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On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides. Polymers (Basel) 2020; 13:polym13010099. [PMID: 33383731 PMCID: PMC7795291 DOI: 10.3390/polym13010099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 12/02/2022] Open
Abstract
Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.
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2
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Kennedy AC, Belgi A, Husselbee BW, Spanswick D, Norton RS, Robinson AJ. α-Conotoxin Peptidomimetics: Probing the Minimal Binding Motif for Effective Analgesia. Toxins (Basel) 2020; 12:E505. [PMID: 32781580 PMCID: PMC7472027 DOI: 10.3390/toxins12080505] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022] Open
Abstract
Several analgesic α-conotoxins have been isolated from marine cone snails. Structural modification of native peptides has provided potent and selective analogues for two of its known biological targets-nicotinic acetylcholine and γ-aminobutyric acid (GABA) G protein-coupled (GABAB) receptors. Both of these molecular targets are implicated in pain pathways. Despite their small size, an incomplete understanding of the structure-activity relationship of α-conotoxins at each of these targets has hampered the development of therapeutic leads. This review scrutinises the N-terminal domain of the α-conotoxin family of peptides, a region defined by an invariant disulfide bridge, a turn-inducing proline residue and multiple polar sidechain residues, and focusses on structural features that provide analgesia through inhibition of high-voltage-activated Ca2+ channels. Elucidating the bioactive conformation of this region of these peptides may hold the key to discovering potent drugs for the unmet management of debilitating chronic pain associated with a wide range of medical conditions.
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Affiliation(s)
- Adam C. Kennedy
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
| | - Alessia Belgi
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
| | - Benjamin W. Husselbee
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
| | - David Spanswick
- Biomedicine Discovery Institute and the Department of Physiology, Monash University, Victoria 3800, Australia;
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- NeuroSolutions Ltd., Coventry CV4 7AL, UK
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia;
- ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria 3052, Australia
| | - Andrea J. Robinson
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
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3
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Mansbach RA, Travers T, McMahon BH, Fair JM, Gnanakaran S. Snails In Silico: A Review of Computational Studies on the Conopeptides. Mar Drugs 2019; 17:E145. [PMID: 30832207 PMCID: PMC6471681 DOI: 10.3390/md17030145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 12/26/2022] Open
Abstract
Marine cone snails are carnivorous gastropods that use peptide toxins called conopeptides both as a defense mechanism and as a means to immobilize and kill their prey. These peptide toxins exhibit a large chemical diversity that enables exquisite specificity and potency for target receptor proteins. This diversity arises in terms of variations both in amino acid sequence and length, and in posttranslational modifications, particularly the formation of multiple disulfide linkages. Most of the functionally characterized conopeptides target ion channels of animal nervous systems, which has led to research on their therapeutic applications. Many facets of the underlying molecular mechanisms responsible for the specificity and virulence of conopeptides, however, remain poorly understood. In this review, we will explore the chemical diversity of conopeptides from a computational perspective. First, we discuss current approaches used for classifying conopeptides. Next, we review different computational strategies that have been applied to understanding and predicting their structure and function, from machine learning techniques for predictive classification to docking studies and molecular dynamics simulations for molecular-level understanding. We then review recent novel computational approaches for rapid high-throughput screening and chemical design of conopeptides for particular applications. We close with an assessment of the state of the field, emphasizing important questions for future lines of inquiry.
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Affiliation(s)
- Rachael A Mansbach
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Benjamin H McMahon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Jeanne M Fair
- Biosecurity and Public Health Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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4
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Mutagenesis of α-Conotoxins for Enhancing Activity and Selectivity for Nicotinic Acetylcholine Receptors. Toxins (Basel) 2019; 11:toxins11020113. [PMID: 30781866 PMCID: PMC6409848 DOI: 10.3390/toxins11020113] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 02/04/2023] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are found throughout the mammalian body and have been studied extensively because of their implication in a myriad of diseases. α-Conotoxins (α-CTxs) are peptide neurotoxins found in the venom of marine snails of genus Conus. α-CTxs are potent and selective antagonists for a variety of nAChR isoforms. Over the past 40 years, α-CTxs have proven to be valuable molecular probes capable of differentiating between closely related nAChR subtypes and have contributed greatly to understanding the physiological role of nAChRs in the mammalian nervous system. Here, we review the amino acid composition and structure of several α-CTxs that selectively target nAChR isoforms and explore strategies and outcomes for introducing mutations in native α-CTxs to direct selectivity and enhance binding affinity for specific nAChRs. This review will focus on structure-activity relationship studies involving native α-CTxs that have been rationally mutated and molecular interactions that underlie binding between ligand and nAChR isoform.
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5
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Biabanikhankahdani R, Bayat S, Ho KL, Alitheen NBM, Tan WS. A Simple Add-and-Display Method for Immobilisation of Cancer Drug on His-tagged Virus-like Nanoparticles for Controlled Drug Delivery. Sci Rep 2017; 7:5303. [PMID: 28706267 PMCID: PMC5509718 DOI: 10.1038/s41598-017-05525-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/30/2017] [Indexed: 01/19/2023] Open
Abstract
pH-responsive virus-like nanoparticles (VLNPs) hold promising potential as drug delivery systems for cancer therapy. In the present study, hepatitis B virus (HBV) VLNPs harbouring His-tags were used to display doxorubicin (DOX) via nitrilotriacetic acid (NTA) conjugation. The His-tags served as pH-responsive nanojoints which released DOX from VLNPs in a controlled manner. The His-tagged VLNPs conjugated non-covalently with NTA-DOX, and cross-linked with folic acid (FA) were able to specifically target and deliver the DOX into ovarian cancer cells via folate receptor (FR)-mediated endocytosis. The cytotoxicity and cellular uptake results revealed that the His-tagged VLNPs significantly increased the accumulation of DOX in the ovarian cancer cells and enhanced the uptake of DOX, which improved anti-tumour effects. This study demonstrated that NTA-DOX can be easily displayed on His-tagged VLNPs by a simple Add-and-Display step with high coupling efficiency and the drug was only released at low pH in a controlled manner. This approach facilitates specific attachment of any drug molecule on His-tagged VLNPs at the very mild conditions without changing the biological structure and native conformation of the VLNPs.
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Affiliation(s)
- Roya Biabanikhankahdani
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Saadi Bayat
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Noorjahan Banu Mohamed Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Wen Siang Tan
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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6
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Xu M, Zhu X, Yu J, Yu J, Luo S, Wang X. The crystal structure of Ac-AChBP in complex with α-conotoxin LvIA reveals the mechanism of its selectivity towards different nAChR subtypes. Protein Cell 2017; 8:675-685. [PMID: 28585176 PMCID: PMC5563285 DOI: 10.1007/s13238-017-0426-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/27/2017] [Indexed: 12/15/2022] Open
Abstract
The α3* nAChRs, which are considered to be promising drug targets for problems such as pain, addiction, cardiovascular function, cognitive disorders etc., are found throughout the central and peripheral nervous system. The α-conotoxin (α-CTx) LvIA has been identified as the most selective inhibitor of α3β2 nAChRs known to date, and it can distinguish the α3β2 nAChR subtype from the α6/α3β2β3 and α3β4 nAChR subtypes. However, the mechanism of its selectivity towards α3β2, α6/α3β2β3, and α3β4 nAChRs remains elusive. Here we report the co-crystal structure of LvIA in complex with Aplysia californica acetylcholine binding protein (Ac-AChBP) at a resolution of 3.4 Å. Based on the structure of this complex, together with homology modeling based on other nAChR subtypes and binding affinity assays, we conclude that Asp-11 of LvIA plays an important role in the selectivity of LvIA towards α3β2 and α3/α6β2β3 nAChRs by making a salt bridge with Lys-155 of the rat α3 subunit. Asn-9 lies within a hydrophobic pocket that is formed by Met-36, Thr-59, and Phe-119 of the rat β2 subunit in the α3β2 nAChR model, revealing the reason for its more potent selectivity towards the α3β2 nAChR subtype. These results provide molecular insights that can be used to design ligands that selectively target α3β2 nAChRs, with significant implications for the design of new therapeutic α-CTxs.
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Affiliation(s)
- Manyu Xu
- The Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing, 100084, China
| | - Xiaopeng Zhu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, 570228, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing, 100084, China
| | - Jinpeng Yu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, 570228, China
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, 570228, China.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing, 100084, China.
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7
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Wu X, Lee J, Brooks BR. Origin of pK a Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water. J Phys Chem B 2016; 121:3318-3330. [PMID: 27700118 DOI: 10.1021/acs.jpcb.6b08249] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein internal ionizable groups can exhibit large shifts in pKa values. Although the environment and interaction changes have been extensively studied both experimentally and computationally, direct calculation of pKa values of these internal ionizable groups in explicit water is challenging due to energy barriers in solvent interaction and in conformational transition. The virtual mixture of multiple states (VMMS) method is a new approach designed to study chemical state equilibrium. This method constructs a virtual mixture of multiple chemical states in order to sample the conformational space of all states simultaneously and to avoid crossing energy barriers related to state transition. By applying VMMS to 25 variants of staphylococcal nuclease with lysine residues at internal positions, we obtained the pKa values of these lysine residues and investigated the physics underlining the pKa shifts. Our calculation results agree reasonably well with experimental measurements, validating the VMMS method for pKa calculation and providing molecular details of the protonation equilibrium for protein internal ionizable groups. Based on our analyses of protein conformation relaxation, lysine side chain flexibility, water penetration, and the microenvironment, we conclude that the hydrophobicity of the microenvironment around the lysine side chain (which affects water penetration differently for different protonation states) plays an important role in the pKa shifts.
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Affiliation(s)
- Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Juyong Lee
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
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8
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Daniel Phillips P, Andersen T, M. McDougal O. Assessing the utility and limitations of high throughput virtual screening. AIMS MOLECULAR SCIENCE 2016. [DOI: 10.3934/molsci.2016.2.238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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9
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Chu C, Lundeen RA, Sander M, McNeill K. Assessing the Indirect Photochemical Transformation of Dissolved Combined Amino Acids through the Use of Systematically Designed Histidine-Containing Oligopeptides. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:12798-12807. [PMID: 26425803 DOI: 10.1021/acs.est.5b03498] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Photooxidation is an important abiotic transformation pathway for amino acids (AAs) in sunlit waters. Although dissolved free AAs are well studied, the photooxidation of dissolved combined AAs (DCAAs) remains poorly investigated. This study is a systematic investigation of the effect of neighboring photostable AA residues (i.e., aliphatic, cationic, anionic, or aromatic residues) on the environmental indirect photochemical transformation of histidine (His) in His-containing oligopeptides. The pKa values of His residues in the studied oligopeptides were found to be between 4.3 and 8.1. Accordingly, the phototransformation rate constants of the His-containing oligopeptides were highly pH-dependent in an environmentally relevant pH range with higher reactivity for neutral His than for the protonated species. The photostable AA residues significantly modulated the photoreactivity of oligopeptides either through altering the accessibility of His to photochemically produced oxidants or through shifting the pKa values of His residues. In addition, the influence of neighboring photostable AA residues on the sorption-enhanced phototransformation of oligopeptides in solutions containing chromophoric dissolved organic matter (CDOM) was assessed. The constituent photostable AA residues promoted sorption of His-containing oligopeptides to CDOM macromolecules through electrostatic attraction, hydrophobic effects, and/or low-barrier hydrogen bonds, and subsequently increased the apparent phototransformation rate constants by up to 2 orders of magnitude.
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Affiliation(s)
- Chiheng Chu
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
| | - Rachel A Lundeen
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
| | - Kristopher McNeill
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
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10
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Schutt TC, Bharadwaj VS, Granum DM, Maupin CM. The impact of active site protonation on substrate ring conformation in Melanocarpus albomyces cellobiohydrolase Cel7B. Phys Chem Chem Phys 2015; 17:16947-58. [DOI: 10.1039/c5cp01801c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding how the protonation state of active site residues impacts the enzyme's structure and substrate conformation is important for improving the efficiency and economic viability of the degradation of cellulosic materials as feedstock for liquid fuel and value-added chemicals.
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Affiliation(s)
- Timothy C. Schutt
- Chemical and Biological Engineering Department
- Colorado School of Mines
- Golden
- USA
| | - Vivek S. Bharadwaj
- Chemical and Biological Engineering Department
- Colorado School of Mines
- Golden
- USA
| | - David M. Granum
- Chemical and Biological Engineering Department
- Colorado School of Mines
- Golden
- USA
| | - C. Mark Maupin
- Chemical and Biological Engineering Department
- Colorado School of Mines
- Golden
- USA
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11
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Chen W, Morrow BH, Shi C, Shen JK. Recent development and application of constant pH molecular dynamics. MOLECULAR SIMULATION 2014; 40:830-838. [PMID: 25309035 DOI: 10.1080/08927022.2014.907492] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Solution pH is a critical environmental factor for chemical and biological processes. Over the last decade, significant efforts have been made in the development of constant pH molecular dynamics (pHMD) techniques for gaining detailed insights into pH-coupled dynamical phenomena. In this article we review the advancement of this field in the past five years, placing a special emphasis on the development of the all-atom continuous pHMD technique. We discuss various applications, including the prediction of pKa shifts for proteins, nucleic acids and surfactant assemblies, elucidation of pH-dependent population shifts, protein-protein and protein-RNA binding, as well as the mechanisms of pH-dependent self-assembly and phase transitions of surfactants and peptides. We also discuss future directions for the further improvement of the pHMD techniques.
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Affiliation(s)
- Wei Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Brian H Morrow
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Chuanyin Shi
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Jana K Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
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12
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Granum DM, Schutt TC, Maupin CM. Computational Evaluation of the Dynamic Fluctuations of Peripheral Loops Enclosing the Catalytic Tunnel of a Family 7 Cellobiohydrolase. J Phys Chem B 2014; 118:5340-9. [DOI: 10.1021/jp5011555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David M. Granum
- Chemical
and Biological Engineering
Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Timothy C. Schutt
- Chemical
and Biological Engineering
Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - C. Mark Maupin
- Chemical
and Biological Engineering
Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
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13
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Sambasivarao SV, Roberts J, Bharadwaj VS, Slingsby JG, Rohleder C, Mallory C, Groome JR, McDougal OM, Maupin CM. Acetylcholine promotes binding of α-conotoxin MII at α3 β2 nicotinic acetylcholine receptors. Chembiochem 2014; 15:413-24. [PMID: 24420650 DOI: 10.1002/cbic.201300577] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Indexed: 11/09/2022]
Abstract
α-Conotoxin MII (α-CTxMII) is a 16-residue peptide with the sequence GCCSNPVCHLEHSNLC, containing Cys2-Cys8 and Cys3-Cys16 disulfide bonds. This peptide, isolated from the venom of the marine cone snail Conus magus, is a potent and selective antagonist of neuronal nicotinic acetylcholine receptors (nAChRs). To evaluate the impact of channel-ligand interactions on ligand-binding affinity, homology models of the heteropentameric α3β2-nAChR were constructed. The models were created in MODELLER with the aid of experimentally characterized structures of the Torpedo marmorata-nAChR (Tm-nAChR, PDB ID: 2BG9) and the Aplysia californica-acetylcholine binding protein (Ac-AChBP, PDB ID: 2BR8) as templates for the α3- and β2-subunit isoforms derived from rat neuronal nAChR primary amino acid sequences. Molecular docking calculations were performed with AutoDock to evaluate interactions of the heteropentameric nAChR homology models with the ligands acetylcholine (ACh) and α-CTxMII. The nAChR homology models described here bind ACh with binding energies commensurate with those of previously reported systems, and identify critical interactions that facilitate both ACh and α-CTxMII ligand binding. The docking calculations revealed an increased binding affinity of the α3β2-nAChR for α-CTxMII with ACh bound to the receptor, and this was confirmed through two-electrode voltage clamp experiments on oocytes from Xenopus laevis. These findings provide insights into the inhibition and mechanism of electrostatically driven antagonist properties of the α-CTxMIIs on nAChRs.
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Affiliation(s)
- Somisetti V Sambasivarao
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden, CO 80401 (USA)
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14
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Granum DM, Vyas S, Sambasivarao SV, Maupin CM. Computational Evaluations of Charge Coupling and Hydrogen Bonding in the Active Site of a Family 7 Cellobiohydrolase. J Phys Chem B 2014; 118:434-48. [DOI: 10.1021/jp408536s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David M. Granum
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Shubham Vyas
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Somisetti V. Sambasivarao
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - C. Mark Maupin
- Chemical and Biological Engineering Department and ‡Chemistry and Geochemistry Department, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
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