1
|
Lobato JCM, Arouche TDS, Nero JD, Filho T, Borges RDS, Neto AMDJC. Interactions between carbon nanotubes and external structures of SARS-CoV-2 using molecular docking and molecular dynamics. J Mol Struct 2023; 1286:135604. [PMID: 37089815 PMCID: PMC10111146 DOI: 10.1016/j.molstruc.2023.135604] [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: 01/08/2023] [Revised: 04/01/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
Molecular modeling techniques are used to describe the process of interaction between nanotubes and the main structures of the Covid-19 virus: the envelope protein, the main protease, and the Spike glycoprotein. Molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics simulations provide information on the mean squared deviation of atomic positions between 0.5 and 3.0 Å. The Gibbs free energy model and solvent accessible surface area approaches are used. Through the results obtained through molecular dynamics simulations, it is noted that the zig-zag nanotube prefers to interact with E-pro, M-pro, and S-gly, respectively. Molecular couplings and free energy showed that the S-gly active site residues strongly interact with zigzag, chiral, and armchair nanotubes, in this order. The interactions demonstrated in this manuscript may predict some promising candidates for virus antagonists, which may be confirmed through experimental approaches.
Collapse
Affiliation(s)
- Júlio Cesar Mendes Lobato
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil
- Proderna, Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil
| | - Tiago da Silva Arouche
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil
| | - Jordan Del Nero
- Physics Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, 66075-110, Belém, PA, Brazil
| | - TarcisoAndrade Filho
- Federal University of the South and Southeast of Pará. 68507-590, Marabá - PA, Brazil
| | - Rosivaldo Dos Santos Borges
- Pharmacy Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil
| | - Antonio Maia de Jesus Chaves Neto
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil
- Physics Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, 66075-110, Belém, PA, Brazil
- Chemistry and Biochemistry, The University of Texas at Arlington, Box 19065, 700 Planetarium Place, Room 130, Arlington, TX 76019-0065
| |
Collapse
|
2
|
Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
Collapse
Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
3
|
Lee OS, Petrenko VI, Šipošová K, Musatov A, Park H, Lanceros-Méndez S. How fullerenes inhibit the amyloid fibril formation of hen lysozyme. J IND ENG CHEM 2022. [DOI: 10.1016/j.jiec.2021.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
4
|
Lee OS, Madjet ME, Mahmoud KA. Antibacterial Mechanism of Multifunctional MXene Nanosheets: Domain Formation and Phase Transition in Lipid Bilayer. NANO LETTERS 2021; 21:8510-8517. [PMID: 34402623 DOI: 10.1021/acs.nanolett.1c01986] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
MXenes, two-dimensional metal carbides or nitrides with multifunctional surfaces, are one of the most promising antibacterial nanoscale materials. However, their putative bactericidal mechanism is elusive. To study their bactericidal mechanism, we investigated the interaction between a MXene nanosheet and a model bacterial membrane by molecular dynamics simulations and found that an adsorbed MXene on a membrane surface induced a local phase transition in a domain where the fluidity of the phospholipid in this domain at room temperature was comparable with that of the gel phase. The domain also showed a denser and thinner phospholipid membrane structure than the peripheral phospholipids. By comparing it with our previous experiments of the bactericidal activity of MXenes, we proposed the leakage of intercellular molecules at the phase boundary defects as a possible bactericidal mechanism of MXenes that leads to cell lysis. This study provides a useful model for tailoring new bactericidal nanomaterials.
Collapse
Affiliation(s)
- One-Sun Lee
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, PO Box 34110 Doha, Qatar
| | - Mohamed E Madjet
- Max-Planck-Institut für Physik, Komplexer Systeme, Nöthnitzer Straße 38, 01187 Dresden, Germany
| | - Khaled A Mahmoud
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, PO Box 34110 Doha, Qatar
| |
Collapse
|
5
|
Abstract
Membrane proteins play crucial roles in cellular processes and are often important pharmacological drug targets. The hydrophobic properties of these proteins make full structural and functional characterization challenging because of the need to use detergents or other solubilizing agents when extracting them from their native lipid membranes. To aid membrane protein research, new methodologies are required to allow these proteins to be expressed and purified cheaply, easily, in high yield and to provide water soluble proteins for subsequent study. This mini review focuses on the relatively new area of water soluble membrane proteins and in particular two innovative approaches: the redesign of membrane proteins to yield water soluble variants and how adding solubilizing fusion proteins can help to overcome these challenges. This review also looks at naturally occurring membrane proteins, which are able to exist as stable, functional, water soluble assemblies with no alteration to their native sequence.
Collapse
|
6
|
Characterization of a computationally designed water-soluble human μ-opioid receptor variant using available structural information. Anesthesiology 2014; 121:866-75. [PMID: 24835677 DOI: 10.1097/aln.0000000000000308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The recent X-ray crystal structure of the murine μ-opioid receptor (MUR) allowed the authors to reengineer a previously designed water-soluble variant of the transmembrane portion of the human MUR (wsMUR-TM). METHODS The new variant of water-soluble MUR (wsMUR-TM_v2) was engineered based on the murine MUR crystal structure. This novel variant was expressed in Escherichia coli and purified. The properties of the receptor were characterized and compared with those of wsMUR-TM. RESULTS Seven residues originally included for mutation in the design of the wsMUR-TM were reverted to their native identities. wsMUR-TM_v2 contains 16% mutations of the total sequence. It was overexpressed and purified with high yield. Although dimers and higher oligomers were observed to form over time, the wsMUR-TM_v2 stayed predominantly monomeric at concentrations as high as 7.5 mg/ml in buffer within a 2-month period. Its secondary structure was predominantly helical and comparable with those of both the original wsMUR-TM variant and the native MUR. The binding affinity of wsMUR-TM_v2 for naltrexone (K(d) approximately 70 nM) was in close agreement with that for wsMUR-TM. The helical content of wsMUR-TM_v2 decreased cooperatively with increasing temperature, and the introduction of sucrose was able to stabilize the protein. CONCLUSIONS A novel functional wsMUR-TM_v2 with only 16% mutations was successfully engineered, expressed in E. coli, and purified based on information from the crystal structure of murine MUR. This not only provides a novel alternative tool for MUR studies in solution conditions but also offers valuable information for protein engineering and structure-function relations.
Collapse
|
7
|
Perez-Aguilar JM, Xi J, Matsunaga F, Cui X, Selling B, Saven JG, Liu R. A computationally designed water-soluble variant of a G-protein-coupled receptor: the human mu opioid receptor. PLoS One 2013; 8:e66009. [PMID: 23799068 PMCID: PMC3682944 DOI: 10.1371/journal.pone.0066009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/30/2013] [Indexed: 11/19/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) play essential roles in various physiological processes, and are widely targeted by pharmaceutical drugs. Despite their importance, studying GPCRs has been problematic due to difficulties in isolating large quantities of these membrane proteins in forms that retain their ligand binding capabilities. Creating water-soluble variants of GPCRs by mutating the exterior, transmembrane residues provides a potential method to overcome these difficulties. Here we present the first study involving the computational design, expression and characterization of water-soluble variant of a human GPCR, the human mu opioid receptor (MUR), which is involved in pain and addiction. An atomistic structure of the transmembrane domain was built using comparative (homology) modeling and known GPCR structures. This structure was highly similar to the subsequently determined structure of the murine receptor and was used to computationally design 53 mutations of exterior residues in the transmembrane region, yielding a variant intended to be soluble in aqueous media. The designed variant expressed in high yield in Escherichia coli and was water soluble. The variant shared structural and functionally related features with the native human MUR, including helical secondary structure and comparable affinity for the antagonist naltrexone (Kd = 65 nM). The roles of cholesterol and disulfide bonds on the stability of the receptor variant were also investigated. This study exemplifies the potential of the computational approach to produce water-soluble variants of GPCRs amenable for structural and functionally related characterization in aqueous solution.
Collapse
Affiliation(s)
- Jose Manuel Perez-Aguilar
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jin Xi
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Felipe Matsunaga
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Xu Cui
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Bernard Selling
- Impact Biologicals Inc., Swarthmore, Pennsylvania, United States of America
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RL); (JGS)
| | - Renyu Liu
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RL); (JGS)
| |
Collapse
|
8
|
Perez-Aguilar JM, Saven JG. Computational design of membrane proteins. Structure 2012; 20:5-14. [PMID: 22244752 DOI: 10.1016/j.str.2011.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/21/2011] [Accepted: 12/21/2011] [Indexed: 11/26/2022]
Abstract
Membrane proteins are involved in a wide variety of cellular processes, and are typically part of the first interaction a cell has with extracellular molecules. As a result, these proteins comprise a majority of known drug targets. Membrane proteins are among the most difficult proteins to obtain and characterize, and a structure-based understanding of their properties can be difficult to elucidate. Notwithstanding, the design of membrane proteins can provide stringent tests of our understanding of these crucial biological systems, as well as introduce novel or targeted functionalities. Computational design methods have been particularly helpful in addressing these issues, and this review discusses recent studies that tailor membrane proteins to display specific structures or functions and examines how redesigned membrane proteins are being used to facilitate structural and functional studies.
Collapse
|
9
|
Cui T, Mowrey D, Bondarenko V, Tillman T, Ma D, Landrum E, Perez-Aguilar JM, He J, Wang W, Saven JG, Eckenhoff RG, Tang P, Xu Y. NMR structure and dynamics of a designed water-soluble transmembrane domain of nicotinic acetylcholine receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:617-26. [PMID: 22155685 DOI: 10.1016/j.bbamem.2011.11.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 11/22/2011] [Indexed: 11/29/2022]
Abstract
The nicotinic acetylcholine receptor (nAChR) is an important therapeutic target for a wide range of pathophysiological conditions, for which rational drug designs often require receptor structures at atomic resolution. Recent proof-of-concept studies demonstrated a water-solubilization approach to structure determination of membrane proteins by NMR (Slovic et al., PNAS, 101: 1828-1833, 2004; Ma et al., PNAS, 105: 16537-42, 2008). We report here the computational design and experimental characterization of WSA, a water-soluble protein with ~83% sequence identity to the transmembrane (TM) domain of the nAChR α1 subunit. Although the design was based on a low-resolution structural template, the resulting high-resolution NMR structure agrees remarkably well with the recent crystal structure of the TM domains of the bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC), demonstrating the robustness and general applicability of the approach. NMR T(2) dispersion measurements showed that the TM2 domain of the designed protein was dynamic, undergoing conformational exchange on the NMR timescale. Photoaffinity labeling with isoflurane and propofol photolabels identified a common binding site in the immediate proximity of the anesthetic binding site found in the crystal structure of the anesthetic-GLIC complex. Our results illustrate the usefulness of high-resolution NMR analyses of water-solubilized channel proteins for the discovery of potential drug binding sites.
Collapse
Affiliation(s)
- Tanxing Cui
- Department of Anesthesiology, University of Pittsburgh School of Medicine, PA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Kim HJ, Howell SC, Van Horn WD, Jeon YH, Sanders CR. Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 55:335-360. [PMID: 20161395 PMCID: PMC2782866 DOI: 10.1016/j.pnmrs.2009.07.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Hak Jun Kim
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, 406-840, Korea
| | - Stanley C. Howell
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Wade D. Van Horn
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Young Ho Jeon
- Center for Magnetic Resonance, Korea Basic Research Institute, Daejon, 305-333, Korea
| | - Charles R. Sanders
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
- Corresponding Author: ; phone: 615-936-3756; fax: 615-936-2211
| |
Collapse
|
11
|
Kang SG, Saven JG. Computational protein design: structure, function and combinatorial diversity. Curr Opin Chem Biol 2007; 11:329-34. [PMID: 17524729 DOI: 10.1016/j.cbpa.2007.05.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Accepted: 05/10/2007] [Indexed: 11/26/2022]
Abstract
Computational protein design has blossomed with the development of methods for addressing the complexities involved in specifying the structure, sequence and function of proteins. Recent applications include the design of novel functional membrane and soluble proteins, proteins incorporating non-biological components and protein combinatorial libraries.
Collapse
Affiliation(s)
- Seung-gu Kang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | | |
Collapse
|