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Zhu Z, Deng Z, Wang Q, Wang Y, Zhang D, Xu R, Guo L, Wen H. Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design. Front Pharmacol 2022; 13:939555. [PMID: 35837274 PMCID: PMC9275593 DOI: 10.3389/fphar.2022.939555] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Ion channels are expressed in almost all living cells, controlling the in-and-out communications, making them ideal drug targets, especially for central nervous system diseases. However, owing to their dynamic nature and the presence of a membrane environment, ion channels remain difficult targets for the past decades. Recent advancement in cryo-electron microscopy and computational methods has shed light on this issue. An explosion in high-resolution ion channel structures paved way for structure-based rational drug design and the state-of-the-art simulation and machine learning techniques dramatically improved the efficiency and effectiveness of computer-aided drug design. Here we present an overview of how simulation and machine learning-based methods fundamentally changed the ion channel-related drug design at different levels, as well as the emerging trends in the field.
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Affiliation(s)
- Zhengdan Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Institute of Big Data Research, Beijing, China
| | - Zhenfeng Deng
- DP Technology, Beijing, China
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | | | | | - Duo Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- DP Technology, Beijing, China
| | - Ruihan Xu
- DP Technology, Beijing, China
- National Engineering Research Center of Visual Technology, Peking University, Beijing, China
| | | | - Han Wen
- DP Technology, Beijing, China
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2
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Mao J, Akhtar J, Zhang X, Sun L, Guan S, Li X, Chen G, Liu J, Jeon HN, Kim MS, No KT, Wang G. Comprehensive strategies of machine-learning-based quantitative structure-activity relationship models. iScience 2021; 24:103052. [PMID: 34553136 PMCID: PMC8441174 DOI: 10.1016/j.isci.2021.103052] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Early quantitative structure-activity relationship (QSAR) technologies have unsatisfactory versatility and accuracy in fields such as drug discovery because they are based on traditional machine learning and interpretive expert features. The development of Big Data and deep learning technologies significantly improve the processing of unstructured data and unleash the great potential of QSAR. Here we discuss the integration of wet experiments (which provide experimental data and reliable verification), molecular dynamics simulation (which provides mechanistic interpretation at the atomic/molecular levels), and machine learning (including deep learning) techniques to improve QSAR models. We first review the history of traditional QSAR and point out its problems. We then propose a better QSAR model characterized by a new iterative framework to integrate machine learning with disparate data input. Finally, we discuss the application of QSAR and machine learning to many practical research fields, including drug development and clinical trials.
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Affiliation(s)
- Jiashun Mao
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen, Guangdong 518055 China
| | - Javed Akhtar
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, Guangdong 518055, China
| | - Xiao Zhang
- Shanghai Rural Commercial Bank Co., Ltd, Shanghai 200002, China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Shenghui Guan
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen, Guangdong 518055 China
| | - Xinyu Li
- School of Life and Health Sciences and Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Guangming Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, Guangdong 518055, China
| | - Jiaxin Liu
- Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyeon-Nae Jeon
- Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Min Sung Kim
- Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Kyoung Tai No
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea
| | - Guanyu Wang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Computational Science and Material Design, Shenzhen, Guangdong 518055 China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, Guangdong 518055, China
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Borah SM, Jha AN. Identification and analysis of structurally critical fragments in HopS2. BMC Bioinformatics 2019; 19:552. [PMID: 30717655 PMCID: PMC7394326 DOI: 10.1186/s12859-018-2551-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/30/2018] [Indexed: 12/02/2022] Open
Abstract
Background Among the diverse roles of the Type III secretion-system (T3SS), one of the notable functions is that it serves as unique nano machineries in gram-negative bacteria that facilitate the translocation of effector proteins from bacteria into their host. These effector proteins serve as potential targets to control the pathogenicity conferred to the bacteria. Despite being ideal choices to disrupt bacterial systems, it has been quite an ordeal in the recent times to experimentally reveal and establish a concrete sequence-structure-function relationship for these effector proteins. This work focuses on the disease-causing spectrum of an effector protein, HopS2 secreted by the phytopathogen Pseudomonas syringae pv. tomato DC3000. Results The study addresses the structural attributes of HopS2 via a bioinformatics approach to by-pass some of the experimental shortcomings resulting in mining some critical regions in the effector protein. We have elucidated the functionally important regions of HopS2 with the assistance of sequence and structural analyses. The sequence based data supports the presence of important regions in HopS2 that are present in the other functional parts of Hop family proteins. Furthermore, these regions have been validated by an ab-initio structure prediction of the protein followed by 100 ns long molecular dynamics (MD) simulation. The assessment of these secondary structural regions has revealed the stability and importance of these regions in the protein structure. Conclusions The analysis has provided insights on important functional regions that may be vital to the effector functioning. In dearth of ample experimental evidence, such a bioinformatics approach has helped in the revelation of a few structural regions which will aid in future experiments to attain and evaluate the structural and functional aspects of this protein family. Electronic supplementary material The online version of this article (10.1186/s12859-018-2551-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sapna M Borah
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Anupam Nath Jha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India.
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Song J, Yang Y, Mauvais-Jarvis F, Wang YP, Niu T. KCNJ11, ABCC8 and TCF7L2 polymorphisms and the response to sulfonylurea treatment in patients with type 2 diabetes: a bioinformatics assessment. BMC MEDICAL GENETICS 2017; 18:64. [PMID: 28587604 PMCID: PMC5461698 DOI: 10.1186/s12881-017-0422-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 05/11/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Type 2 diabetes (T2D) is a worldwide epidemic with considerable health and economic consequences. Sulfonylureas are widely used drugs for the treatment of patients with T2D. KCNJ11 and ABCC8 encode the Kir6.2 (pore-forming subunit) and SUR1 (regulatory subunit that binds to sulfonylurea) of pancreatic β cell KATP channel respectively with a critical role in insulin secretion and glucose homeostasis. TCF7L2 encodes a transcription factor expressed in pancreatic β cells that regulates insulin production and processing. Because mutations of these genes could affect insulin secretion stimulated by sulfonylureas, the aim of this study is to assess associations between molecular variants of KCNJ11, ABCC8 and TCF7L2 genes and response to sulfonylurea treatment and to predict their potential functional effects. METHODS Based on a comprehensive literature search, we found 13 pharmacogenetic studies showing that single nucleotide polymorphisms (SNPs) located in KCNJ11: rs5219 (E23K), ABCC8: rs757110 (A1369S), rs1799854 (intron 15, exon 16 -3C/T), rs1799859 (R1273R), and TCF7L2: rs7903146 (intron 4) were significantly associated with responses to sulfonylureas. For in silico bioinformatics analysis, SIFT, PolyPhen-2, PANTHER, MutPred, and SNPs3D were applied for functional predictions of 36 coding (KCNJ11: 10, ABCC8: 24, and TCF7L2: 2; all are missense), and HaploReg v4.1, RegulomeDB, and Ensembl's VEP were used to predict functions of 7 non-coding (KCNJ11: 1, ABCC8: 1, and TCF7L2: 5) SNPs, respectively. RESULTS Based on various in silico tools, 8 KCNJ11 missense SNPs, 23 ABCC8 missense SNPs, and 2 TCF7L2 missense SNPs could affect protein functions. Of them, previous studies showed that mutant alleles of 4 KCNJ11 missense SNPs and 5 ABCC8 missense SNPs can be successfully rescued by sulfonylurea treatments. Further, 3 TCF7L2 non-coding SNPs (rs7903146, rs11196205 and rs12255372), can change motif(s) based on HaploReg v4.1 and are predicted as risk factors by Ensembl's VEP. CONCLUSIONS Our study indicates that a personalized medicine approach by tailoring sulfonylurea therapy of T2D patients according to their genotypes of KCNJ11, ABCC8, and TCF7L2 could attain an optimal treatment efficacy.
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Affiliation(s)
- Jingwen Song
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Yunzhong Yang
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Franck Mauvais-Jarvis
- Division of Endocrinology and Metabolism, Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112 USA
| | - Yu-Ping Wang
- Department of Biomedical Engineering, Tulane University School of Science and Engineering, New Orleans, LA 70118 USA
| | - Tianhua Niu
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
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Rational design of xylose dehydrogenase for improved thermostability and its application in development of efficient enzymatic biofuel cell. Enzyme Microb Technol 2016; 84:78-85. [DOI: 10.1016/j.enzmictec.2015.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 11/25/2015] [Accepted: 12/01/2015] [Indexed: 11/22/2022]
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Unraveling the mechanism of selective ion transport in hydrophobic subnanometer channels. Proc Natl Acad Sci U S A 2015; 112:10851-6. [PMID: 26283377 DOI: 10.1073/pnas.1513718112] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently reported synthetic organic nanopore (SONP) can mimic a key feature of natural ion channels, i.e., selective ion transport. However, the physical mechanism underlying the K(+)/Na(+) selectivity for the SONPs is dramatically different from that of natural ion channels. To achieve a better understanding of the selective ion transport in hydrophobic subnanometer channels in general and SONPs in particular, we perform a series of ab initio molecular dynamics simulations to investigate the diffusivity of aqua Na(+) and K(+) ions in two prototype hydrophobic nanochannels: (i) an SONP with radius of 3.2 Å, and (ii) single-walled carbon nanotubes (CNTs) with radii of 3-5 Å (these radii are comparable to those of the biological potassium K(+) channels). We find that the hydration shell of aqua Na(+) ion is smaller than that of aqua K(+) ion but notably more structured and less yielding. The aqua ions do not lower the diffusivity of water molecules in CNTs, but in SONP the diffusivity of aqua ions (Na(+) in particular) is strongly suppressed due to the rugged inner surface. Moreover, the aqua Na(+) ion requires higher formation energy than aqua K(+) ion in the hydrophobic nanochannels. As such, we find that the ion (K(+) vs. Na(+)) selectivity of the (8, 8) CNT is ∼20× higher than that of SONP. Hence, the (8, 8) CNT is likely the most efficient artificial K(+) channel due in part to its special interior environment in which Na(+) can be fully solvated, whereas K(+) cannot. This work provides deeper insights into the physical chemistry behind selective ion transport in nanochannels.
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Shahlaei M, Mousavi A. A Conformational Analysis Study on the Melanocortin 4 Receptor Using Multiple Molecular Dynamics Simulations. Chem Biol Drug Des 2015; 86:309-21. [DOI: 10.1111/cbdd.12495] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 05/29/2014] [Accepted: 06/13/2014] [Indexed: 12/28/2022]
Affiliation(s)
- Mohsen Shahlaei
- Novel Drug Delivery Research Center; School of Pharmacy; Kermanshah University of Medical Sciences; Parastar Bolvar 6734667149 Kermanshah Iran
| | - Atefeh Mousavi
- Student Research Committee; School of Pharmacy; Kermanshah University of Medical Sciences; Parastar Bolvar 6734667149 Kermanshah Iran
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Martin GM, Chen PC, Devaraneni P, Shyng SL. Pharmacological rescue of trafficking-impaired ATP-sensitive potassium channels. Front Physiol 2013; 4:386. [PMID: 24399968 PMCID: PMC3870925 DOI: 10.3389/fphys.2013.00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/09/2013] [Indexed: 12/25/2022] Open
Abstract
ATP-sensitive potassium (KATP) channels link cell metabolism to membrane excitability and are involved in a wide range of physiological processes including hormone secretion, control of vascular tone, and protection of cardiac and neuronal cells against ischemic injuries. In pancreatic β-cells, KATP channels play a key role in glucose-stimulated insulin secretion, and gain or loss of channel function results in neonatal diabetes or congenital hyperinsulinism, respectively. The β-cell KATP channel is formed by co-assembly of four Kir6.2 inwardly rectifying potassium channel subunits encoded by KCNJ11 and four sulfonylurea receptor 1 subunits encoded by ABCC8. Many mutations in ABCC8 or KCNJ11 cause loss of channel function, thus, congenital hyperinsulinism by hampering channel biogenesis and hence trafficking to the cell surface. The trafficking defects caused by a subset of these mutations can be corrected by sulfonylureas, KATP channel antagonists that have long been used to treat type 2 diabetes. More recently, carbamazepine, an anticonvulsant that is thought to target primarily voltage-gated sodium channels has been shown to correct KATP channel trafficking defects. This article reviews studies to date aimed at understanding the mechanisms by which mutations impair channel biogenesis and trafficking and the mechanisms by which pharmacological ligands overcome channel trafficking defects. Insight into channel structure-function relationships and therapeutic implications from these studies are discussed.
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Affiliation(s)
- Gregory M Martin
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University Portland, OR, USA
| | - Pei-Chun Chen
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University Portland, OR, USA
| | - Prasanna Devaraneni
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University Portland, OR, USA
| | - Show-Ling Shyng
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University Portland, OR, USA
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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10
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Vyas VK, Ukawala RD, Ghate M, Chintha C. Homology modeling a fast tool for drug discovery: current perspectives. Indian J Pharm Sci 2012. [PMID: 23204616 PMCID: PMC3507339 DOI: 10.4103/0250-474x.102537] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery.
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Affiliation(s)
- V K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad-382 481, India
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Conductance properties of the inwardly rectifying channel, Kir3.2: molecular and Brownian dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:471-8. [PMID: 23022491 DOI: 10.1016/j.bbamem.2012.09.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 09/17/2012] [Accepted: 09/20/2012] [Indexed: 02/08/2023]
Abstract
Using the recently unveiled crystal structure, and molecular and Brownian dynamics simulations, we elucidate several conductance properties of the inwardly rectifying potassium channel, Kir3.2, which is implicated in cardiac and neurological disorders. We show that the pore is closed by a hydrophobic gating mechanism similar to that observed in Kv1.2. Once open, potassium ions move into, but not out of, the cell. The asymmetrical current-voltage relationship arises from the lack of negatively charged residues at the narrow intracellular mouth of the channel. When four phenylalanine residues guarding the intracellular gate are mutated to glutamate residues, the channel no longer shows inward rectification. Inward rectification is restored in the mutant Kir3.2 when it becomes blocked by intracellular Mg(2+). Tertiapin, a polypeptide toxin isolated from the honey bee, is known to block several subtypes of the inwardly rectifying channels with differing affinities. We identify critical residues in the toxin and Kir3.2 for the formation of the stable complex. A lysine residue of tertiapin protrudes into the selectivity filter of Kir3.2, while two other basic residues of the toxin form hydrogen bonds with acidic residues located just outside the channel entrance. The depth of the potential of mean force encountered by tertiapin is -16.1kT, thus indicating that the channel will be half-blocked by 0.4μM of the toxin.
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12
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Baker J, Wright SH, Tama F. Simulations of substrate transport in the multidrug transporter EmrD. Proteins 2012; 80:1620-32. [PMID: 22434745 DOI: 10.1002/prot.24056] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 01/22/2012] [Accepted: 01/27/2012] [Indexed: 11/07/2022]
Abstract
EmrD is a multidrug resistance (MDR) transporter from Escherichia coli, which is involved in the efflux of amphipathic compounds from the cytoplasm, and the first MDR member of the major facilitator superfamily to be crystallized. Molecular dynamics simulation of EmrD in a phospholipid bilayer was used to characterize the conformational dynamics of the protein. Motions that support a previously proposed lateral diffusion pathway for substrate from the cytoplasmic membrane leaflet into the EmrD central cavity were observed. In addition, the translocation pathway of meta-chloro carbonylcyanide phenylhydrazone (CCCP) was probed using both standard and steered molecular dynamics simulation. In particular, interactions of a few specific residues with CCCP have been identified. Finally, a large motion of two residues, Val 45 and Leu 233, was observed with the passage of CCCP into the periplasmic space, placing a lower bound on the extent of opening required at this end of the protein for substrate transport. Overall, our simulations probe details of the transport pathway, motions of EmrD at an atomic level of detail, and offer new insights into the functioning of MDR transporters.
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Affiliation(s)
- Joseph Baker
- Department of Physics, The University of Arizona, Tucson, AZ 85721, USA
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13
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Raja M, Olrichs NK, Vales E, Schrempf H. Transferring knowledge towards understanding the pore stabilizing variations in K+ channels. J Bioenerg Biomembr 2012; 44:199-205. [DOI: 10.1007/s10863-012-9407-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Ganoth A, Alhadeff R, Kohen D, Arkin IT. Characterization of the Na⁺/H⁺ antiporter from Yersinia pestis. PLoS One 2011; 6:e26115. [PMID: 22102858 PMCID: PMC3216949 DOI: 10.1371/journal.pone.0026115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 09/19/2011] [Indexed: 11/30/2022] Open
Abstract
Yersinia pestis, the bacterium that historically accounts for the Black Death epidemics, has nowadays gained new attention as a possible biological warfare agent. In this study, its Na/H antiporter is investigated for the first time, by a combination of experimental and computational methodologies. We determined the protein's substrate specificity and pH dependence by fluorescence measurements in everted membrane vesicles. Subsequently, we constructed a model of the protein's structure and validated the model using molecular dynamics simulations. Taken together, better understanding of the Yersinia pestis Na/H antiporter's structure-function relationship may assist in studies on ion transport, mechanism of action and designing specific blockers of Na/H antiporter to help in fighting Yersinia pestis -associated infections. We hope that our model will prove useful both from mechanistic and pharmaceutical perspectives.
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Affiliation(s)
- Assaf Ganoth
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Raphael Alhadeff
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dovrat Kohen
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isaiah T. Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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15
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Raja M. Diverse gating in K+ channels: differential role of the pore-helix glutamate in stabilizing the channel pore. Biochem Biophys Res Commun 2011; 413:1-4. [PMID: 21872570 DOI: 10.1016/j.bbrc.2011.08.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 08/13/2011] [Indexed: 10/17/2022]
Abstract
The selectivity filter and adjacent regions in the bacterial KcsA and inwardly rectifying K(+) (Kir) channels reveal significant conformational changes that cause the channel pore to transition from an activated to inactive state (C-type inactivation) once the channel is open. The meshwork of residues stabilizing the pore of KcsA involves Glu71-Asp80 carboxyl-carboxylate interaction 'behind' the selectivity filter. Interestingly, the Kir channels do not have this exact interaction, but instead have a Glu-Arg salt bridge where the Glu is in the same position but the Arg is one position N-terminal compared to the Asp in KcsA. Also, the Kir channels lack the Trp that hydrogen bonds to Asp80 in KcsA. Here, the sequence and structural information are combined to understand the dissimilarity in the role of the pore-helix Glu in stabilizing the pore structure in KcsA and Kir channels. This review illustrates that although Glu is quite conserved among both types of channels, the network of interactions is not translatable from one channel to the other; thereby suggesting a unique phenomenon of diverse gating patterns in K(+) channels.
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Affiliation(s)
- Mobeen Raja
- School of Molecular and Systems Medicine, 6126 HRIF East, Alberta Diabetes Institute, University of Alberta, Edmonton AB, Canada T6G 2E1.
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16
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Li W, Zhou F, Liu B, Feng D, He Y, Qi K, Wang H, Wang J. Comparative characterization, expression pattern and function analysis of the 12-oxo-phytodienoic acid reductase gene family in rice. PLANT CELL REPORTS 2011; 30:981-995. [PMID: 21249367 DOI: 10.1007/s00299-011-1002-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/02/2011] [Accepted: 01/05/2011] [Indexed: 05/30/2023]
Abstract
The 12-oxo-phytodienoic acid reductases (OPRs) belong to the old yellow enzyme family of flavoenzymes and form multiple subfamilies in angiosperm plants. In our previous study, a comparative genomic analysis showed that five OPR subfamilies (subs. I-V) occur in monocots, and two subfamilies (subs. I and II) in dicots. Here, a comparative study of five OsOPR genes, representing five subfamilies (I-V) in rice, was performed to provide insights into OPR biochemical properties and physiological importance. Comparative analysis of the three-dimensional structure by homology modeling indicated all five OsOPR proteins contained a highly conserved backbone with (α/β)(8)-barrels, while two middle variable regions (MVR i and ii) were also detected and defined. Analysis of enzymatic characteristics revealed that all five OsOPR fusion proteins exhibit distinct substrate specificity. Different catalytic activity was observed using racemic OPDA and trans-2-hexen-1-al as substrates, suggesting OsOPR family genes participate in two main branches of the octadecanoid pathway, including the allene oxide synthase and hydroperoxide lyase pathways which regulate various developmental processes and/or defense responses. The transcript profiles of five OsOPR genes exhibited strong tissue-specific and inducible expression patterns under abiotic stress, hormones and plant wounding treatments. Furthermore, the transcriptions of OsOPR04-1 (OsOPR11) and OsOPR08-1 (OsOPR7), representing subs. I and II, respectively, were observed in all six selected tissues and with all above-stress treatments. This suggests that these two subfamilies play an important role during different developmental stages and in response to stresses; while the expressions of OsOPR06-1 (OsOPR6), OsOPR01-1 (OsOPR10) and OsOPR02-1 (OsOPR8), representing subs. III, IV and V respectively, were strongly up-regulated with abscisic acid (ABA) and indoleacetic acid (IAA) treatments in roots, suggesting these three subfamilies play an important role in responding to hormones especially ABA and IAA signals in roots.
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Affiliation(s)
- Wenyan Li
- State Key Laboratory for Biocontrol and Key Laboratory of Gene Engineering of Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
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17
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Ganoth A, Alhadeff R, Arkin IT. Computational study of the Na+/H + antiporter from Vibrio parahaemolyticus. J Mol Model 2010; 17:1877-90. [PMID: 21107625 DOI: 10.1007/s00894-010-0883-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 10/19/2010] [Indexed: 11/25/2022]
Abstract
Sodium proton antiporters are ubiquitous membrane proteins that catalyze the exchange of Na(+) for protons throughout the biological world. The Escherichia coli NhaA is the archetypal Na(+)/H(+) antiporter and is absolutely essential for survival in high salt concentrations under alkaline conditions. Its crystal structure, accompanied by extensive molecular dynamics simulations, have provided an atomically detailed model of its mechanism. In this study, we utilized a combination of computational methodologies in order to construct a structural model for the Na(+)/H(+) antiporter from the gram-negative bacterium Vibrio parahaemolyticus. We explored its overall architecture by computational means and validated its stability and robustness. This protein belongs to a novel group of NhaA proteins that transports not only Na(+) and Li(+) as substrate ions, but K(+) as well, and was also found to miss a β-hairpin segment prevalent in other homologs of the Bacteria domain. We propose, for the first time, a structure of a prototype model of a β-hairpin-less NhaA that is selective to K(+). Better understanding of the Vibrio parahaemolyticus NhaA structure-function may assist in studies on ion transport, pH regulation and designing selective blockers.
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Affiliation(s)
- Assaf Ganoth
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus Givat-Ram, Jerusalem 91904, Israel.
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18
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Musiani F, Bertoša B, Magistrato A, Zambelli B, Turano P, Losasso V, Micheletti C, Ciurli S, Carloni P. Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+ 2 Francesco Musiani and Branimir Bertoša contributed equally to the simulations presented here. J Chem Theory Comput 2010; 6:3503-15. [DOI: 10.1021/ct900635z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Branimir Bertoša
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Alessandra Magistrato
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Paola Turano
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Valeria Losasso
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Cristian Micheletti
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Paolo Carloni
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
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19
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Denning EJ, Woolf TB. Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations. Proteins 2010; 78:1105-19. [PMID: 19950367 DOI: 10.1002/prot.22632] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The growing dataset of K(+) channel x-ray structures provides an excellent opportunity to begin a detailed molecular understanding of voltage-dependent gating. These structures, while differing in sequence, represent either a stable open or closed state. However, an understanding of the molecular details of gating will require models for the transitions and experimentally testable predictions for the gating transition. To explore these ideas, we apply dynamic importance sampling to a set of homology models for the molecular conformations of K(+) channels for four different sets of sequences and eight different states. In our results, we highlight the importance of particular residues upstream from the Pro-Val-Pro (PVP) region to the gating transition. This supports growing evidence that the PVP region is important for influencing the flexibility of the S6 helix and thus the opening of the gating domain. The results further suggest how gating on the molecular level depends on intra-subunit motions to influence the cooperative behavior of all four subunits of the K(+) channel. We hypothesize that the gating process occurs in steps: first sidechain movement, then inter-S5-S6 subunit motions, and lastly the large-scale domain rearrangements.
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Affiliation(s)
- Elizabeth J Denning
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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20
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Kim T, Kim E, Park SJ, Joo H. PCHM: A bioinformatic resource for high-throughput human mitochondrial proteome searching and comparison. Comput Biol Med 2009; 39:689-96. [DOI: 10.1016/j.compbiomed.2009.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022]
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21
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Mankoo PK, Sukumar S, Karchin R. PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations. Proteins 2009; 75:499-508. [PMID: 18951408 DOI: 10.1002/prot.22265] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Somatic mutations in PIK3CA (phosphatidylinositol-3 kinase, catalytic subunit, alpha isoform) are reported in breast and other human cancers to concentrate at hotspots within its kinase and helical domains. Most of these mutations cause kinase gain of function in vitro and are associated with oncogenicity in vivo. However, little is known about the mechanisms driving tumor development. We have performed computational structural studies on a homology model of wildtype PIK3CA plus recurrent H1047R, H1047L, and P539R mutations, located in the kinase and helical domains, respectively. The time evolution of the structures show that H1047R/L mutants exhibit a larger area of the catalytic cleft between the kinase N- and C-lobes compared with the wildtype that could facilitate the entrance of substrates. This larger area might yield enhanced substrate-to-product turnover associated with oncogenicity. In addition, the H1047R/L mutants display increased kinase activation loop mobility, compared with the wildtype. The P539R mutant forms more hydrogen bonds and salt-bridge interactions than the wildtype, properties that are associated with enhanced thermostability. Mutant-specific differences in the catalytic cleft and activation loop behavior suggest that structure-based mutant-specific inhibitors can be designed for PIK3CA-positive breast cancers.
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Affiliation(s)
- Parminder K Mankoo
- Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21218, USA
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22
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Shen R, Guo W. Ion binding properties and structure stability of the NaK channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1024-32. [DOI: 10.1016/j.bbamem.2009.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 01/09/2009] [Accepted: 01/13/2009] [Indexed: 10/21/2022]
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23
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Tayefeh S, Kloss T, Kreim M, Gebhardt M, Baumeister D, Hertel B, Richter C, Schwalbe H, Moroni A, Thiel G, Kast SM. Model development for the viral Kcv potassium channel. Biophys J 2009; 96:485-98. [PMID: 19167299 DOI: 10.1016/j.bpj.2008.09.050] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 09/29/2008] [Indexed: 11/24/2022] Open
Abstract
A computational model for the open state of the short viral Kcv potassium channel was created and tested based on homology modeling and extensive molecular-dynamics simulation in a membrane environment. Particular attention was paid to the structure of the highly flexible N-terminal region and to the protonation state of membrane-exposed lysine residues. Data from various experimental sources, NMR spectroscopy, and electrophysiology, as well as results from three-dimensional reference interaction site model integral equation theory were taken into account to select the most reasonable model among possible variants. The final model exhibits spontaneous ion transitions across the complete pore, with and without application of an external field. The nonequilibrium transport events could be induced reproducibly without abnormally large driving potential and without the need to place ions artificially at certain key positions along the transition path. The transport mechanism through the filter region corresponds to the classic view of single-file motion, which in our case is coupled to frequent exchange of ions between the innermost filter position and the cavity.
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Affiliation(s)
- Sascha Tayefeh
- Eduard Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Darmstadt, Germany
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24
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Jørgensen AM, Tagmose L, Jørgensen AMM, Bøgesø KP, Peters GH. Molecular dynamics simulations of Na+/Cl(-)-dependent neurotransmitter transporters in a membrane-aqueous system. ChemMedChem 2008; 2:827-40. [PMID: 17436258 DOI: 10.1002/cmdc.200600243] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have performed molecular dynamics simulations of a homology model of the human serotonin transporter (hSERT) in a membrane environment and in complex with either the natural substrate 5-HT or the selective serotonin reuptake inhibitor escitalopram. We have also included a transporter homologue, the Aquifex aeolicus leucine transporter (LeuT), in our study to evaluate the applicability of a simple and computationally attractive membrane system. Fluctuations in LeuT extracted from simulations are in good agreement with crystallographic B factors. Furthermore, key interactions identified in the X-ray structure of LeuT are maintained throughout the simulations indicating that our simple membrane system is suitable for studying the transmembrane protein hSERT in complex with 5-HT or escitalopram. For these transporter complexes, only relatively small fluctuations are observed in the ligand-binding cleft. Specific interactions responsible for ligand recognition, are identified in the hSERT-5HT and hSERT-escitalopram complexes. Our findings are in good agreement with predictions from mutagenesis studies.
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Affiliation(s)
- Anne Marie Jørgensen
- MEMPHYS-Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, Building 206, 2800 Kgs. Lyngby, Denmark
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25
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Shrivastava IH, Jiang J, Amara SG, Bahar I. Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter. J Biol Chem 2008; 283:28680-90. [PMID: 18678877 PMCID: PMC2568915 DOI: 10.1074/jbc.m800889200] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Glutamate transporters, also referred to as excitatory amino acid
transporters (EAATs), are membrane proteins that regulate glutamatergic signal
transmission by clearing excess glutamate after its release at synapses. A
structure-based understanding of their molecular mechanisms of function has
been elusive until the recent determination of the x-ray structure of an
archaeal transporter, GltPh. GltPh exists as a trimer,
with each subunit containing a core region that mediates substrate
translocation. In the present study a series of molecular dynamics simulations
have been conducted and analyzed in light of new experimental data on
substrate binding properties of EAATs. The simulations provide for the first
time a full atomic description of the time-resolved events that drive the
recognition and binding of substrate. The core region of each subunit exhibits
an intrinsic tendency to open the helical hairpin HP2 loop, the extracellular
gate, within tens of nanoseconds exposing conserved polar residues that serve
as attractors for substrate binding. The NMDGT motif on the partially unwound
part of the transmembrane helix TM7 and the residues Asp-390 and Asp-394 on
TM8 are also distinguished by their important role in substrate binding and
close interaction with mediating water molecules and/or sodium ions. The
simulations reveal a Na+ binding site comprised in part of Leu-303
on TM7 and Asp-405 on TM8 and support a role for sodium ions in stabilizing
substrate-bound conformers. The functional importance of Leu-303 or its
counterpart Leu-391 in human EAAT1 (hEAAT1) is confirmed by site-directed
mutagenesis and Na+ dependence assays conducted with hEAAT1 mutants
L391C and L391A.
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Affiliation(s)
- Indira H Shrivastava
- Department of Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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26
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Róg T, Murzyn K, Karttunen M, Pasenkiewicz-Gierula M. Nonpolar interactions between trans-membrane helical EGF peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies. J Pept Sci 2008; 14:374-82. [DOI: 10.1002/psc.936] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects. Biophys J 2008; 94:3565-76. [PMID: 18222999 DOI: 10.1529/biophysj.107.116335] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Differences of ionic concentrations across lipid bilayers are some of the primary energetic driving forces for cellular electrophysiology. While macroscopic models of asymmetric ionic solutions are well-developed, their connection to ion, water, and lipid interactions at the atomic scale are much more poorly understood. In this study, we used molecular dynamics to examine a system of two chambers of equal ionic strength, but differing amounts of NaCl and KCl, separated by a lipid bilayer. Our expectation was that the net electrostatic potential difference between the two chambers should be small or zero. Contrary to our expectation, a large potential difference (-70 mV) slowly evolved across the two water chambers over the course of our 172-ns simulation. This potential primarily originated from strong Na(+) binding to the carbonyls of the phosphatidylcholine lipids. This ion adsorption also led to significant structural and mechanical changes in the lipid bilayer. We discuss this surprising result in the context of indirect experimental evidence for Na(+) interaction with bilayers as well as potential caveats in current biomembrane simulation methodology, including force-field parameters and finite size effects.
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28
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Masetti M, Cavalli A, Recanatini M. Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies. J Comput Chem 2008; 29:795-808. [DOI: 10.1002/jcc.20842] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Debret G, Valadié H, Stadler AM, Etchebest C. New insights of membrane environment effects on MscL channel mechanics from theoretical approaches. Proteins 2007; 71:1183-96. [DOI: 10.1002/prot.21810] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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30
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Molecular dynamics simulations and membrane protein structure quality. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 37:403-9. [PMID: 17960373 DOI: 10.1007/s00249-007-0225-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 09/28/2007] [Accepted: 10/03/2007] [Indexed: 10/22/2022]
Abstract
Despite a growing repertoire of membrane protein structures (currently approximately 120 unique structures), considerations of low resolution and crystallization in the absence of a lipid bilayer require the development of techniques to assess the global quality of membrane protein folds. This is also the case for assessment of, e.g. homology models of human membrane proteins based on structures of (distant) bacterial homologues. Molecular dynamics (MD) simulations may be used to help evaluate the quality of a membrane protein structure or model. We have used a structure of the bacterial ABC transporter MsbA which has the correct transmembrane helices but an incorrect handedness and topology of their packing to test simulation methods of quality assessment. An MD simulation of the MsbA model in a lipid bilayer is compared to a simulation of another bacterial ABC transporter, BtuCD. The latter structure has demonstrated good conformational stability in the same bilayer environment and over the same timescale (20 ns) as for the MsbA model simulation. A number of comparative analyses of the two simulations were performed to assess changes in the structural integrity of each protein. The results show a significant difference between the two simulations, chiefly due to the dramatic structural deformations of MsbA. We therefore propose that MD could become a useful quality control tool for membrane protein structural biology. In particular, it provides a way in which to explore the global conformational stability of a model membrane protein fold.
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31
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Haider S, Tarasov AI, Craig TJ, Sansom MSP, Ashcroft FM. Identification of the PIP2-binding site on Kir6.2 by molecular modelling and functional analysis. EMBO J 2007; 26:3749-59. [PMID: 17673911 PMCID: PMC1952224 DOI: 10.1038/sj.emboj.7601809] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 07/03/2007] [Indexed: 12/25/2022] Open
Abstract
ATP-sensitive potassium (K(ATP)) channels couple cell metabolism to electrical activity by regulating K(+) fluxes across the plasma membrane. Channel closure is facilitated by ATP, which binds to the pore-forming subunit (Kir6.2). Conversely, channel opening is potentiated by phosphoinositol bisphosphate (PIP(2)), which binds to Kir6.2 and reduces channel inhibition by ATP. Here, we use homology modelling and ligand docking to identify the PIP(2)-binding site on Kir6.2. The model is consistent with a large amount of functional data and was further tested by mutagenesis. The fatty acyl tails of PIP(2) lie within the membrane and the head group extends downwards to interact with residues in the N terminus (K39, N41, R54), transmembrane domains (K67) and C terminus (R176, R177, E179, R301) of Kir6.2. Our model suggests how PIP(2) increases channel opening and decreases ATP binding and channel inhibition. It is likely to be applicable to the PIP(2)-binding site of other Kir channels, as the residues identified are conserved and influence PIP(2) sensitivity in other Kir channel family members.
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Affiliation(s)
- Shozeb Haider
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Tim J Craig
- Laboratory of Physiology, University of Oxford, Oxford, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
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32
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Tayefeh S, Kloss T, Thiel G, Hertel B, Moroni A, Kast SM. Molecular Dynamics Simulation of the Cytosolic Mouth in Kcv-Type Potassium Channels. Biochemistry 2007; 46:4826-39. [PMID: 17397187 DOI: 10.1021/bi602468r] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The functional effect of mutations near the intracellular mouth of the short viral Kcv potassium channel was studied by molecular dynamics simulations. As a model system we used the analogously mutated and truncated KirBac1.1, a channel with known crystal structure that shares genuine local sequence motifs with Kcv. By a novel simulated annealing methodology for structural averaging, information about the structure and dynamics of the intracellular mouth was extracted and complemented by Poisson-Boltzmann and 3D-RISM (reference interaction site model) integral equation theory for the determination of the K+ free energy surface. Besides the wild-type analogue of Kcv with its experimental reference activity (truncated KirBac1.1), two variants were studied: a deletion mutant where the N-terminus is further truncated by eight amino acids, showing inactivity in the Kcv reference system, and a point mutant where the kink-forming proline at position 13 is substituted by alanine, resulting in hyperactivity. The computations reveal that the change of activity is closely related to a hydrophilic intracellular constriction formed by the C-terminal residues of the monomers. Hyperactivity of the point mutant is correlated with both sterical and electrostatic factors, while inactivity of the deletion mutant is related to a loss of specific salt bridge patterns between the C- and N-terminus at the constriction and to the consequences for ion passage barriers, as revealed by integral equation theory. The cytosolic gate, however, is probably formed by the N-terminal segment up to the proline kink and not by the constriction. The results are compared with design principles found for other channels.
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Affiliation(s)
- Sascha Tayefeh
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 20, 64287 Darmstadt, Germany
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33
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Haider S, Khalid S, Tucker SJ, Ashcroft FM, Sansom MSP. Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: a comparative study. Biochemistry 2007; 46:3643-52. [PMID: 17326663 DOI: 10.1021/bi062210f] [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] [Indexed: 11/29/2022]
Abstract
Inward rectifier potassium (Kir) channels regulate cell excitability and transport K+ ions across membranes. Homotetrameric models of three mammalian Kir channels (Kir1.1, Kir3.1, and Kir6.2) have been generated, using the KirBac3.1 transmembrane and rat Kir3.1 intracellular domain structures as templates. All three models have been explored by 10 ns molecular dynamics simulations in phospholipid bilayers. Analysis of the initial structures revealed conservation of potential lipid interaction residues (Trp/Tyr and Arg/Lys side chains near the lipid headgroup-water interfaces). Examination of the intracellular domains revealed key structural differences between Kir1.1 and Kir6.2 which may explain the difference in channel inhibition by ATP. The behavior of all three models in the MD simulations revealed that they have conformational stability similar to that seen for comparable simulations of, for example, structures derived from cryoelectron microscopy data. Local distortions of the selectivity filter were seen during the simulations, as observed in previous simulations of KirBac and in simulations and structures of KcsA. These may be related to filter gating of the channel. The intracellular hydrophobic gate does not undergo any substantial changes during the simulations and thus remains functionally closed. Analysis of lipid-protein interactions of the Kir models emphasizes the key role of the M0 (or "slide") helix which lies approximately parallel to the bilayer-water interface and forms a link between the transmembrane and intracellular domains of the channel.
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Affiliation(s)
- Shozeb Haider
- Department of Biochemistry, University of Oxford, UK
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34
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Kóňa J, Minozzi M, Torre V, Carloni P. A gate mechanism indicated in the selectivity filter of the potassium channel KscA. Theor Chem Acc 2007. [DOI: 10.1007/s00214-006-0226-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Carrillo-Tripp M, San-Román ML, Hernańdez-Cobos J, Saint-Martin H, Ortega-Blake I. Ion hydration in nanopores and the molecular basis of selectivity. Biophys Chem 2006; 124:243-50. [PMID: 16765508 DOI: 10.1016/j.bpc.2006.04.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 04/26/2006] [Accepted: 04/27/2006] [Indexed: 11/25/2022]
Abstract
Using a simple model, it is shown that the cost of constraining a hydrated potassium ion inside a narrow pore is smaller than the cost of constraining hydrated sodium or lithium ions in pores of radius around 1.5 A. The opposite is true for pores of radius around 2.5 A. The reason for the selectivity in the first region is that the potassium ion allows for a greater distortion of its hydration shell and can therefore maintain a better coordination, and the reason for the reverse selectivity in the second region is that the smaller ions retain their hydration shells in these pores. This is relevant to the molecular basis of ion selective channels, and since this mechanism does not depend on the molecular details of the pore, it could also operate in all sorts of nanotubes.
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36
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Rojas A, Wu J, Wang R, Jiang C. Gating of the ATP-sensitive K+ channel by a pore-lining phenylalanine residue. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1768:39-51. [PMID: 16970907 DOI: 10.1016/j.bbamem.2006.06.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Revised: 06/27/2006] [Accepted: 06/28/2006] [Indexed: 11/26/2022]
Abstract
ATP-sensitive K(+) (K(ATP)) channels are gated by intracellular ATP, proton and phospholipids. The pore-forming Kir6.2 subunit has all essential machineries for channel gating by these ligands. It is known that channel gating involves the inner helix bundle of crossing in which a phenylalanine residue (Phe168) is found in the TM2 at the narrowest region of the ion-conduction pathway in the Kir6.2. Here we present evidence that Phe168-Kir6.2 functions as an ATP- and proton-activated gate via steric hindrance and hydrophobic interactions. Site-specific mutations of Phe168 to a small amino acid resulted in losses of the ATP- and proton-dependent gating, whereas the channel gating was well maintained after mutation to a bulky tryptophan, supporting the steric hindrance effect. The steric hindrance effect, though necessary, was insufficient for the gating, as mutating Phe168 to a bulky hydrophilic residue severely compromised the channel gating. Single-channel kinetics of the F168W mutant resembled the wild-type channel. Small residues increased P(open), and displayed long-lasting closures and long-lasting openings. Kinetic modeling showed that these resulted from stabilization of the channel to open and long-lived closed states, suggesting that a bulky and hydrophobic residue may lower the energy barrier for the switch between channel openings and closures. Thus, it is likely that the Phe168 acts as not only a steric hindrance gate but also potentially a facilitator of gating transitions in the Kir6.2 channel.
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Affiliation(s)
- Asheebo Rojas
- Department of Biology, Georgia State University, 24 Peachtree Center Avenue, Atlanta, GA 30302-4010, USA
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37
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Khalid S, Bond PJ, Deol SS, Sansom MSP. Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa. Proteins 2006; 63:6-15. [PMID: 16397890 DOI: 10.1002/prot.20845] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OprF is a major outer membrane protein from Pseudomonas aeruginosa, a homolog of OmpA from Escherichia coli. The N-terminal domains of both proteins have been demonstrated to form low conductance channels in lipid bilayers. Homology models, consisting of an eight-stranded beta-barrel, of the N-terminal domain OprF have been constructed based on the crystal structure of the corresponding domain from E. coli OmpA. OprF homology models have been evaluated via a set (6 x 10 ns) of simulations of the beta-barrel embedded within a solvated dimyristoyl-phosphatidylcholine (DMPC) bilayer. The conformational stability of the models is similar to that of the crystal structure of OmpA in comparable simulations. There is a degree of water penetration into the pore-like center of the OprF barrel. The presence of an acidic/basic (E8/K121) side-chain interaction within the OprF barrel may form a "gate" able to close/open a central pore. Lipid-protein interactions within the simulations were analyzed and revealed that aromatic side-chains (Trp, Tyr) of OprF interact with lipid headgroups. Overall, the behavior of the OprF model in simulations supports the suggestion that this molecule is comparable to OmpA. The simulations help to explain the mechanism of formation of low conductance pores within the outer membrane.
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Affiliation(s)
- Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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38
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Sengupta D, Meinhold L, Langosch D, Ullmann GM, Smith JC. Understanding the energetics of helical peptide orientation in membranes. Proteins 2006; 58:913-22. [PMID: 15657932 DOI: 10.1002/prot.20383] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Understanding the energetic factors determining the positioning and orientation of single-helical peptides in membranes is of fundamental interest in structural biology. Here, a simple 5-slab continuum dielectric model for the membrane is examined that distinguishes between the solvent, headgroup, and core regions. An analytical solution for the electrostatic solvation of a single dipole and an all-atom model of N-methylacetamide are used to demonstrate the effect of the dielectric boundaries in the system on peptide dipole orientation. The dipole orientation energy is shown to dominate the electrostatic solvation energy of a polyalanine helix in the membrane. With an additional surface-area-dependent term to account for the cavity formation in the aqueous region, the continuum electrostatics description is used to examine several helical peptides, the atoms of which are explicitly represented with a molecular mechanics force field. The experimentally determined tilt angles of a number of peptides of alternating alanine and leucine residues, and of glycophorin and melittin, are accurately reproduced by the model. The factors determining the tilt angles and their fluctuations are analyzed. The tilt angles of the simpler peptides are found to increase approximately linearly with peptide length; this effect is also rationalized. The analysis and model presented here provide a step toward the prediction of helical membrane protein structure.
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Affiliation(s)
- Durba Sengupta
- IWR-Computational Molecular Biophysics, University of Heidelberg, Heidelberg, Germany
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39
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Shrivastava IH, Bahar I. Common mechanism of pore opening shared by five different potassium channels. Biophys J 2006; 90:3929-40. [PMID: 16533848 PMCID: PMC1459499 DOI: 10.1529/biophysj.105.080093] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A fundamental question associated with the function of ion channels is the conformational changes that allow for reversibly opening/occluding the pore through which the cations permeate. The recently elucidated crystal structures of potassium channels reveal similar structural motifs at their pore-forming regions, suggesting that they share a common gating mechanism. The validity of this hypothesis is explored by analyzing the collective dynamics of five known K(+) channel structures. Normal-mode analysis using the Gaussian network model strikingly reveals that all five structures display the same intrinsic motions at their pore-forming region despite the differences in their sequences, structures, and activation mechanisms. Superposition of the most cooperative mode profiles shows that the identified common mechanism is a global corkscrew-like counterrotation of the extracellular and cytoplasmic (CP) regions, leading to the opening of the CP end of the pore. A second cooperative mode shared by all five K(+) channels is the extension of the extracellular and/or CP ends via alternating anticorrelated fluctuations of pairs of diagonally opposite monomers. Residues acting as hinges/anchors in both modes are highly conserved across the members of the family of K(+) channel proteins, consistent with their presently disclosed critical mechanical role in pore gating.
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Affiliation(s)
- Indira H Shrivastava
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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40
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Grottesi A, Domene C, Hall B, Sansom MSP. Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations. Biochemistry 2006; 44:14586-94. [PMID: 16262258 DOI: 10.1021/bi0510429] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
KirBac1.1 and 3.1 are bacterial homologues of mammalian inward rectifier K channels. We have performed extended molecular dynamics simulations (five simulations, each of >20 ns duration) of the transmembrane domain of KirBac in two membrane environments, a palmitoyl oleoyl phosphatidylcholine bilayer and an octane slab. Analysis of these simulations has focused on the conformational dynamics of the pore-lining M2 helices, which form the cytoplasmic hydrophobic gate of the channel. Principal components analysis reveals bending of M2, with a molecular hinge at the conserved glycine (Gly134 in KirBac1.1, Gly120 in KirBac3.1). More detailed analysis reveals a dimer-of-dimers type motion. The first two eigenvectors describing the motions of M2 correspond to helix kink and swivel motions. The conformational flexibility of M2 seen in these simulations correlates with differences in M2 conformation between that seen in the X-ray structures of closed channels (KcsA and KirBac) in which the helix is undistorted, and in open channels (e.g. MthK) in which the M2 helix is kinked. Thus, the simulations, albeit on a time scale substantially shorter than that required for channel gating, suggest a gating model in which the intrinsic flexibility of M2 about a molecular hinge is coupled to conformational transitions of an intracellular 'gatekeeper' domain, the latter changing conformation in response to ligand binding.
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41
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Ivanov AA, Baskin II, Palyulin VA, Piccagli L, Baraldi PG, Zefirov NS. Molecular modeling and molecular dynamics simulation of the human A2B adenosine receptor. The study of the possible binding modes of the A2B receptor antagonists. J Med Chem 2005; 48:6813-20. [PMID: 16250640 DOI: 10.1021/jm049418o] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A molecular model of the human A(2B) adenosine receptor containing seven transmembrane alpha helices connected by three intracellular and three extracellular hydrophilic loops had been constructed. A molecular docking of seven structurally diverse xanthine antagonists of the A(2B) receptor was performed, and the differences in their binding modes were investigated. The 1 ns molecular dynamics (MD) simulations of several obtained ligand-receptor complexes inserted into the phospholipid bilayer were carried out. The conformational changes of the A(2B) receptor occurring during MD simulations were explored, and the stable binding modes of the studied antagonists were determined. According to the models presented in this work, the involvement of the His251, Asn282, Ser92, Thr89, and some aromatic residues in ligand recognition was determined. The obtained binding modes of the A(2B) antagonists demonstrate good agreement with the site-directed mutagenesis data.
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Affiliation(s)
- Andrei A Ivanov
- Department of Chemistry, M. V. Lomonosov Moscow State University, 119992 Moscow, Russian Federation
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42
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Chapman ML, Blanke ML, Krovetz HS, VanDongen AMJ. Allosteric effects of external K+ ions mediated by the aspartate of the GYGD signature sequence in the Kv2.1 K+ channel. Pflugers Arch 2005; 451:776-92. [PMID: 16283201 DOI: 10.1007/s00424-005-1515-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 08/12/2005] [Accepted: 08/31/2005] [Indexed: 11/30/2022]
Abstract
K+ channels achieve exquisite ion selectivity without jeopardizing efficient permeation by employing multiple, interacting K+-binding sites. Introduction ofa cadmium (Cd2+)-binding site in the external vestibule of Kv2.1 (drk1), allowed us to functionally characterize a binding site for external monovalent cations. Permeant ions displayed higher affinity for this site than non-permeant monovalent cations, although the selectivity profile was different from that of the channel. Point mutations identified the highly conserved aspartate residue immediately following the selectivity filter as a critical determinant of the antagonism between external K+ and Cd2+ ions. A conservative mutation at this position (D378E) significantly affected the open-state stability. Moreover, the mean open time was found to be modulated by external K+ concentration, suggesting a coupling between channel closing and the permeation process. Reducing the Rb+ conductance by mutating the selectivity filter to the sequence found inKv4.1, also significantly reduced the effectiveness ofRb+ ions to antagonize Cd2+ inhibition, thereby implicating the selectivity filter as the site at which K+ions exert their antagonistic effect on Cd2+ block. The equivalent of D378 in KcsA, D80, takes part in an inter-subunit hydrogen-bond network that allows D80to functionally interact with the selectivity filter. The results suggest that external K+ ions antagonize Cd2+inhibition (in I379C) and modulate the mean open time(in the wild-type Kv2.1) by altering the occupancy profile of the K+-binding sites in the selectivity filter.
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Affiliation(s)
- Mark L Chapman
- Department of Pharmacology, Duke University, Durham, NC, USA.
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43
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Abstract
Organ function (the heart beat for example) can only be understood through knowledge of molecular and cellular processes within the constraints of structure-function relations at the tissue level. A quantitative modeling framework that can deal with these multiscale issues is described here under the banner of the International Union of Physiological Sciences Physiome Project.
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Affiliation(s)
- Peter Hunter
- Bioengineering Institute, University of Auckland, Auckland, New Zealand.
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44
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Abstract
Potassium (K(+)) channels are tetrameric membrane-spanning proteins that provide a selective pore for the conductance of K(+) across the cell membranes. These channels are most remarkable in their ability to discriminate K(+) from Na(+) by more than a thousandfold and conduct at a throughput rate near diffusion limit. The recent progress in the structural characterization of K(+) channel provides us with a unique opportunity to understand their function at the atomic level. With their ability to go beyond static structures, molecular dynamics simulations based on atomic models can play an important role in shaping our view of how ion channels carry out their function. The purpose of this review is to summarize the most important findings from experiments and computations and to highlight a number of fundamental mechanistic questions about ion conduction and selectivity that will require further work.
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Affiliation(s)
- Benoît Roux
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA.
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45
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Grottesi A, Domene C, Haider S, Sansom MSP. Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function. IEEE Trans Nanobioscience 2005; 4:112-20. [PMID: 15816177 DOI: 10.1109/tnb.2004.842473] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Molecular modeling and simulations enable extrapolation for the structure of bacterial potassium channels to the function of their mammalian homologues. Molecular dynamics simulations have revealed the concerted single-file motion of potassium ions and water molecules through the selectivity filter of K channels and the role of filter flexibility in ion permeation and in "fast gating." Principal components analysis of extended K channel simulations suggests that hinge-bending of pore-lining M2 (or S6) helices plays a key role in K channel gating. Based on these and other simulations, a molecular model for gating of inward rectifier K channel gating is presented.
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Affiliation(s)
- Alessandro Grottesi
- Department of Biochemistry, University of Oxford, Oxford OX 3QU, United Kingdom.
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46
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Yesylevskyy S, Kharkyanen V. Barrier-less knock-on conduction in ion channels: peculiarity or general mechanism? Chem Phys 2005. [DOI: 10.1016/j.chemphys.2004.11.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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47
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Shrivastava IH, Durell SR, Guy HR. A model of voltage gating developed using the KvAP channel crystal structure. Biophys J 2005; 87:2255-70. [PMID: 15454428 PMCID: PMC1304651 DOI: 10.1529/biophysj.104.040592] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Having inspected the crystal structure of the complete KvAP channel protein, we suspect that the voltage-sensing domain is too distorted to provide reliable information about its native tertiary structure or its interactions with the central pore-forming domain. On the other hand, a second crystal structure of the isolated voltage-sensing domain may well correspond to a native open conformation. We also observe that the paddle model of gating developed from these two structures is inconsistent with many experimental results, and suspect it to be energetically unrealistic. Here we show that the isolated voltage-sensing domain crystal structure can be docked onto the pore domain portion of the full-length KvAP crystal structure in an energetically favorable way to create a model of the open conformation. Using this as a starting point, we have developed rather conventional models of resting and transition conformations based on the helical screw mechanism for the transition from the open to the resting conformation. Our models are consistent with both theoretical considerations and experimental results.
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Affiliation(s)
- Indira H Shrivastava
- Laboratory of Experimental and Computational Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5567, USA
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48
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Liu HL, Chen CW, Lin JC. Homology Models of the Tetramerization Domain of Six Eukaryotic Voltage-gated Potassium Channels Kv1.1-Kv1.6. J Biomol Struct Dyn 2005; 22:387-98. [PMID: 15588103 DOI: 10.1080/07391102.2005.10507011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The homology models of the tetramerization (T1) domain of six eukaryotic potassium channels, Kv1.1-Kv1.6, were constructed based on the crystal structure of the Shaker T1 domain. The results of amino acid sequence alignment indicate that the T1 domains of these K+ channels are highly conserved, with the similarities varying from 77% between Shaker and Kv1.6 to 93% between Kv1.2 and Kv1.3. The homology models reveal that the T1 domains of these Kv channels exhibit similar folds as those of Shaker K+ channel. These models also show that each T1 monomer consists of three distinct layers, with N-terminal layer 1 and C-terminal layer 3 facing the cytoplasm and the membrane, respectively. Layer 2 exhibits the highest structural conservation because it is located around the central hydrophobic core. For each Kv channel, four identical subunits assemble into the homotetramer architecture around a four-fold axis through the hydrogen bonds and salt bridges formed by 15 highly conserved polar residues. The narrowest opening of the pore is formed by the four conserved residues corresponding to R115 of the Shaker T1 domain. The homology models of these Kv T1 domains provide particularly attractive targets for further structure-based studies.
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Affiliation(s)
- Hsuan-Liang Liu
- Department of Chemical Engineering and Graduate Institute of Biotechnology, National Taipei University of Technology, No. 1 Sec. 3 Chung-Hsiao E. Rd., Taipei, Taiwan 10608.
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49
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Domene C, Grottesi A, Sansom MSP. Filter flexibility and distortion in a bacterial inward rectifier K+ channel: simulation studies of KirBac1.1. Biophys J 2005; 87:256-67. [PMID: 15240462 PMCID: PMC1304348 DOI: 10.1529/biophysj.104.039917] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial channel KirBac1.1 provides a structural homolog of mammalian inward rectifier potassium (Kir) channels. The conformational dynamics of the selectivity filter of Kir channels are of some interest in the context of possible permeation and gating mechanisms for this channel. Molecular dynamics simulations of KirBac have been performed on a 10-ns timescale, i.e., comparable to that of ion permeation. The results of five simulations (total simulation time 50 ns) based on three different initial ion configurations and two different model membranes are reported. These simulation data provide evidence for limited (<0.1 nm) filter flexibility during the concerted motion of ions and water molecules within the filter, such local changes in conformation occurring on an approximately 1-ns timescale. In the absence of K(+) ions, the KirBac selectivity filter undergoes more substantial distortions. These resemble those seen in comparable simulations of other channels (e.g., KcsA and KcsA-based homology models) and are likely to lead to functional closure of the channel. This suggests filter distortions may provide a mechanism of K-channel gating in addition to changes in the hydrophobic gate formed at the intracellular crossing point of the M2 helices. The simulation data also provide evidence for interactions of the "slide" (pre-M1) helix of KirBac with phospholipid headgroups.
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Affiliation(s)
- Carmen Domene
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU United Kingdom
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50
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Abstract
KATP channels assemble from four regulatory SUR1 and four pore-forming Kir6.2 subunits. At the single-channel current level, ATP-dependent gating transitions between the active burst and the inactive interburst conformations underlie inhibition of the KATP channel by intracellular ATP. Previously, we identified a slow gating mutation, T171A in the Kir6.2 subunit, which dramatically reduces rates of burst to interburst transitions in Kir6.2DeltaC26 channels without SUR1 in the absence of ATP. Here, we constructed all possible mutations at position 171 in Kir6.2DeltaC26 channels without SUR1. Only four substitutions, 171A, 171F, 171H, and 171S, gave rise to functional channels, each increasing Ki,ATP for ATP inhibition by >55-fold and slowing gating to the interburst by >35-fold. Moreover, we investigated the role of individual Kir6.2 subunits in the gating by comparing burst to interburst transition rates of channels constructed from different combinations of slow 171A and fast T171 "wild-type" subunits. The relationship between gating transition rate and number of slow subunits is exponential, which excludes independent gating models where any one subunit is sufficient for inhibition gating. Rather, our results support mechanisms where four ATP sites independently can control a single gate formed by the concerted action of all four Kir6.2 subunit inner helices of the KATP channel.
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Affiliation(s)
- Peter Drain
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA.
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