidasept and Aspidasept II and their part structures were analysed with respect to their toxic behavior in different established models against a variety of relevant cells, and in electrophysiological experiments targeting the hERG channel according to ICH S7B. Furthermore, the effects in mouse models of neurobiological behavior and the local lymph node according to OECD test guideline 429 were investigated, as well as a rat model of repeated dose toxicology according to ICH M3. The data provide conclusive information about potential toxic effects, thus specifying a therapeutic window for the application of the peptides. Therefore, these data allow us to define Aspidasept concentrations for their use in clinical studies as parenteral application.
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14
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Yang F, Jiang W, Chen X, Chen X, Wu J, Huang J, Cai X, Wang S. Identification of Novel Antifreeze Peptides from Takifugu obscurus Skin and Molecular Mechanism in Inhibiting Ice Crystal Growth. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14148-14156. [PMID: 36314886 DOI: 10.1021/acs.jafc.2c04393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Foodborne hydrolyzed antifreeze peptides have been widely used in the food industry and the biomedical field. However, the components of hydrolyzed peptides are complex and the molecular mechanism remains unclear. This study focused on identification and mechanism analysis of novel antifreeze peptides from Takifugu obscurus skin by traditional methods and computer-assisted techniques. Results showed that three peptides (EGPRAGGAPG, GDAGPSGPAGPTG, and GEAGPAGPAG) possessed cryoprotection via reducing the freezing point and inhibiting ice crystal growth. Molecular docking confirmed that the cryoprotective property was related to peptide structure, especially α-helix, and hydrogen bond sites. Moreover, the antifreeze peptides were double-faces, which controlled ice crystals while affecting the arrangement of surrounding water molecules, thus exhibiting a strong antifreeze activity. This investigation deepens the comprehension of the mechanism of antifreeze peptides at molecular scale, and the novel efficient antifreeze peptides can be developed in antifreeze materials design and applied in food industry.
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Affiliation(s)
- Fujia Yang
- College of Chemical Engineering, Fuzhou University, Fuzhou350108, P.R. China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Wenting Jiang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Xu Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Xuan Chen
- College of Chemical Engineering, Fuzhou University, Fuzhou350108, P.R. China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai200240, P.R. China
| | - Jianlian Huang
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing of Ministry of Agriculture and Rural Affairs, Xiamen361022, P.R. China
- Fujian Anjoy Foods Co. Ltd., Xiamen361022, P.R. China
| | - Xixi Cai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
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15
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Jin J, Pak AJ, Durumeric AEP, Loose TD, Voth GA. Bottom-up Coarse-Graining: Principles and Perspectives. J Chem Theory Comput 2022; 18:5759-5791. [PMID: 36070494 PMCID: PMC9558379 DOI: 10.1021/acs.jctc.2c00643] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 01/14/2023]
Abstract
Large-scale computational molecular models provide scientists a means to investigate the effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship between variations on the molecular scale and macroscopic observable properties facilitates an understanding of the molecular interactions driving the properties of real world materials and complex systems (e.g., those found in biology, chemistry, and materials science). As a result, discovering an explicit, systematic connection between microscopic nature and emergent mesoscopic behavior is a fundamental goal for this type of investigation. The molecular forces critical to driving the behavior of complex heterogeneous systems are often unclear. More problematically, simulations of representative model systems are often prohibitively expensive from both spatial and temporal perspectives, impeding straightforward investigations over possible hypotheses characterizing molecular behavior. While the reduction in resolution of a study, such as moving from an atomistic simulation to that of the resolution of large coarse-grained (CG) groups of atoms, can partially ameliorate the cost of individual simulations, the relationship between the proposed microscopic details and this intermediate resolution is nontrivial and presents new obstacles to study. Small portions of these complex systems can be realistically simulated. Alone, these smaller simulations likely do not provide insight into collectively emergent behavior. However, by proposing that the driving forces in both smaller and larger systems (containing many related copies of the smaller system) have an explicit connection, systematic bottom-up CG techniques can be used to transfer CG hypotheses discovered using a smaller scale system to a larger system of primary interest. The proposed connection between different CG systems is prescribed by (i) the CG representation (mapping) and (ii) the functional form and parameters used to represent the CG energetics, which approximate potentials of mean force (PMFs). As a result, the design of CG methods that facilitate a variety of physically relevant representations, approximations, and force fields is critical to moving the frontier of systematic CG forward. Crucially, the proposed connection between the system used for parametrization and the system of interest is orthogonal to the optimization used to approximate the potential of mean force present in all systematic CG methods. The empirical efficacy of machine learning techniques on a variety of tasks provides strong motivation to consider these approaches for approximating the PMF and analyzing these approximations.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander J. Pak
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Aleksander E. P. Durumeric
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Timothy D. Loose
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
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16
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Oyama LB, Olleik H, Teixeira ACN, Guidini MM, Pickup JA, Hui BYP, Vidal N, Cookson AR, Vallin H, Wilkinson T, Bazzolli DMS, Richards J, Wootton M, Mikut R, Hilpert K, Maresca M, Perrier J, Hess M, Mantovani HC, Fernandez-Fuentes N, Creevey CJ, Huws SA. In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus. NPJ Biofilms Microbiomes 2022; 8:58. [PMID: 35835775 PMCID: PMC9283466 DOI: 10.1038/s41522-022-00320-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 06/21/2022] [Indexed: 12/29/2022] Open
Abstract
Here we report two antimicrobial peptides (AMPs), HG2 and HG4 identified from a rumen microbiome metagenomic dataset, with activity against multidrug-resistant (MDR) bacteria, especially methicillin-resistant Staphylococcus aureus (MRSA) strains, a major hospital and community-acquired pathogen. We employed the classifier model design to analyse, visualise, and interpret AMP activities. This approach allowed in silico discrimination of promising lead AMP candidates for experimental evaluation. The lead AMPs, HG2 and HG4, are fast-acting and show anti-biofilm and anti-inflammatory activities in vitro and demonstrated little toxicity to human primary cell lines. The peptides were effective in vivo within a Galleria mellonella model of MRSA USA300 infection. In terms of mechanism of action, HG2 and HG4 appear to interact with the cytoplasmic membrane of target cells and may inhibit other cellular processes, whilst preferentially binding to bacterial lipids over human cell lipids. Therefore, these AMPs may offer additional therapeutic templates for MDR bacterial infections.
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Affiliation(s)
- Linda B. Oyama
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland BT9 5DL UK
| | - Hamza Olleik
- grid.6227.10000000121892165CNRS Enzyme and Cell Engineering Laboratory, Université de Technologie de Compiègne, Sorbonne Universités, Rue du Docteur Schweitzer, CS 60319, CEDEX, 60203 Compiègne, France
| | - Ana Carolina Nery Teixeira
- grid.12799.340000 0000 8338 6359Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, 36570-900 Brasil
| | - Matheus M. Guidini
- grid.12799.340000 0000 8338 6359Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, 36570-900 Brasil
| | - James A. Pickup
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland BT9 5DL UK
| | - Brandon Yeo Pei Hui
- University College Fairview (UCF), 4178, Jalan 1/27D, Section 6, Wangsa Maju, 53300 Kuala Lumpur, Malaysia
| | - Nicolas Vidal
- grid.5399.60000 0001 2176 4817Yelen Analytics, Aix-Marseille University ICR, 13013 Marseille, France
| | - Alan R. Cookson
- grid.8186.70000 0001 2168 2483Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales SY23 3DA UK
| | - Hannah Vallin
- grid.8186.70000 0001 2168 2483Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales SY23 3DA UK
| | - Toby Wilkinson
- grid.4305.20000 0004 1936 7988The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Denise M. S. Bazzolli
- grid.12799.340000 0000 8338 6359Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, 36570-900 Brasil
| | - Jennifer Richards
- grid.241103.50000 0001 0169 7725Specialist Antimicrobial Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW UK
| | - Mandy Wootton
- grid.241103.50000 0001 0169 7725Specialist Antimicrobial Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW UK
| | - Ralf Mikut
- grid.7892.40000 0001 0075 5874Karlsruhe Institute of Technology, Institute for Automation and Applied Informatics, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein, Leopoldshafen Germany
| | - Kai Hilpert
- grid.4464.20000 0001 2161 2573Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London, SW17 0RE UK
| | - Marc Maresca
- grid.5399.60000 0001 2176 4817Aix Marseille University, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Josette Perrier
- grid.5399.60000 0001 2176 4817Aix Marseille University, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Matthias Hess
- grid.27860.3b0000 0004 1936 9684UC Davis, College of Agricultural and Environmental Sciences, California, 95616 CA USA
| | - Hilario C. Mantovani
- grid.12799.340000 0000 8338 6359Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, 36570-900 Brasil
| | - Narcis Fernandez-Fuentes
- grid.8186.70000 0001 2168 2483Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales SY23 3DA UK
| | - Christopher J. Creevey
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland BT9 5DL UK
| | - Sharon A. Huws
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland BT9 5DL UK
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17
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Zhi T, Li X, Sadiq FA, Mao K, Gao J, Mi S, Liu X, Deng W, Chitrakar B, Sang Y. Novel antioxidant peptides from protein hydrolysates of scallop (Argopecten irradians) mantle using enzymatic and microbial methods: Preparation, purification, identification and characterization. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Cai X, Han W. Development of a Hybrid-Resolution Force Field for Peptide Self-Assembly Simulations: Optimizing Peptide-Peptide and Peptide-Solvent Interactions. J Chem Inf Model 2022; 62:2744-2760. [PMID: 35561002 DOI: 10.1021/acs.jcim.2c00066] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Atomic descriptions of peptide self-assembly are crucial to an understanding of disease-related peptide aggregation and the design of peptide-assembled materials. Obtaining these descriptions through computer simulation is challenging because current force fields, which were not designed for this process and are often unable to describe correctly peptide self-assembly behavior and the sequence dependence. Here, we developed a framework using dipeptide aggregation as a model system to improve force fields for simulations of self-assembly. Aggregation-related structural properties were designed and used to guide the optimization of peptide-peptide and peptide-solvent interactions. With this framework, we developed a self-assembly force field, termed PACE-ASM, by reoptimizing a hybrid-resolution force field that was originally developed for folding simulation. With its applicability in folding simulations, the new PACE was used to simulate the self-assembly of two disease-related short peptides, Aβ16-21 and PHF6, into β-sheet-rich cross-β amyloids. These simulations reproduced the crystal structures of Aβ16-21 and PHF6 amyloids at near-atomic resolution and captured the difference in packing orientations between the two sequences, a task which is challenging even with all-atom force fields. Apart from cross-β amyloids, the self-assembly of emerging helix-rich cross-α amyloids by another peptide PSMα3 can also be correctly described with the new PACE, manifesting the versatility of the force field. We demonstrated that the ability of the PACE-ASM to model peptide self-assembly is based largely on its improved description of peptide-peptide and peptide-solvent interactions. This was achieved with our optimization framework that can readily identify and address the deficiency in describing these interactions.
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Affiliation(s)
- Xiang Cai
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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19
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Sajid M, Marriam S, Mukhtar H, Sohail S, Sajid M, Sehgal SA. Epitope-based peptide vaccine design and elucidation of novel compounds against 3C like protein of SARS-CoV-2. PLoS One 2022; 17:e0264700. [PMID: 35324925 PMCID: PMC8947391 DOI: 10.1371/journal.pone.0264700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/15/2022] [Indexed: 12/23/2022] Open
Abstract
Coronaviruses (CoVs) are positive-stranded RNA viruses with short clubs on their edges. CoVs are pathogenic viruses that infect several animals and plant organisms, as well as humans (lethal respiratory dysfunctions). A noval strain of CoV has been reported and named as SARS-CoV-2. Numerous COVID-19 cases were being reported all over the World. COVID-19 and has a high mortality rate. In the present study, immunoinformatics techniques were utilized to predict the antigenic epitopes against 3C like protein. B-cell epitopes and Cytotoxic T-lymphocyte (CTL) were designed computationally against SARS-CoV-2. Multiple Sequence Alignment (MSA) of seven complete strains (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2) was performed to elucidate the binding domain and interacting residues. MHC-I binding epitopes were evaluated by analyzing the binding affinity of the top-ranked peptides having HLA molecule. By utilizing the docked complexes of CTL epitopes with antigenic sites, the binding relationship and affinity of top-ranked predicted peptides with the MHC-I HLA protein were investigated. The molecular docking analyses were conducted on the ZINC database library and twelve compounds having least binding energy were scrutinized. In conclusion, twelve CTL epitopes (GTDLEGNFY, TVNVLAWLY, GSVGFNIDY, SEDMLNPNY, LSQTGIAV, VLDMCASLK, LTQDHVDIL, TTLNDFNLV, CTSEDMLNP, TTITVNVLA, YNGSPSGVY, and SMQNCVLKL) were identified against SARS-CoV-2.
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Affiliation(s)
- Muhammad Sajid
- Department of Biotechnology, University of Okara, Okara, Pakistan
| | - Saigha Marriam
- Department of Microbiology and Molecular Genetics, University of Okara, Okara, Pakistan
| | | | - Summar Sohail
- Department of Forestry, Kohsar University Murree, Murree, Pakistan
| | - Muhammad Sajid
- Department of Biotechnology, University of Okara, Okara, Pakistan
- * E-mail: (MS); (SAS)
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics, University of Okara, Okara, Pakistan
- * E-mail: (MS); (SAS)
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20
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Roterman I, Sieradzan A, Stapor K, Fabian P, Wesołowski P, Konieczny L. On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field. J Mol Graph Model 2022; 114:108166. [PMID: 35325843 DOI: 10.1016/j.jmgm.2022.108166] [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: 08/02/2021] [Revised: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
During the protein folding process in computer simulations involving the use of a United RESidue (UNRES) force field, an additional module was introduced to represent directly the presence of a polar solvent in water form. This module implements the fuzzy oil drop model (FOD) where the 3D Gauss function expresses the presence of a polar environment which directs the polypeptide chain folding process towards the generation of a centric hydrophobic core. Sample test polypeptide chains of 8 proteins with chain lengths ranging from 37 to 75 aa were simulated in silico using the UNRES (U) package with an implicit solvent model and a built-in module expressing the FOD model (UNRES-FOD-UNRES (U + F) interleaved simulation). The protein structure obtained by both *** simulation schemes, i.e., accordingly***U and U + F, for all the analyzed protein models shows the presence of a hydrophobic core including where it is absent in the native structure. The proposed FOD-M model (M-modified) explaining the source of this phenomenon reveals the need to modify the external field expressing the role of a folding environment. The modification takes into account the influence of other than polar factors present in the folding environment.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College Medyczna 7, 30-688, Kraków, Poland.
| | - Adam Sieradzan
- Faculty of Chemistry, Gdansk University, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Katarzyna Stapor
- Faculty of Automatic, Electronics and Computer Science, Department of Applied Informatics, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
| | - Piotr Fabian
- Faculty of Automatic, Electronics and Computer Science, Department of Algorithmics and Software, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
| | - Patryk Wesołowski
- Faculty of Chemistry, Gdansk University, Wita Stwosza 63, 80-308, Gdańsk, Poland; Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, ul. Abrahama 58, 80-307, Gdańsk, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry - Jagiellonian University - Medical College, Kopernika 7, 31-034, Kraków, Poland.
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21
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Binette V, Mousseau N, Tuffery P. A Generalized Attraction-Repulsion Potential and Revisited Fragment Library Improves PEP-FOLD Peptide Structure Prediction. J Chem Theory Comput 2022; 18:2720-2736. [PMID: 35298162 DOI: 10.1021/acs.jctc.1c01293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fast and accurate structure prediction is essential to the study of peptide function, molecular targets, and interactions and has been the subject of considerable efforts in the past decade. In this work, we present improvements to the popular simplified PEP-FOLD technique for small peptide structure prediction. PEP-FOLD originality is threefold: (i) it uses a predetermined structural alphabet, (ii) it uses a sequential algorithm to reconstruct the tridimensional structures of these peptides in a discrete space using a fragment library, and (iii) it assesses the energy of these structures using a coarse-grained representation in which all of the backbone atoms but the α-hydrogen are present, and the side chain corresponds to a unique bead. In former versions of PEP-FOLD, a van der Waals formulation was used for non-bonded interactions, with each side chain being associated with a fixed radius. Here, we explore the relevance of using instead a generalized formulation in which not only the optimal distance of interaction and the energy at this distance are parameters but also the distance at which the potential is zero. This allows each side chain to be associated with a different radius and potential energy shape, depending on its interaction partner, and in principle to make more effective the coarse-grained representation. In addition, the new PEP-FOLD version is associated with an updated library of fragments. We show that these modifications lead to important improvements for many of the problematic targets identified with the former PEP-FOLD version while maintaining already correct predictions. The improvement is in terms of both model ranking and model accuracy. We also compare the PEP-FOLD enhanced version to state-of-the-art techniques for both peptide and structure predictions: APPTest, RaptorX, and AlphaFold2. We find that the new predictions are superior, in particular with respect to the prediction of small β-targets, to those of APPTest and RaptorX and bring, with its original approach, additional understanding on folded structures, even when less precise than AlphaFold2. With their strong physical influence, the revised structural library and coarse-grained potential offer, however, the means for a deeper understanding of the nature of folding and open a solid basis for studying flexibility and other dynamical properties not accessible to IA structure prediction approaches.
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Affiliation(s)
- Vincent Binette
- Départment de Physique, Université de Montréal, Case postale 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Normand Mousseau
- Départment de Physique, Université de Montréal, Case postale 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Pierre Tuffery
- Université de Paris, INSERM U1133, CNRS UMR 8251, F-75205 Paris, France
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22
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Gokcan H, Isayev O. Learning molecular potentials with neural networks. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hatice Gokcan
- Department of Chemistry, Mellon College of Science Carnegie Mellon University Pittsburgh Pennsylvania USA
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science Carnegie Mellon University Pittsburgh Pennsylvania USA
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23
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Nguyen TH, Nguyen PH, Ngo ST, Derreumaux P. Effect of Cholesterol Molecules on Aβ1-42 Wild-Type and Mutants Trimers. Molecules 2022; 27:molecules27041395. [PMID: 35209177 PMCID: PMC8879133 DOI: 10.3390/molecules27041395] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Alzheimer’s disease displays aggregates of the amyloid-beta (Aβ) peptide in the brain, and there is increasing evidence that cholesterol may contribute to the pathogenesis of the disease. Though many experimental and theoretical studies have focused on the interactions of Aβ oligomers with membrane models containing cholesterol, an understanding of the effect of free cholesterol on small Aβ42 oligomers is not fully established. To address this question, we report on replica exchange with a solute tempering simulation of an Aβ42 trimer with cholesterol and compare it with a previous replica exchange molecular dynamics simulation. We show that the binding hot spots of cholesterol are rather complex, involving hydrophobic residues L17–F20 and L30–M35 with a non-negligible contribution of loop residues D22–K28 and N-terminus residues. We also examine the effects of cholesterol on the trimers of the disease-causing A21G and disease-protective A2T mutations by molecular dynamics simulations. We show that these two mutations moderately impact cholesterol-binding modes. In our REST2 simulations, we find that cholesterol is rarely inserted into aggregates but rather attached as dimers and trimers at the surface of Aβ42 oligomers. We propose that cholesterol acts as a glue to speed up the formation of larger aggregates; this provides a mechanistic link between cholesterol and Alzheimer’s disease.
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Affiliation(s)
- Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam; (T.H.N.); (S.T.N.)
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam; (T.H.N.); (S.T.N.)
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
- Correspondence:
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24
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Co NT, Li MS, Krupa P. Computational Models for the Study of Protein Aggregation. Methods Mol Biol 2022; 2340:51-78. [PMID: 35167070 DOI: 10.1007/978-1-0716-1546-1_4] [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] [Indexed: 06/14/2023]
Abstract
Protein aggregation has been studied by many groups around the world for many years because it can be the cause of a number of neurodegenerative diseases that have no effective treatment. Obtaining the structure of related fibrils and toxic oligomers, as well as describing the pathways and main factors that govern the self-organization process, is of paramount importance, but it is also very difficult. To solve this problem, experimental and computational methods are often combined to get the most out of each method. The effectiveness of the computational approach largely depends on the construction of a reasonable molecular model. Here we discussed different versions of the four most popular all-atom force fields AMBER, CHARMM, GROMOS, and OPLS, which have been developed for folded and intrinsically disordered proteins, or both. Continuous and discrete coarse-grained models, which were mainly used to study the kinetics of aggregation, are also summarized.
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Affiliation(s)
- Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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25
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Nguyen PH, Tufféry P, Derreumaux P. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations. Methods Mol Biol 2022; 2405:95-113. [PMID: 35298810 DOI: 10.1007/978-1-0716-1855-4_5] [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] [Indexed: 06/14/2023]
Abstract
Amyloid fibril formation is an intrinsic property of short peptides, non-disease proteins, and proteins associated with neurodegenerative diseases. Aggregates of the Aβ and tau proteins, the α-synuclein protein, and the prion protein are observed in the brain of Alzheimer's, Parkinson's, and prion disease patients, respectively. Due to the transient short-range and long-range interactions of all species and their high aggregation propensities, the conformational ensemble of these devastating proteins, the exception being for the monomeric prion protein, remains elusive by standard structural biology methods in bulk solution and in lipid membranes. To overcome these limitations, an increasing number of simulations using different sampling methods and protein models have been performed. In this chapter, we first review our main contributions to the field of amyloid protein simulations aimed at understanding the early aggregation steps of short linear amyloid peptides, the conformational ensemble of the Aβ40/42 dimers in bulk solution, and the stability of Aβ aggregates in lipid membrane models. Then we focus on our studies on the interactions of amyloid peptides/inhibitors to prevent aggregation, and long amyloid sequences, including new results on a monomeric tau construct.
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Affiliation(s)
- Phuong Hoang Nguyen
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Pierre Tufféry
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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26
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Liwo A, Czaplewski C, Sieradzan AK, Lipska AG, Samsonov SA, Murarka RK. Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems. Biomolecules 2021; 11:1347. [PMID: 34572559 PMCID: PMC8465211 DOI: 10.3390/biom11091347] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022] Open
Abstract
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink's group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Agnieszka G. Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Sergey A. Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Rajesh K. Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, MP, India;
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27
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Greener JG, Jones DT. Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins. PLoS One 2021; 16:e0256990. [PMID: 34473813 PMCID: PMC8412298 DOI: 10.1371/journal.pone.0256990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/19/2021] [Indexed: 11/26/2022] Open
Abstract
Finding optimal parameters for force fields used in molecular simulation is a challenging and time-consuming task, partly due to the difficulty of tuning multiple parameters at once. Automatic differentiation presents a general solution: run a simulation, obtain gradients of a loss function with respect to all the parameters, and use these to improve the force field. This approach takes advantage of the deep learning revolution whilst retaining the interpretability and efficiency of existing force fields. We demonstrate that this is possible by parameterising a simple coarse-grained force field for proteins, based on training simulations of up to 2,000 steps learning to keep the native structure stable. The learned potential matches chemical knowledge and PDB data, can fold and reproduce the dynamics of small proteins, and shows ability in protein design and model scoring applications. Problems in applying differentiable molecular simulation to all-atom models of proteins are discussed along with possible solutions and the variety of available loss functions. The learned potential, simulation scripts and training code are made available at https://github.com/psipred/cgdms.
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Affiliation(s)
- Joe G. Greener
- Department of Computer Science, University College London, London, United Kingdom
| | - David T. Jones
- Department of Computer Science, University College London, London, United Kingdom
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28
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Giulini M, Rigoli M, Mattiotti G, Menichetti R, Tarenzi T, Fiorentini R, Potestio R. From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules. Front Mol Biosci 2021; 8:676976. [PMID: 34164432 PMCID: PMC8215203 DOI: 10.3389/fmolb.2021.676976] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/06/2021] [Indexed: 12/18/2022] Open
Abstract
The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.
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Affiliation(s)
- Marco Giulini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Marta Rigoli
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Giovanni Mattiotti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Roberto Menichetti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Thomas Tarenzi
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaele Fiorentini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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29
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Crooke SN, Ovsyannikova IG, Kennedy RB, Poland GA. Identification of naturally processed Zika virus peptides by mass spectrometry and validation of memory T cell recall responses in Zika convalescent subjects. PLoS One 2021; 16:e0252198. [PMID: 34077451 PMCID: PMC8171893 DOI: 10.1371/journal.pone.0252198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Once an obscure pathogen, Zika virus (ZIKV) has emerged as a significant global public health concern. Several studies have linked ZIKV infection in pregnant women with the development of microcephaly and other neurological abnormalities, emphasizing the need for a safe and effective vaccine to combat the spread of this disease. Preclinical studies and vaccine development efforts have largely focused on the role of humoral immunity in disease protection. Consequently, relatively little is known in regard to cellular immunity against ZIKV, although an effective vaccine will likely need to engage both the humoral and cellular arms of the immune system. To that end, we utilized two-dimensional liquid chromatography coupled with tandem mass spectrometry to identify 90 ZIKV peptides that were naturally processed and presented on HLA class I and II molecules (HLA-A*02:01/HLA-DRB1*04:01) of an immortalized B cell line infected with ZIKV (strain PRVABC59). Sequence identity clustering was used to filter the number of candidate peptides prior to evaluating memory T cell recall responses in ZIKV convalescent subjects. Peptides that individually elicited broad (4 of 7 subjects) and narrow (1 of 7 subjects) T cell responses were further analyzed using a suite of predictive algorithms and in silico modeling to evaluate HLA binding and peptide structural properties. A subset of nine broadly reactive peptides was predicted to provide robust global population coverage (97.47% class I; 70.74% class II) and to possess stable structural properties amenable for vaccine formulation, highlighting the potential clinical benefit for including ZIKV T cell epitopes in experimental vaccine formulations.
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Affiliation(s)
- Stephen N. Crooke
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Inna G. Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Richard B. Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
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30
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Olotu FA, Soliman MES. Immunoinformatics prediction of potential B-cell and T-cell epitopes as effective vaccine candidates for eliciting immunogenic responses against Epstein-Barr virus. Biomed J 2021; 44:317-337. [PMID: 34154948 PMCID: PMC8358216 DOI: 10.1016/j.bj.2020.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/15/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The ongoing search for viable treatment options to curtail Epstein Barr Virus (EBV) pathogenicity has necessitated a paradigmatic shift towards the design of peptide-based vaccines. Potential B-cell and T-cell epitopes were predicted for nine antigenic EBV proteins that mediate epithelial cell-attachment and spread, capsid self-assembly, DNA replication and processivity. METHODS Predictive algorithms incorporated in the Immune Epitope Database (IEDB) resources were used to determine potential B-cell epitopes based on their physicochemical attributes. These were combined with a string-kernel method and an antigenicity predictive AlgPred tool to enhance accuracy in the end-point selection of highly potential antigenic EBV B-cell epitopes. NetCTL 1.2 algorithms enabled the prediction of probable T-cell epitopes which were structurally modeled and subjected to blind peptide-protein docking with HLA-A*02:01. All-atom molecular dynamics (MD) simulation and Molecular Mechanics Generalized-Born Surface Area methods were used to investigate interaction dynamics and affinities of predicted T-cell peptide-protein complexes. RESULTS Computational predictions and sequence overlapping analysis yielded 18 linear (continuous) and discontinuous (conformational) subunit epitopes from the antigenic proteins with characteristic surface accessibility, flexibility and antigenicity, and predictive scores above the threshold value (1) set. A novel site was identified on HLA-A*02:01 with preferential affinity binding for modeled BMRF2, BXLF1 and BGLF4 T-cell epitopes. Interaction dynamics and energies were also computed in addition to crucial residues that mediated complex formation and stability. CONCLUSION This study implemented an integrative meta-analytical approach to model highly probable B-cell and T-cell epitopes as potential peptide-vaccine candidates for the treatment of EBV-related diseases.
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Affiliation(s)
- Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa.
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31
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Onime LA, Oyama LB, Thomas BJ, Gani J, Alexander P, Waddams KE, Cookson A, Fernandez-Fuentes N, Creevey CJ, Huws SA. The rumen eukaryotome is a source of novel antimicrobial peptides with therapeutic potential. BMC Microbiol 2021; 21:105. [PMID: 33832427 PMCID: PMC8034185 DOI: 10.1186/s12866-021-02172-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The rise of microbial antibiotic resistance is a leading threat to the health of the human population. As such, finding new approaches to tackle these microbes, including development of novel antibiotics is vital. RESULTS In this study, we mined a rumen eukaryotic metatranscriptomic library for novel Antimicrobial peptides (AMPs) using computational approaches and thereafter characterised the therapeutic potential of the AMPs. We identified a total of 208 potentially novel AMPs from the ruminal eukaryotome, and characterised one of those, namely Lubelisin. Lubelisin (GIVAWFWRLAR) is an α-helical peptide, 11 amino acid long with theoretical molecular weight of 1373.76 D. In the presence of Lubelisin, strains of methicillin-resistant Staphylococcus aureus (MRSA) USA300 and EMRSA-15 were killed within 30 min of exposure with ≥103 and 104 CFU/mL reduction in viable cells respectively. Cytotoxicity of Lubelisin against both human and sheep erythrocytes was low resulting in a therapeutic index of 0.43. Membrane permeabilisation assays using propidium iodide alongside transmission electron microscopy revealed that cytoplasmic membrane damage may contribute to the antimicrobial activities of Lubelisin. CONCLUSIONS We demonstrate that the rumen eukaryotome is a viable source for the discovery of antimicrobial molecules for the treatment of bacterial infections and further development of these may provide part of the potential solution to the ongoing problem of antimicrobial resistance. The role of these AMPs in the ecological warfare within the rumen is also currently unknown.
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Affiliation(s)
- Lucy A Onime
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Linda B Oyama
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Benjamin J Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Jurnorain Gani
- Institute of Infection and Immunity, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Peter Alexander
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Kate E Waddams
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Alan Cookson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Christopher J Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Sharon A Huws
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK.
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32
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Zhong Q, Li G. Adaptively Iterative Multiscale Switching Simulation Strategy and Applications to Protein Folding and Structure Prediction. J Phys Chem Lett 2021; 12:3151-3162. [PMID: 33755493 DOI: 10.1021/acs.jpclett.1c00618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Structure prediction is an important means to quickly understand new protein functions. However, the prediction of effects of proteins that have no detectable templates is still to be improved. Molecular dynamics simulation is supposed to be the primary research tool for structure predictions, but it still has limitations of huge computational cost in all-atom (AA) models and rough accuracy in coarse-grained (CG) models. We propose a universal multiscale simulation strategy named AIMS in which simulations can iteratively switch among multiple resolutions in order to adaptively trade off AA accuracy and CG high-efficiency. AIMS follows the idea of CG-guided enhanced sampling so that final results always keep AA accuracy. We successfully achieve four ab initio and four data-assisted protein structure predictions using AIMS. The prediction result is an ensemble rather than a structure and provides special insights on folding metastable states. AIMS is estimated to achieve a computational speed about 40 times faster than that of conventional AA simulations.
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Affiliation(s)
- Qinglu Zhong
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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33
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Waqas M, Haider A, Rehman A, Qasim M, Umar A, Sufyan M, Akram HN, Mir A, Razzaq R, Rasool D, Tahir RA, Sehgal SA. Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening. BIOMED RESEARCH INTERNATIONAL 2021; 2021:1596834. [PMID: 33728324 PMCID: PMC7910514 DOI: 10.1155/2021/1596834] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/13/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Coronaviruses (CoVs) are enveloped positive-strand RNA viruses which have club-like spikes at the surface with a unique replication process. Coronaviruses are categorized as major pathogenic viruses causing a variety of diseases in birds and mammals including humans (lethal respiratory dysfunctions). Nowadays, a new strain of coronaviruses is identified and named as SARS-CoV-2. Multiple cases of SARS-CoV-2 attacks are being reported all over the world. SARS-CoV-2 showed high death rate; however, no specific treatment is available against SARS-CoV-2. METHODS In the current study, immunoinformatics approaches were employed to predict the antigenic epitopes against SARS-CoV-2 for the development of the coronavirus vaccine. Cytotoxic T-lymphocyte and B-cell epitopes were predicted for SARS-CoV-2 coronavirus protein. Multiple sequence alignment of three genomes (SARS-CoV, MERS-CoV, and SARS-CoV-2) was used to conserved binding domain analysis. RESULTS The docking complexes of 4 CTL epitopes with antigenic sites were analyzed followed by binding affinity and binding interaction analyses of top-ranked predicted peptides with MHC-I HLA molecule. The molecular docking (Food and Drug Regulatory Authority library) was performed, and four compounds exhibiting least binding energy were identified. The designed epitopes lead to the molecular docking against MHC-I, and interactional analyses of the selected docked complexes were investigated. In conclusion, four CTL epitopes (GTDLEGNFY, TVNVLAWLY, GSVGFNIDY, and QTFSVLACY) and four FDA-scrutinized compounds exhibited potential targets as peptide vaccines and potential biomolecules against deadly SARS-CoV-2, respectively. A multiepitope vaccine was also designed from different epitopes of coronavirus proteins joined by linkers and led by an adjuvant. CONCLUSION Our investigations predicted epitopes and the reported molecules that may have the potential to inhibit the SARS-CoV-2 virus. These findings can be a step towards the development of a peptide-based vaccine or natural compound drug target against SARS-CoV-2.
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Affiliation(s)
- Muhammad Waqas
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Ali Haider
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Abdur Rehman
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Ahitsham Umar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Sufyan
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Hafiza Nisha Akram
- Department of Environmental Sciences, Quaid-e-Azam University, Islamabad, Pakistan
| | - Asif Mir
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Roha Razzaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Danish Rasool
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Rana Adnan Tahir
- Department of Biosciences, COMSATS University, Sahiwal Campus, Islamabad, Pakistan
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- Department of Bioinformatics, University of Okara, Okara, Pakistan
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34
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Klein F, Barrera EE, Pantano S. Assessing SIRAH's Capability to Simulate Intrinsically Disordered Proteins and Peptides. J Chem Theory Comput 2021; 17:599-604. [PMID: 33411518 DOI: 10.1021/acs.jctc.0c00948] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The challenges posed by intrinsically disordered proteins (IDPs) to atomistic and coarse-grained (CG) simulations are boosting efforts to develop and reparametrize current force fields. An assessment of the dynamical behavior of IDPs' and unstructured peptides with the CG SIRAH force field suggests that the current version achieves a fair description of IDPs' conformational flexibility. Moreover, we found a remarkable capability to capture the effect of point mutations in loosely structured peptides.
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Affiliation(s)
- Florencia Klein
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, CP 11400, Uruguay.,Graduate Program in Chemistry, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay
| | - Exequiel E Barrera
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, CP 11400, Uruguay.,Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), M5500 Mendoza, Argentina
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, CP 11400, Uruguay.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
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35
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Krishnan G S, Joshi A, Akhtar N, Kaushik V. Immunoinformatics designed T cell multi epitope dengue peptide vaccine derived from non structural proteome. Microb Pathog 2021; 150:104728. [PMID: 33400987 DOI: 10.1016/j.micpath.2020.104728] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 12/20/2020] [Accepted: 12/27/2020] [Indexed: 12/20/2022]
Abstract
Dengue viral disease has been reported as an Aedes aegypti mosquito-borne human disease and causing a severe global public health concern. In this study, immunoinformatics methods was deployed for crafting CTL T-cell epitopes as dengue vaccine candidates. The NS1 protein sequence of dengue serotype 1 strain retrieved from the protein database and T-cell epitopes (n = 85) were predicted by the artificial neural network. The conserved epitopes (n = 10) were predicted and selected for intensive computational analysis. The machine learning technique and quantitative matrix-based toxicity analysis assured nontoxic peptide selection. Hidden Markov Model derived Structural Alphabet (SA) based algorithm predicted the 3D molecular structure and all-atom structure of peptide ligand validated by Ramachandran-plot. Three-tier molecular docking approaches were used to predictthe peptide - HLA docking complex. Molecular dynamics (MD) simulation study confirmed the docking complex was stable in the time frame of 100ns. Population coverage analysis predicted the interaction epitope interaction with a particular population of HLA. These results concluded that the computationally designed HTLWSNGVL and FTTNIWLKL epitope peptides could be used as putative agents for the multi CTL T cell epitope vaccine. The vaccine protein sequence expression and translation were analyzed in the prokaryotic vector adapted by codon usage. Such in silico formulated CTL T-cell-based prophylactic vaccines could encourage the commercial development of dengue vaccines.
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Affiliation(s)
- Sunil Krishnan G
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India.
| | - Amit Joshi
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India.
| | - Nahid Akhtar
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India.
| | - Vikas Kaushik
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India.
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36
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Menichetti R, Giulini M, Potestio R. A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules. THE EUROPEAN PHYSICAL JOURNAL. B 2021; 94:204. [PMID: 34720709 PMCID: PMC8550479 DOI: 10.1140/epjb/s10051-021-00205-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/13/2021] [Indexed: 05/04/2023]
Abstract
ABSTRACT A mapping of a macromolecule is a prescription to construct a simplified representation of the system in which only a subset of its constituent atoms is retained. As the specific choice of the mapping affects the analysis of all-atom simulations as well as the construction of coarse-grained models, the characterisation of the mapping space has recently attracted increasing attention. We here introduce a notion of scalar product and distance between reduced representations, which allows the study of the metric and topological properties of their space in a quantitative manner. Making use of a Wang-Landau enhanced sampling algorithm, we exhaustively explore such space, and examine the qualitative features of mappings in terms of their squared norm. A one-to-one correspondence with an interacting lattice gas on a finite volume leads to the emergence of discontinuous phase transitions in mapping space, which mark the boundaries between qualitatively different reduced representations of the same molecule.
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Affiliation(s)
- Roberto Menichetti
- Physics Department, University of Trento, via Sommarive, 14, 38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, via Sommarive, 14, 38123 Trento, Italy
| | - Marco Giulini
- Physics Department, University of Trento, via Sommarive, 14, 38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, via Sommarive, 14, 38123 Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, via Sommarive, 14, 38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, via Sommarive, 14, 38123 Trento, Italy
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37
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Waqas M, Haider A, Sufyan M, Siraj S, Sehgal SA. Determine the Potential Epitope Based Peptide Vaccine Against Novel SARS-CoV-2 Targeting Structural Proteins Using Immunoinformatics Approaches. Front Mol Biosci 2020; 7:227. [PMID: 33195402 PMCID: PMC7593713 DOI: 10.3389/fmolb.2020.00227] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/11/2020] [Indexed: 12/23/2022] Open
Abstract
Coronaviruses (CoVs) belong to the Coronaviridae-family. The genus Beta-coronaviruses, are enveloped positive strand RNA viruses with club-like spikes at the surface with a unique replication process and a large RNA genome (∼25 kb). CoVs are known as one of the major pathogenic viruses causing a variety of diseases in birds and mammals including humans (lethal respiratory dysfunctions). Recently, a new strain of coronavirus has been identified and named as SARS-CoV-2. A large number of COVID-19 (disease caused by SARS-CoV-2) cases are being diagnosed all over the World especially in China (Wuhan). COVID-19 showed high mortality rate exponentially, however, not even a single effective cure is being introduced yet against COVID-19. In the current study, immunoinformatics approaches were employed to predict the antigenic epitopes against COVID-19 for the development of a coronavirus peptide vaccine. Cytotoxic T-lymphocyte (CTL) and B-cell epitopes were predicted for SARS-CoV-2 coronavirus structural proteins (Spikes, Membrane, Envelope, and Nucleocapsid). The docking complexes of the top 10 epitopes having antigenic sites were analyzed led by binding affinity and binding interactional analyses of top ranked predicted peptides with the MHC-I HLA molecule. The predicted peptides may have potential to be used as peptide vaccine against COVID-19.
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Affiliation(s)
- Muhammad Waqas
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ali Haider
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Sufyan
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Sami Siraj
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
- Department of Bioinformatics, University of Okara, Okara, Pakistan
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38
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Joshi SY, Deshmukh SA. A review of advancements in coarse-grained molecular dynamics simulations. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1828583] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Soumil Y. Joshi
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
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39
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Khan S, Ali SS, Zaheer I, Saleem S, Ziaullah, Zaman N, Iqbal A, Suleman M, Wadood A, Rehman AU, Khan A, Khan A, Wei DQ. Proteome-wide mapping and reverse vaccinology-based B and T cell multi-epitope subunit vaccine designing for immune response reinforcement against Porphyromonas gingivalis. J Biomol Struct Dyn 2020; 40:833-847. [PMID: 32928063 DOI: 10.1080/07391102.2020.1819423] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Porphyromonas gingivalis, a prominent pathogen responsible for acute periodontal diseases, is widely studied by the scientific community for its successful evasion of the host immune system. P. gingivalis is associated with rheumatoid arthritis, dementia, and Alzheimer's. The pathogen successfully survives itself against the heavy load of conventional antibiotics because of its ability to evade the host immune system. Subtractive proteomics and reverse vaccinology approaches were employed in order to prioritize the best proteins for vaccine designing. Three vaccine candidates with Uniprot ID: Q7MWZ2 (histidine Kinase), Q7MVL1 (Fe (2+) transporter), and Q7MWZ2 (Capsular polysaccharide transport protein) were identified for vaccine designing. These proteins are antigenic and essential for pathogen survival. A wide range of immunoinformatics tools was applied for the prediction of epitopes, B, and T cells, for the vaccine candidate proteins. Molecular docking of the predicted epitopes against the MHC molecules were carried out. In-silico vaccine was constructed using carefully evaluated epitopes and consequently modeled for docking with human Toll-like receptor 2. Chain C of Pam3CSK4 (PDB ID; 2Z7X) was linked to the vaccine as an adjuvant to boost immune response towards the vaccine. For stability evaluation of the vaccine-TLR-2 docked complex, Molecular Dynamics simulations were performed. The reverse-translated nucleotide sequence cloned in Eschericia coli to attain the maximal expression of the vaccine protein. The maximal expression was ensured by CAI score of 0.96. The current vaccine requires future experimental validation to confirm its effectiveness. The vaccine developed will be helpful to protect against P. gingivalis associated infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shahzeb Khan
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Iqra Zaheer
- Faculty of Life Sciences, Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Shoaib Saleem
- National Center for Bioinformatics, Quaid-e-azam University, Islamabad, Pakistan
| | - Ziaullah
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Nasib Zaman
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Arshad Iqbal
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Abdul Wadood
- Research and Development Technician at Infineum L.P, Linden, New Jersey, USA
| | - Ashfaq Ur Rehman
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R China
| | - Asghar Khan
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R China.,State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China.,Peng Cheng Laboratory, Shanghai Jiao Tong University, Shanghai, P.R China
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40
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Shivgan AT, Marzinek JK, Huber RG, Krah A, Henchman RH, Matsudaira P, Verma CS, Bond PJ. Extending the Martini Coarse-Grained Force Field to N-Glycans. J Chem Inf Model 2020; 60:3864-3883. [PMID: 32702979 DOI: 10.1021/acs.jcim.0c00495] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glycans play a vital role in a large number of cellular processes. Their complex and flexible nature hampers structure-function studies using experimental techniques. Molecular dynamics (MD) simulations can help in understanding dynamic aspects of glycans if the force field parameters used can reproduce key experimentally observed properties. Here, we present optimized coarse-grained (CG) Martini force field parameters for N-glycans, calibrated against experimentally derived binding affinities for lectins. The CG bonded parameters were obtained from atomistic (ATM) simulations for different glycan topologies including high mannose and complex glycans with various branching patterns. In the CG model, additional elastic networks are shown to improve maintenance of the overall conformational distribution. Solvation free energies and octanol-water partition coefficients were also calculated for various N-glycan disaccharide combinations. When using standard Martini nonbonded parameters, we observed that glycans spontaneously aggregated in the solution and required down-scaling of their interactions for reproduction of ATM model radial distribution functions. We also optimized the nonbonded interactions for glycans interacting with seven lectin candidates and show that a relatively modest scaling down of the glycan-protein interactions can reproduce free energies obtained from experimental studies. These parameters should be of use in studying the role of glycans in various glycoproteins and carbohydrate binding proteins as well as their complexes, while benefiting from the efficiency of CG sampling.
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Affiliation(s)
- Aishwary T Shivgan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Roland G Huber
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Alexander Krah
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Paul Matsudaira
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Chandra S Verma
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
| | - Peter J Bond
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
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41
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Saldaño TE, Freixas VM, Tosatto SCE, Parisi G, Fernandez-Alberti S. Exploring Conformational Space with Thermal Fluctuations Obtained by Normal-Mode Analysis. J Chem Inf Model 2020; 60:3068-3080. [PMID: 32216314 DOI: 10.1021/acs.jcim.9b01136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Proteins in their native states can be represented as ensembles of conformers in dynamical equilibrium. Thermal fluctuations are responsible for transitions between these conformers. Normal-modes analysis (NMA) using elastic network models (ENMs) provides an efficient procedure to explore global dynamics of proteins commonly associated with conformational transitions. In the present work, we present an iterative approach to explore protein conformational spaces by introducing structural distortions according to their equilibrium dynamics at room temperature. The approach can be used either to perform unbiased explorations of conformational space or to explore guided pathways connecting two different conformations, e.g., apo and holo forms. In order to test its performance, four proteins with different magnitudes of structural distortions upon ligand binding have been tested. In all cases, the conformational selection model has been confirmed and the conformational space between apo and holo forms has been encompassed. Different strategies have been tested that impact on the efficiency either to achieve a desired conformational change or to achieve a balanced exploration of the protein conformational multiplicity.
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Affiliation(s)
- Tadeo E Saldaño
- Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD Bernal, Argentina
| | - Victor M Freixas
- Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD Bernal, Argentina
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 5131 Padova, Italy
| | - Gustavo Parisi
- Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD Bernal, Argentina
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42
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Liwo A, Czaplewski C, Sieradzan AK, Lubecka EA, Lipska AG, Golon Ł, Karczyńska A, Krupa P, Mozolewska MA, Makowski M, Ganzynkowicz R, Giełdoń A, Maciejczyk M. Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:73-122. [PMID: 32145953 DOI: 10.1016/bs.pmbts.2019.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this chapter the scale-consistent approach to the derivation of coarse-grained force fields developed in our laboratory is presented, in which the effective energy function originates from the potential of mean force of the system under consideration and embeds atomistically detailed interactions in the resulting energy terms through use of Kubo's cluster-cumulant expansion, appropriate selection of the major degrees of freedom to be averaged out in the derivation of analytical approximations to the energy terms, and appropriate expression of the interaction energies at the all-atom level in these degrees of freedom. Our approach enables the developers to find correct functional forms of the effective coarse-grained energy terms, without having to import them from all-atom force fields or deriving them on a heuristic basis. In particular, the energy terms derived in such a way exhibit correct dependence on coarse-grained geometry, in particular on site orientation. Moreover, analytical formulas for the multibody (correlation) terms, which appear to be crucial for coarse-grained modeling of many of the regular structures such as, e.g., protein α-helices and β-sheets, can be derived in a systematic way. Implementation of the developed theory to the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules, which consists of the UNRES (for proteins), NARES-2P (for nucleic acids), and SUGRES-1P (for polysaccharides) components, and is being developed in our laboratory is described. Successful applications of UNICORN to the prediction of protein structure, simulating the folding and stability of proteins and nucleic acids, and solving biological problems are discussed.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea.
| | | | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Emilia A Lubecka
- Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Gdańsk, Poland
| | | | - Łukasz Golon
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | | | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | | | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Maciej Maciejczyk
- Department of Physics and Biophysics, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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43
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Jorgenson TD, Yucesoy DT, Sarikaya M, Overney RM. Thermal Selection of Aqueous Molecular Conformations for Tailored Energetics of Peptide Assemblies at Solid Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:318-327. [PMID: 31829632 DOI: 10.1021/acs.langmuir.9b02425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Key to the development of functional bioinorganic soft interfaces is the predictive control over the micron-scale assembly structure and energetics of biomolecules at solid interfaces. While assembly of labile biomolecules, such as short peptides, at interfaces is a great deal affected by the shape of the molecule, biomolecular conformations are prompted by external solution conditions, involving temperature, pH, and salt concentration. In this light, one can expect that the environmental conformational selection of aqueous biomolecules could potentially allow for fine-tuning of the equilibrium assembly structure at interfaces, as well as, the binding strength and molecular mobility within these assemblies. Here, we demonstrate the energetic and structural tailoring of two-dimensional surface assemblies of graphite-binding dodecapeptides, through the thermal selection of aqueous peptide conformations. Our findings based on a scanning probe energetic analysis, supplemented by molecular dynamics modeling, show that peptide-graphite and peptide-peptide intermolecular interactions strongly depend on the thermally selected molecular conformation and that the extent of the conformational change is directly related to the observed assembled structure. Enabled by these results was the design of a peptide with predictable binding and assembled structure, thus, suggesting environmental preconditioning of peptides as a means for controlling self-assembling active bioinorganic interfaces for bioelectronic implementations such as biomolecular fuel cells and biosensors.
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Affiliation(s)
- Tyler D Jorgenson
- Molecular Engineering and Sciences Institute , University of Washington , Box 351653, Seattle , Washington 98195-1653 , United States
- GEMSEC, Genetically Engineered Materials Science and Engineering Center , University of Washington , Seattle , Washington 98195 , United States
| | - Deniz T Yucesoy
- GEMSEC, Genetically Engineered Materials Science and Engineering Center , University of Washington , Seattle , Washington 98195 , United States
- Department of Material Science and Engineering , University of Washington , Roberts Hall , Box 352120, Seattle , Washington 98195-2120 , United States
| | - Mehmet Sarikaya
- Molecular Engineering and Sciences Institute , University of Washington , Box 351653, Seattle , Washington 98195-1653 , United States
- GEMSEC, Genetically Engineered Materials Science and Engineering Center , University of Washington , Seattle , Washington 98195 , United States
- Department of Material Science and Engineering , University of Washington , Roberts Hall , Box 352120, Seattle , Washington 98195-2120 , United States
- Department of Chemical Engineering , University of Washington , Benson Hall , Box 351750, Seattle , Washington 98195-1750 , United States
| | - René M Overney
- Molecular Engineering and Sciences Institute , University of Washington , Box 351653, Seattle , Washington 98195-1653 , United States
- Department of Chemical Engineering , University of Washington , Benson Hall , Box 351750, Seattle , Washington 98195-1750 , United States
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44
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Nguyen PH, Sterpone F, Derreumaux P. Aggregation of disease-related peptides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:435-460. [PMID: 32145950 DOI: 10.1016/bs.pmbts.2019.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein misfolding and aggregation of amyloid proteins is the fundamental cause of more than 20 diseases. Molecular mechanisms of the self-assembly and the formation of the toxic aggregates are still elusive. Computer simulations have been intensively used to study the aggregation of amyloid peptides of various amino acid lengths related to neurodegenerative diseases. We review atomistic and coarse-grained simulations of short amyloid peptides aimed at determining their transient oligomeric structures and the early and late aggregation steps.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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Mehmood A, Kaushik AC, Wei DQ. Prediction and validation of potent peptides against herpes simplex virus type 1 via immunoinformatic and systems biology approach. Chem Biol Drug Des 2019; 94:1868-1883. [PMID: 31437863 DOI: 10.1111/cbdd.13602] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/23/2019] [Accepted: 08/10/2019] [Indexed: 12/19/2022]
Abstract
The human herpes simplex virus type 1 (HSV-1) is an extremely rampant human pathogen, and its infection could cause life-long diseases, including the central nervous system disorders. The glycoproteins of HSV-1 such as glycoprotein B, glycoprotein C, glycoprotein D, glycoprotein H, and glycoprotein L are highly involved in mediating the viral attachment and infection of the host cell. Therefore, immunoinformatic approaches followed by molecular dynamics simulation and systems biology has been used to analyze these glycoproteins in order to propose effective peptide-based vaccine candidates against the HSV-1 infection. The ElliPro and NetCTL.1.2 online tools were employed to forecast the B- and T-lymphocyte (CTL) epitopes for gB, gC, gD, gH, and gL. The 3D coordinates of these epitopes were modeled and docked against the human major histocompatibility complex molecule-1. The outcomes obtained from postdocking analysis along with TAP (Transporter associated with antigen processing), MHC binding, and C-terminal cleavage score assisted in the selection of potential epitopes. These epitopes were further subjected to molecular dynamics simulation and systems biology approach which showed significant results. On the basis of these substantial outcomes, peptides are proposed that could be used to provoke immunity against the HSV-1 infection.
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Affiliation(s)
- Aamir Mehmood
- State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Aman Chandra Kaushik
- State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Krupa P, Quoc Huy PD, Li MS. Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components. J Chem Phys 2019. [DOI: 10.1063/1.5093184] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Pawel Krupa
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Pham Dinh Quoc Huy
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
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Park S, Jackman JA, Cho NJ. Comparing the Membrane-Interaction Profiles of Two Antiviral Peptides: Insights into Structure-Function Relationship. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:9934-9943. [PMID: 31291111 DOI: 10.1021/acs.langmuir.9b01052] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In recent years, certain amphipathic, α-helical peptides have been discovered that inhibit medically important enveloped viruses by disrupting the lipid membrane surrounding individual virus particles. Interestingly, only a small subset of amphipathic, α-helical peptides demonstrate inhibitory activity, and there is broad interest in understanding how the structures of these peptides contribute to functional activity against lipid membranes. To address this question, herein, we employed multiple surface-sensitive measurement techniques along with computational simulations in order to investigate how AH and C5A peptides, two of the most biologically active peptides in this class, interact with model lipid membranes while gaining insight into membrane-induced peptide conformational changes. Circular dichroism spectroscopy experiments revealed that both AH and C5A peptides undergo pronounced coil-to-helix transitions in the presence of lipid membrane environments, and the C5A conformational change was the largest. Time-lapsed fluorescence microscopy measurements were conducted to monitor the interaction of peptides with arrays of tethered, individual lipid vesicles and showed that C5A potently lyses lipid vesicles indiscriminate of vesicle size at peptide concentrations as low as 10 nM whereas AH peptide preferentially lyses lipid vesicles with high membrane curvature and is less potent than C5A. These findings were complemented by electrochemical impedance spectroscopy measurements on a tethered lipid bilayer membrane platform, which indicated that C5A solubilizes lipid membranes in a manner that is distinct from how AH disrupts lipid membranes via pore formation. Computational simulations supported that the distinct membrane-interaction profiles arise from different helical folding patterns, whereby AH monomers predominantly exist as two shorter helices with a hinge in-between and C5A monomers form a single helix. Taken together, our findings demonstrate that membrane-active antiviral peptides can exhibit distinct membrane-interaction profiles that confer different degrees of targeting selectivity, and the corresponding structural insights will be useful for peptide engineering applications.
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Affiliation(s)
- Soohyun Park
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue 639798 , Singapore
| | - Joshua A Jackman
- School of Chemical Engineering , Sungkyunkwan University , Suwon 16419 , Republic of Korea
| | - Nam-Joon Cho
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue 639798 , Singapore
- School of Chemical and Biomedical Engineering , Nanyang Technological University , 62 Nanyang Drive 637459 , Singapore
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Barroso da Silva FL, Sterpone F, Derreumaux P. OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field. J Chem Theory Comput 2019; 15:3875-3888. [DOI: 10.1021/acs.jctc.9b00202] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fernando Luís Barroso da Silva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do café, s/no, Ribeirão Preto, São Paulo BR-14040-903, Brazil
- Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot − Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Fabio Sterpone
- Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot − Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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Chan-Yao-Chong M, Durand D, Ha-Duong T. Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles. J Chem Inf Model 2019; 59:1743-1758. [PMID: 30840442 DOI: 10.1021/acs.jcim.8b00928] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The concept of intrinsically disordered proteins (IDPs) has emerged relatively slowly, but over the past 20 years, it has become an intense research area in structural biology. Indeed, because of their considerable flexibility and structural heterogeneity, the determination of IDP conformational ensemble is particularly challenging and often requires a combination of experimental measurements and computational approaches. With the improved accuracy of all-atom force fields and the increasing computing performances, molecular dynamics (MD) simulations have become more and more reliable to generate realistic conformational ensembles. And the combination of MD simulations with experimental approaches, such as nuclear magnetic resonance (NMR) and/or small-angle X-ray scattering (SAXS) allows one to converge toward a more accurate and exhaustive description of IDP structures. In this Review, we discuss the state of the art of MD simulations of IDP conformational ensembles, with a special focus on studies that back-calculated and directly compared theoretical and experimental NMR or SAXS observables, such as chemical shifts (CS), 3J-couplings (3Jc), residual dipolar couplings (RDC), or SAXS intensities. We organize the review in three parts. In the first section, we discuss the studies which used NMR and/or SAXS data to test and validate the development of force fields or enhanced sampling techniques. In the second part, we explore different methods for the refinement of MD-derived structural ensembles, such as NMR or SAXS data-restrained MD simulations or ensemble reweighting to better fit experiments. Finally, we survey some recent studies combining MD simulations with NMR and/or SAXS measurements to investigate the relationship between IDP conformational ensemble and biological activity, as well as their implication in human diseases. From this review, we noticed that quite a few studies compared MD-generated conformational ensembles with both NMR and SAXS measurements to validate IDP structures at both local and global levels. Yet, beside the IDP propensity to form local secondary structures, their dynamic extension or compactness also appears important for their activity. Thus, we believe that a close synergy between MD simulations, NMR, and SAXS experiments would be greatly appropriate to address the challenges of characterizing the disordered structures of proteins and their complexes, relative to their biological functions.
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Affiliation(s)
- Maud Chan-Yao-Chong
- BioCIS, Université Paris-Sud, CNRS , Université Paris-Saclay , 92290 Châtenay-Malabry , France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex, France
| | - Tâp Ha-Duong
- BioCIS, Université Paris-Sud, CNRS , Université Paris-Saclay , 92290 Châtenay-Malabry , France
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Ali A, Khan A, Kaushik AC, Wang Y, Ali SS, Junaid M, Saleem S, Cho WCS, Mao X, Wei DQ. Immunoinformatic and systems biology approaches to predict and validate peptide vaccines against Epstein-Barr virus (EBV). Sci Rep 2019; 9:720. [PMID: 30679646 PMCID: PMC6346095 DOI: 10.1038/s41598-018-37070-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/30/2018] [Indexed: 12/19/2022] Open
Abstract
Epstein-Barr virus (EBV), also known as human herpesvirus 4 (HHV-4), is a member of the Herpesviridae family and causes infectious mononucleosis, Burkitt's lymphoma, and nasopharyngeal carcinoma. Even in the United States of America, the situation is alarming, as EBV affects 95% of the young population between 35 and 40 years of age. In this study, both linear and conformational B-cell epitopes as well as cytotoxic T-lymphocyte (CTL) epitopes were predicted by using the ElliPro and NetCTL.1.2 webservers for EBV proteins (GH, GL, GB, GN, GM, GP42 and GP350). Molecular modelling tools were used to predict the 3D coordinates of peptides, and these peptides were then docked against the MHC molecules to obtain peptide-MHC complexes. Studies of their post-docking interactions helped to select potential candidates for the development of peptide vaccines. Our results predicted a total of 58 T-cell epitopes of EBV; where the most potential were selected based on their TAP, MHC binding and C-terminal Cleavage score. The top most peptides were subjected to MD simulation and stability analysis. Validation of our predicted epitopes using a 0.45 µM concentration was carried out by using a systems biology approach. Our results suggest a panel of epitopes that could be used to immunize populations to protect against multiple diseases caused by EBV.
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Affiliation(s)
- Arif Ali
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Aman Chandra Kaushik
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjie Wang
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Junaid
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shoaib Saleem
- Center for Biotechnology and Microbiology, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Xueying Mao
- Qianweichang College, Shanghai University, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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