1
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Reyes Romero A, Kubica K, Kitel R, Rodríguez I, Magiera-Mularz K, Dömling A, Holak TA, Surmiak E. Computer- and NMR-Aided Design of Small-Molecule Inhibitors of the Hub1 Protein. Molecules 2022; 27:8282. [PMID: 36500376 PMCID: PMC9738620 DOI: 10.3390/molecules27238282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
By binding to the spliceosomal protein Snu66, the human ubiquitin-like protein Hub1 is a modulator of the spliceosome performance and facilitates alternative splicing. Small molecules that bind to Hub1 would be of interest to study the protein-protein interaction of Hub1/Snu66, which is linked to several human pathologies, such as hypercholesterolemia, premature aging, neurodegenerative diseases, and cancer. To identify small molecule ligands for Hub1, we used the interface analysis, peptide modeling of the Hub1/Snu66 interaction and the fragment-based NMR screening. Fragment-based NMR screening has not proven sufficient to unambiguously search for fragments that bind to the Hub1 protein. This was because the Snu66 binding pocket of Hub1 is occupied by pH-sensitive residues, making it difficult to distinguish between pH-induced NMR shifts and actual binding events. The NMR analyses were therefore verified experimentally by microscale thermophoresis and by NMR pH titration experiments. Our study found two small peptides that showed binding to Hub1. These peptides are the first small-molecule ligands reported to interact with the Hub1 protein.
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Affiliation(s)
- Atilio Reyes Romero
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kubica
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Radoslaw Kitel
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Ismael Rodríguez
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Department of Innovative Chemistry, Palackӯ University, CATRIN, Šlechtitelů 241/27, 779 00 Olomouc, Czech Republic
| | - Tad A. Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Ewa Surmiak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
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2
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Jakhmola S, Sk MF, Chatterjee A, Jain K, Kar P, Jha HC. A plausible contributor to multiple sclerosis; presentation of antigenic myelin protein epitopes by major histocompatibility complexes. Comput Biol Med 2022; 148:105856. [PMID: 35863244 DOI: 10.1016/j.compbiomed.2022.105856] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/17/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Multiple sclerosis (MS) can be induced upon successful presentation of myelin antigens by MHC I/II. Antigenic similarity between the myelin and viral proteins may worsen the immunological responses. METHODOLOGY Antigenic regions within myelin proteins; PLP1, MBP, MOG, and MAG were analyzed using SVMTrip and EMBOSS. Homology search identified sequence similarity between the predicted host epitopes and viral proteins. NetMHCpan predicted MHC I/II binding followed by peptide-protein docking through the HPEPDOCK server. Thereafter we analyzed conformational flexibility and stability of 15 protein-peptide complexes based on high docking scores. The binding free energy was calculated using conventional (MD) and Gaussian accelerated molecular dynamics simulation. RESULTS PLP1, MBP, MAG and MOG contained numerous antigenic epitopes. MBP and MOG epitopes had sequence similarity to HHV-6 BALF5; EBNA1 and CMV glycoprotein M (gM), and EBV LMP2B, gp350/220; HHV-8 ORFs respectively. Many herpes virus proteins like tegument, envelope glycoproteins, and ORFs of EBV, CMV, HHV-6, and HHV-8 demonstrated sequence similarity with MAG and PLP1. Some antigenic peptides were also linear B-cell epitopes and influenced cytokine production by T-cell. MHC I allele HLA-B*57:01 bound to PLP1 peptide and HLA-A*68:02 bound to a MAG peptide strongly. MHC II alleles HLA-DRB1*04:05 and HLA-DR1*01:01 associated with MAG- and MOG-derived peptides, respectively, demonstrating high HPEPDOCK scores. MD simulations established stable binding of certain peptides with the MHC namely HLA-B*51:01-MBP(DYKSAHKGFKGVDAQGTLSKIFKL), HLA-B*57:01-PLP1(PDKFVGITYALTVVWLLVFACSAVPVYIYF), HLA-DR1*01:01-MOG(VEDPFYWVSPGVLVLLAVLPVLLLQITVGLVFLCLQYR) and HLA-DRB1*04:05-MAG(TWVQVSLLHFVPTREA). CONCLUSIONS Cross-reactivity between self-antigens and pathogen derived immunodominant epitopes may induce MS. Our study supported the role of specific MHC alleles as a contributing MS risk factor.
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Affiliation(s)
- Shweta Jakhmola
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India.
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Akash Chatterjee
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Khushboo Jain
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India.
| | - Hem Chandra Jha
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India.
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3
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Najm AAK, Azfaralariff A, Dyari HRE, Othman BA, Shahid M, Khalili N, Law D, Syed Alwi SS, Fazry S. Anti-breast cancer synthetic peptides derived from the Anabas testudineus skin mucus fractions. Sci Rep 2021; 11:23182. [PMID: 34848729 PMCID: PMC8632885 DOI: 10.1038/s41598-021-02007-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/09/2021] [Indexed: 01/17/2023] Open
Abstract
Previous study has shown the antimicrobial activities of mucus protein extracted from Anabastestudineus. In this study, we are interested in characterizing the anticancer activity of the A.testudineus antimicrobial peptides (AMPs). The mucus was extracted, fractioned, and subjected to antibacterial activity testing to confirm the fish's AMPs production. The cytotoxic activity of each fraction was also identified. Fraction 2 (F2), which shows toxicity against MCF7 and MDA-MB-231 were sent for peptide sequencing to identify the bioactive peptide. The two peptides were then synthetically produced and subjected to cytotoxic assay to prove their efficacy against cancer cell lines. The IC50 for AtMP1 against MCF7 and MDA-MB-231 were 8.25 ± 0.14 μg/ml and 9.35 ± 0.25 μg/ml respectively, while for AtMP2 it is 5.89 ± 0.14 μg/ml and 6.97 ± 0.24 μg/ml respectively. AtMP1 and AtMP2 treatment for 48 h induced breast cancer cell cycle arrest and apoptosis by upregulating the p53, which lead to upregulate pro-apoptotic BAX gene and downregulate the anti-apoptotic BCL-2 gene, consequently, trigger the activation of the caspase-3. This interaction was supported by docking analysis (QuickDBD, HPEPDOCK, and ZDOCK) and immunoprecipitation. This study provided new prospects in the development of highly effective and selective cancer therapeutics based on antimicrobial peptides.
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Affiliation(s)
- Ahmed Abdul Kareem Najm
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Ahmad Azfaralariff
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia.,Innovative Center for Confectionery Technology (MANIS), Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Herryawan Ryadi Eziwar Dyari
- Department of Earth Sciences and Environmental, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Babul Airianah Othman
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Muhammad Shahid
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Nahid Khalili
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Douglas Law
- Faculty of Health and Life Sciences, Inti International University, Persiaran Perdana BBN Putra Nilai, 71800, Nilai, Negeri Sembilan, Malaysia
| | - Sharifah Sakinah Syed Alwi
- Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Shazrul Fazry
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia. .,Innovative Center for Confectionery Technology (MANIS), Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia. .,Chini Lake Research Centre, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia.
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4
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Kurcinski M, Kmiecik S, Zalewski M, Kolinski A. Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations. Int J Mol Sci 2021; 22:ijms22147341. [PMID: 34298961 PMCID: PMC8306105 DOI: 10.3390/ijms22147341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/03/2021] [Accepted: 07/04/2021] [Indexed: 12/21/2022] Open
Abstract
Most of the protein–protein docking methods treat proteins as almost rigid objects. Only the side-chains flexibility is usually taken into account. The few approaches enabling docking with a flexible backbone typically work in two steps, in which the search for protein–protein orientations and structure flexibility are simulated separately. In this work, we propose a new straightforward approach for docking sampling. It consists of a single simulation step during which a protein undergoes large-scale backbone rearrangements, rotations, and translations. Simultaneously, the other protein exhibits small backbone fluctuations. Such extensive sampling was possible using the CABS coarse-grained protein model and Replica Exchange Monte Carlo dynamics at a reasonable computational cost. In our proof-of-concept simulations of 62 protein–protein complexes, we obtained acceptable quality models for a significant number of cases.
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5
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Kurcinski M, Pawel Ciemny M, Oleniecki T, Kuriata A, Badaczewska-Dawid AE, Kolinski A, Kmiecik S. CABS-dock standalone: a toolbox for flexible protein-peptide docking. Bioinformatics 2020; 35:4170-4172. [PMID: 30865258 PMCID: PMC6792116 DOI: 10.1093/bioinformatics/btz185] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/30/2019] [Accepted: 03/12/2019] [Indexed: 12/02/2022] Open
Abstract
Summary CABS-dock standalone is a multiplatform Python package for protein–peptide docking with backbone flexibility. The main feature of the CABS-dock method is its ability to simulate significant backbone flexibility of the entire protein–peptide system in a reasonable computational time. In the default mode, the package runs a simulation of fully flexible peptide searching for a binding site on the surface of a flexible protein receptor. The flexibility level of the molecules may be defined by the user. Furthermore, the CABS-dock standalone application provides users with full control over the docking simulation from the initial setup to the analysis of results. The standalone version is an upgrade of the original web server implementation—it introduces a number of customizable options, provides support for large-sized systems and offers a framework for deeper analysis of docking results. Availability and implementation CABS-dock standalone is distributed under the MIT licence, which is free for academic and non-profit users. It is implemented in Python and Fortran. The CABS-dock standalone source code, wiki with documentation and examples of use and installation instructions for Linux, macOS and Windows are available in the CABS-dock standalone repository at https://bitbucket.org/lcbio/cabsdock.
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Affiliation(s)
- Mateusz Kurcinski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Maciej Pawel Ciemny
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.,Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Tymoteusz Oleniecki
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Aleksander Kuriata
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | - Andrzej Kolinski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
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6
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Badaczewska-Dawid AE, Kmiecik S, Koliński M. Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement. Brief Bioinform 2020; 22:5855394. [PMID: 32520310 PMCID: PMC8138832 DOI: 10.1093/bib/bbaa109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022] Open
Abstract
The structural description of peptide ligands bound to G protein-coupled receptors (GPCRs) is important for the discovery of new drugs and deeper understanding of the molecular mechanisms of life. Here we describe a three-stage protocol for the molecular docking of peptides to GPCRs using a set of different programs: (1) CABS-dock for docking fully flexible peptides; (2) PD2 method for the reconstruction of atomistic structures from C-alpha traces provided by CABS-dock and (3) Rosetta FlexPepDock for the refinement of protein–peptide complex structures and model scoring. We evaluated the proposed protocol on the set of seven different GPCR–peptide complexes (including one containing a cyclic peptide), for which crystallographic structures are available. We show that CABS-dock produces high resolution models in the sets of top-scored models. These sets of models, after reconstruction to all-atom representation, can be further improved by Rosetta high-resolution refinement and/or minimization, leading in most of the cases to sub-Angstrom accuracy in terms of interface root-mean-square-deviation measure.
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Affiliation(s)
| | | | - Michał Koliński
- Corresponding author: Michał Koliński, Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawińskiego St, 02-106 Warsaw, Poland. Tel: (+48) 22 849 93 58; Fax: (+48) 22 668 55 32; E-mail:
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7
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Namazi F, Bolhassani A, Sadat SM, Irani S. Delivery of HIV-1 Polyepitope Constructs Using Cationic and Amphipathic Cell Penetrating Peptides into Mammalian Cells. Curr HIV Res 2020; 17:408-428. [DOI: 10.2174/1570162x17666191121114522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022]
Abstract
Background:
An effective vaccine against human immunodeficiency virus 1 (HIV-1) is
an important global health priority. Despite many efforts in the development of the HIV-1 vaccine,
no effective vaccine has been approved yet. Recently, polyepitope vaccines including several immunogenic
and conserved epitopes of HIV-1 proteins have received special attention.
Methods:
In this study, HIV-1 Nef, Tat, Gp160 and P24 proteins were considered for selection of
immunodominant and conserved epitopes due to their critical roles in the viral life cycle and pathogenesis.
At first, the Nef60-84-Nef126-144-Tat29-49-Gp16030-53-Gp160308-323-P248-151 DNA construct was
designed using in silico studies. Then, the DNA construct was subcloned in pEGFP-N1 and pET-
24a (+) expression vectors and the rNef-Tat-Gp160-P24 polyepitope peptide was generated in E.coli
expression system for in vitro delivery using novel cell-penetrating peptides (CPPs), LDP-NLS and
CyLoP-1, in a non-covalent manner. Also, the HR9 and MPG CPPs were used to transfer the DNA
construct.
Results:
Our results showed that the recombinant polyepitope peptide generated in Rosetta strain
migrated as a clear band of ~31 kDa in SDS-PAGE. The SEM data confirmed the formation of stable
nanoparticles with a size below 250 nm. MTT assay revealed that the complexes did not represent
any considerable cytotoxic effect compared to untreated cells. The results of fluorescence microscopy,
flow cytometry and western blotting indicated that these CPPs successfully delivered polyepitope
constructs into HEK-293T cell line.
Conclusion:
These data suggested that these CPPs can be used as a promising approach for the development
of the HIV-1 vaccine.
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Affiliation(s)
- Fatemeh Namazi
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Mehdi Sadat
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Shiva Irani
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
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8
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Kurcinski M, Badaczewska‐Dawid A, Kolinski M, Kolinski A, Kmiecik S. Flexible docking of peptides to proteins using CABS-dock. Protein Sci 2020; 29:211-222. [PMID: 31682301 PMCID: PMC6933849 DOI: 10.1002/pro.3771] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022]
Abstract
Molecular docking of peptides to proteins can be a useful tool in the exploration of the possible peptide binding sites and poses. CABS-dock is a method for protein-peptide docking that features significant conformational flexibility of both the peptide and the protein molecules during the peptide search for a binding site. The CABS-dock has been made available as a web server and a standalone package. The web server is an easy to use tool with a simple web interface. The standalone package is a command-line program dedicated to professional users. It offers a number of advanced features, analysis tools and support for large-sized systems. In this article, we outline the current status of the CABS-dock method, its recent developments, applications, and challenges ahead.
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Affiliation(s)
- Mateusz Kurcinski
- Faculty of Chemistry, Biological and Chemical Research CenterUniversity of WarsawWarsawPoland
| | | | - Michal Kolinski
- Bioinformatics Laboratory, Mossakowski Medical Research CentrePolish Academy of SciencesWarsawPoland
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research CenterUniversity of WarsawWarsawPoland
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research CenterUniversity of WarsawWarsawPoland
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9
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Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein-Peptide Complex Structures. Methods Mol Biol 2020; 2165:273-287. [PMID: 32621231 DOI: 10.1007/978-1-0716-0708-4_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Structural characterizations of protein-peptide complexes may require further improvements. These may include reconstruction of missing atoms and/or structure optimization leading to higher accuracy models. In this work, we describe a workflow that generates accurate structural models of peptide-protein complexes starting from protein-peptide models in C-alpha representation generated using CABS-dock molecular docking. First, protein-peptide models are reconstructed from their C-alpha traces to all-atom representation using MODELLER. Next, they are refined using Rosetta FlexPepDock. The described workflow allows for reliable all-atom reconstruction of CABS-dock models and their further improvement to high-resolution models.
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10
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Blaszczyk M, Ciemny MP, Kolinski A, Kurcinski M, Kmiecik S. Protein-peptide docking using CABS-dock and contact information. Brief Bioinform 2019; 20:2299-2305. [PMID: 30247502 PMCID: PMC6954405 DOI: 10.1093/bib/bby080] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 12/11/2022] Open
Abstract
CABS-dock is a computational method for protein-peptide molecular docking that does not require predefinition of the binding site. The peptide is treated as fully flexible, while the protein backbone undergoes small fluctuations and, optionally, large-scale rearrangements. Here, we present a specific CABS-dock protocol that enhances the docking procedure using fragmentary information about protein-peptide contacts. The contact information is used to narrow down the search for the binding peptide pose to the proximity of the binding site. We used information on a single-chosen and randomly chosen native protein-peptide contact to validate the protocol on the peptiDB benchmark. The contact information significantly improved CABS-dock performance. The protocol has been made available as a new feature of the CABS-dock web server (at http://biocomp.chem.uw.edu.pl/CABSdock/). SHORT ABSTRACT CABS-dock is a tool for flexible docking of peptides to proteins. In this article, we present a protocol for CABS-dock docking driven by information about protein-peptide contact(s). Using information on individual protein-peptide contacts allows to improve the accuracy of CABS-dock docking.
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11
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Ciemny MP, Badaczewska-Dawid AE, Pikuzinska M, Kolinski A, Kmiecik S. Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields. Int J Mol Sci 2019; 20:E606. [PMID: 30708941 PMCID: PMC6386871 DOI: 10.3390/ijms20030606] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/20/2022] Open
Abstract
The description of protein disordered states is important for understanding protein folding mechanisms and their functions. In this short review, we briefly describe a simulation approach to modeling protein interactions, which involve disordered peptide partners or intrinsically disordered protein regions, and unfolded states of globular proteins. It is based on the CABS coarse-grained protein model that uses a Monte Carlo (MC) sampling scheme and a knowledge-based statistical force field. We review several case studies showing that description of protein disordered states resulting from CABS simulations is consistent with experimental data. The case studies comprise investigations of protein⁻peptide binding and protein folding processes. The CABS model has been recently made available as the simulation engine of multiscale modeling tools enabling studies of protein⁻peptide docking and protein flexibility. Those tools offer customization of the modeling process, driving the conformational search using distance restraints, reconstruction of selected models to all-atom resolution, and simulation of large protein systems in a reasonable computational time. Therefore, CABS can be combined in integrative modeling pipelines incorporating experimental data and other modeling tools of various resolution.
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Affiliation(s)
- Maciej Pawel Ciemny
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | | | - Monika Pikuzinska
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
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12
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Blaszczyk M, Gront D, Kmiecik S, Kurcinski M, Kolinski M, Ciemny MP, Ziolkowska K, Panek M, Kolinski A. Protein Structure Prediction Using Coarse-Grained Models. SPRINGER SERIES ON BIO- AND NEUROSYSTEMS 2019. [DOI: 10.1007/978-3-319-95843-9_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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13
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Ding F, Peng W. Probing the local conformational flexibility in receptor recognition: mechanistic insight from an atomic-scale investigation. RSC Adv 2019; 9:13968-13980. [PMID: 35519308 PMCID: PMC9064033 DOI: 10.1039/c9ra01906e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/28/2019] [Indexed: 12/13/2022] Open
Abstract
Inherent protein conformational flexibility is important for biomolecular recognition, but this critical property is often neglected in several studies. This event can lead to large deviations in the research results. In the current contribution, we disclose the effects of the local conformational flexibility on receptor recognition by using an atomic-scale computational method. The results indicated that both static and dynamic reaction modes have noticeable differences, and these originated from the structural features of the protein molecules. Dynamic interaction results displayed that the structural stability and conformational flexibility of the proteins had a significant influence on the recognition processes. This point related closely to the characteristics of the flexible loop regions where bixin located within the protein structures. The energy decomposition analyses and circular dichroism results validated the rationality of the recognition studies. More importantly, the conformational and energy changes of some residues around the bixin binding domain were found to be vital to biological reactions. These microscopic findings clarified the nature of the phenomenon that the local conformational flexibility could intervene in receptor recognition. Obviously, this report may provide biophysical evidence for the exploration of the structure–function relationships of the biological receptors in the human body. The local conformational flexibility and dynamics have significant impacts on the receptor recognition processes, and this phenomenon is related closely to the structural characteristics of the flexible loop domains in biomacromolecules.![]()
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Affiliation(s)
- Fei Ding
- School of Environmental Science and Engineering
- Chang'an University
- Xi'an 710064
- China
- Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education
| | - Wei Peng
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- China
- Department of Chemistry
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14
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Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci 2018; 19:ijms19113496. [PMID: 30404229 PMCID: PMC6274762 DOI: 10.3390/ijms19113496] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022] Open
Abstract
Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this minireview, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions, and highly simplified structure-based elastic network models of protein flexibility. In contrast to classical all-atom molecular dynamics, the modeling strategies discussed here allow the quite accurate modeling of much larger systems and longer-time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.
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