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Srivastava P, Sudevan ST, Thennavan A, Mathew B, Kanthlal SK. Inhibiting Monoamine Oxidase in CNS and CVS would be a Promising Approach to Mitigating Cardiovascular Complications in Neurodegenerative Disorders. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2024; 23:331-341. [PMID: 36872357 DOI: 10.2174/1871527322666230303115236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/17/2022] [Accepted: 01/03/2023] [Indexed: 03/07/2023]
Abstract
The flavoenzyme monoamine oxidases (MAOs) are present in the mitochondrial outer membrane and are responsible for the metabolism of biogenic amines. MAO deamination of biological amines produces toxic byproducts such as amines, aldehydes, and hydrogen peroxide, which are significant in the pathophysiology of multiple neurodegenerative illnesses. In the cardiovascular system (CVS), these by-products target the mitochondria of cardiac cells leading to their dysfunction and producing redox imbalance in the endothelium of the blood vessels. This brings up the biological relationship between the susceptibility of getting cardiovascular disorders in neural patients. In the current scenario, MAO inhibitors are highly recommended by physicians worldwide for the therapy and management of various neurodegenerative disorders. Many interventional studies reveal the benefit of MAO inhibitors in CVS. Drug candidates who can target both the central and peripheral MAO could be a better to compensate for the cardiovascular comorbidities observed in neurodegenerative patients.
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Affiliation(s)
- Princika Srivastava
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, 682 041, Kerala, India
| | - Sachithra Thazhathuveedu Sudevan
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - Arumugam Thennavan
- Central Lab Animal Facility, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, 682 041, Kerala, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - S K Kanthlal
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, 682 041, Kerala, India
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2
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Riedel R, Frese N, Yang F, Wortmann M, Dalpke R, Rhinow D, Hampp N, Gölzhäuser A. Fusion of purple membranes triggered by immobilization on carbon nanomembranes. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2021; 12:93-101. [PMID: 33564606 PMCID: PMC7849249 DOI: 10.3762/bjnano.12.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
A freestanding ultrathin hybrid membrane was synthesized comprising two functional layers, that is, first, a carbon nanomembrane (CNM) produced by electron irradiation-induced cross-linking of a self-assembled monolayer (SAM) of 4'-nitro-1,1'-biphenyl-4-thiol (NBPT) and second, purple membrane (PM) containing genetically modified bacteriorhodopsin (BR) carrying a C-terminal His-tag. The NBPT-CNM was further modified to carry nitrilotriacetic acid (NTA) terminal groups for the interaction with the His-tagged PMs forming a quasi-monolayer of His-tagged PM on top of the CNM-NTA. The formation of the Ni-NTA/His-tag complex leads to the unidirectional orientation of PM on the CNM substrate. Electrophoretic sedimentation was employed to optimize the surface coverage and to close gaps between the PM patches. This procedure for the immobilization of oriented dense PM facilitates the spontaneous fusion of individual PM patches, forming larger membrane areas. This is, to our knowledge, the very first procedure described to induce the oriented fusion of PM on a solid support. The resulting hybrid membrane has a potential application as a light-driven two-dimensional proton-pumping membrane, for instance, for light-driven seawater desalination as envisioned soon after the discovery of PM.
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Affiliation(s)
- René Riedel
- Faculty of Chemistry and Materials Sciences Center, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Natalie Frese
- Physics of Supramolecular Systems and Surfaces, Faculty of Physics, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Fang Yang
- Nano Biomaterials Group, Ningbo Institute of Industrial Technology, Chinese Academy of Science, China
| | - Martin Wortmann
- Faculty of Engineering and Mathematics, Bielefeld University of Applied Sciences, Interaktion 1, D-33619 Bielefeld, Germany
| | - Raphael Dalpke
- Physics of Supramolecular Systems and Surfaces, Faculty of Physics, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Daniel Rhinow
- Faculty of Chemistry and Materials Sciences Center, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
- Max Planck Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany
| | - Norbert Hampp
- Faculty of Chemistry and Materials Sciences Center, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Armin Gölzhäuser
- Physics of Supramolecular Systems and Surfaces, Faculty of Physics, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
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Qiu Z, Liu Q. Protein-protein interaction site prediction using random forest proximity distance. J Bioinform Comput Biol 2020; 19:2050042. [PMID: 33215966 DOI: 10.1142/s0219720020500420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A front-end method based on random forest proximity distance (PD) is used to screen the test set to improve protein-protein interaction site (PPIS) prediction. The assessment of a distance metric is done under the assumption that a distance definition of higher quality leads to higher classification. On an independent test set, the numerical analysis based on statistical inference shows that the PD has the advantage over Mahalanobis and Cosine distance. Based on the fact that the proximity distance depends on the tree composition of the random forest model, an iterative method is designed to optimize the proximity distance, which adjusts the tree composition of the random forest model by adjusting the size of the training set. Two PD metrics, 75PD and 50PD, are obtained by the iterative method. On two independent test sets, compared with the PD produced by the original training set, the values of 75PD in Matthews correlation coefficient and F1 score were higher, and the differences between them were statistically significant. All numerical experiments show that the closer the distance between the test data and the training data, the better the prediction results of the predictor. These indicate that the iterative method can optimize proximity distance definition and the distance information provided by PD can be used to indicate the reliability of prediction results.
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Affiliation(s)
- Zhijun Qiu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, P. R. China.,Henan Engineering Research Center of Food Microbiology, Luoyang 471023, P. R. China
| | - Qingjie Liu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, P. R. China
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Manzoor S, Hoda N. A comprehensive review of monoamine oxidase inhibitors as Anti-Alzheimer's disease agents: A review. Eur J Med Chem 2020; 206:112787. [PMID: 32942081 DOI: 10.1016/j.ejmech.2020.112787] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 07/22/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
Monoamine oxidases (MAO-A and MAO-B) are mammalian flavoenzyme, which catalyze the oxidative deamination of several neurotransmitters like norepinephrine, dopamine, tyramine, serotonin, and some other amines. The oxidative deamination produces several harmful side products like ammonia, peroxides, and aldehydes during the biochemical reaction. The concentration of biochemical neurotransmitter alteration in the brain by MAO is directly related with several neurological disorders like Alzheimer's disease and Parkinson's disease (PD). Activated MAO also contributes to the amyloid beta (Aβ) aggregation by two successive cleft β-secretase and γ-secretase of amyloid precursor protein (APP). Additionally, activated MAO is also involved in aggregation of neurofibrillary tangles and cognitive destruction through the cholinergic neuronal damage and disorder of the cholinergic system. MAO inhibition has general anti-Alzheimer's disease effect as a consequence of oxidative stress reduction prompted by MAO enzymes. In this review, we outlined and addressed recent understanding on MAO enzymes such as their structure, physiological function, catalytic mechanism, and possible therapeutic goals in AD. In addition, it also highlights the current development and discovery of potential MAO inhibitors (MAOIs) from various chemical scaffolds.
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Affiliation(s)
- Shoaib Manzoor
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Nasimul Hoda
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India.
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Shi R, Wu Q, Xin C, Yu H, Lim KL, Li X, Shi Z, Zhang CW, Qian L, Li L, Huang W. Structure-Based Specific Detection and Inhibition of Monoamine Oxidases and Their Applications in Central Nervous System Diseases. Chembiochem 2019; 20:1487-1497. [PMID: 30664830 DOI: 10.1002/cbic.201800813] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Indexed: 12/21/2022]
Abstract
Monoamine oxidases (MAOs) are the enzymes that catalyze the oxidation of monoamines, such as dopamine, norepinephrine, and serotonin, which serve as key neurotransmitters in the central nervous system (CNS). MAOs play important roles in maintaining the homeostasis of monoamines, and the aberrant expression or activation of MAOs underlies the pathogenesis of monoamine neurotransmitter disorders, including neuropsychiatric and neurodegenerative diseases. Clearly, detecting and inhibiting the activities of MAOs is of great value for the diagnosis and therapeutics of these diseases. Accordingly, many specific detection probes and inhibitors have been developed and substantially contributed to basic and clinical studies of these diseases. In this review, progress in the detecting and inhibiting of MAOs and their applications in mechanism exploration and treatment of neurotransmitter-related disorders is summarized. Notably, how the detection probes and inhibitors of MAOs were developed has been specifically addressed. It is hoped that this review will benefit the design of more effective and sensitive probes and inhibitors for MAOs, and eventually the treatment of monoamine neurotransmitter disorders.
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Affiliation(s)
- Riri Shi
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, P.R. China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, P.R. China
| | - Chenqi Xin
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, P.R. China
| | - Houzhi Yu
- Department of Cardiology, Shandong Provincial Hospital affiliated to Shandong University, 324 Jingwu Road, Jinan, 250021, P.R. China
| | - Kah-Leong Lim
- Neuroscience Clinic, National Neuroscience Institute, 11 Jalan Tock Seng, Singapore, 308433, Singapore
| | - Xin Li
- Shaanxi Institute of Flexible Electronics (SIFE), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P.R. China
| | - Zhenxiong Shi
- Shaanxi Institute of Flexible Electronics (SIFE), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P.R. China
| | - Cheng-Wu Zhang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, P.R. China
| | - Linghui Qian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P.R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, P.R. China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, P.R. China.,Shaanxi Institute of Flexible Electronics (SIFE), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P.R. China
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6
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Jaswal SS, O'Hara PB, Williamson PL, Springer AL. Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:351-359. [PMID: 24019219 DOI: 10.1002/bmb.20718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 06/11/2013] [Indexed: 06/02/2023]
Abstract
Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one-semester undergraduate biochemistry course to integrate use of structural representation tools into both laboratory and homework activities. First, early in the course we introduce the use of readily available open-source software for visualizing protein structure, coincident with modules on amino acid and peptide bond properties. Second, we use these same software tools in lectures and incorporate images and other structure representations in homework tasks. Third, we require a capstone project in which teams of students examine a protein-nucleic acid complex and then use the software tools to illustrate for their classmates the salient features of the structure, relating how the structure helps explain biological function. To ensure engagement with a range of software and database features, we generated a detailed template file that can be used to explore any structure, and that guides students through specific applications of many of the software tools. In presentations, students demonstrate that they are successfully interpreting structural information, and using representations to illustrate particular points relevant to function. Thus, over the semester students integrate information about structural features of biological macromolecules into the larger discussion of the chemical basis of function. Together these assignments provide an accessible introduction to structural representation tools, allowing students to add these methods to their biochemical toolboxes early in their scientific development.
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Affiliation(s)
- Sheila S Jaswal
- Department of Chemistry, Amherst College, Amherst, Massachusetts
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7
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Koth CMM, Payandeh J. Strategies for the cloning and expression of membrane proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2009; 76:43-86. [PMID: 20663478 DOI: 10.1016/s1876-1623(08)76002-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Despite the determination of thousands of high-resolution structures of soluble proteins, many features of integral membrane proteins render them difficult targets for the structural biologist. Among these, the most important challenge is in expressing sufficient quantities of active protein to support downstream purification and structure determination efforts. Over 190 unique membrane protein structures have now been solved, and noticeable trends in successful expression strategies are beginning to emerge. A number of groups have also explored high-throughput (HTP) methods for membrane protein expression, with varying degrees of success. Here we review the current state of expressing membrane proteins for functional and structural studies. We first survey successful methods that have already yielded levels of membrane protein expression sufficient for structure determination. HTP methods are also examined since these aim to explore large numbers of targets and can predict reasonable starting points for many membrane proteins. Since HTP techniques may fail, particularly for certain classes of eukaryotic targets, detailed strategies for the expression of two prominent classes of eukaryotic protein families, G-protein-coupled receptors and ion channels, are also summarized.
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Affiliation(s)
- Christopher M M Koth
- Department of Structural Biology, Genentech, South San Francisco, California 94080, USA
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8
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de Planque MRR, Killian JA. Protein–lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring (Review). Mol Membr Biol 2009; 20:271-84. [PMID: 14578043 DOI: 10.1080/09687680310001605352] [Citation(s) in RCA: 240] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Biological membranes are characterized by a heterogeneous composition, which is not only manifested in the wide variety of their components, but also in aspects like the lateral organization, topology, and conformation of proteins and lipids. In bringing about the correct membrane structure, protein-lipid interactions can be expected to play a prominent role. The extent of hydrophobic matching between transmembrane protein segments and lipids potentially constitutes a versatile director of membrane organization, because a tendency to avoid hydrophobic mismatch could result in compensating adaptations such as tilt of the transmembrane segment or segregation into distinct domains. Also, interfacial interactions between lipid headgroups and the aromatic and charged residues that typically flank transmembrane domains may act as an organizing element. In this review, we discuss the numerous model studies that have systematically explored the influence of hydrophobic matching and interfacial anchoring on membrane structure. Designed peptides consisting of a polyleucine or polyleucine/alanine hydrophobic stretch, which is flanked on both sides by tryptophan or lysine residues, reflect the general layout of transmembrane protein segments. It is shown for phosphatidylcholine bilayers and for other model membranes that these peptides adapt a transmembrane topology without extensive peptide or lipid adaptations under conditions of hydrophobic matching, but that significant rearrangements can result from hydrophobic mismatch. Moreover, these effects depend on the nature of the flanking residues, implying a modulation of the mismatch response by interfacial interactions of the flanking residues. The implications of these model studies for the organization of biomembranes are discussed in the context of recent experiments with more complex systems.
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Affiliation(s)
- Maurits R R de Planque
- Department of Biochemistry of Membranes, Center for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands.
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Ma J, Xia D. The use of blue native PAGE in the evaluation of membrane protein aggregation states for crystallization. J Appl Crystallogr 2008; 41:1150-1160. [PMID: 19529836 DOI: 10.1107/s0021889808033797] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 10/16/2008] [Indexed: 02/08/2023] Open
Abstract
Crystallization has long been one of the bottlenecks in obtaining structural information at atomic resolution for membrane proteins. This is largely due to difficulties in obtaining high-quality protein samples. One frequently used indicator of protein quality for successful crystallization is the monodispersity of proteins in solution, which is conventionally obtained by size exclusion chromatography (SEC) or by dynamic light scattering (DLS). Although useful in evaluating the quality of soluble proteins, these methods are not always applicable to membrane proteins either because of the interference from detergent micelles or because of the requirement for large sample quantities. Here, the use of blue native polyacrylamide gel electrophoresis (BN-PAGE) to assess aggregation states of membrane protein samples is reported. A strong correlation is demonstrated between the monodispersity measured by BN-PAGE and the propensity for crystallization of a number of soluble and membrane protein complexes. Moreover, it is shown that there is a direct correspondence between the oligomeric states of proteins as measured by BN-PAGE and those obtained from their crystalline forms. When applied to a membrane protein with unknown structure, BN-PAGE was found to be useful and efficient for selecting well behaved proteins from various constructs and in screening detergents. Comparisons of BN-PAGE with DLS and SEC are provided.
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Affiliation(s)
- Jichun Ma
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Building 37, Room 2122C, Bethesda, MD 20892, USA
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10
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Zubova SV, Ivanov AY, Prokhorenko IR. The effect of composition of the core region of Escherichia coli K-12 lipopolysaccharides on the surface properties of cells. Microbiology (Reading) 2008. [DOI: 10.1134/s0026261708030077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Özdirekcan S, Etchebest C, Killian JA, Fuchs PFJ. On the Orientation of a Designed Transmembrane Peptide: Toward the Right Tilt Angle? J Am Chem Soc 2007; 129:15174-81. [DOI: 10.1021/ja073784q] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suat Özdirekcan
- Contribution from the Department of Chemical Biology and Organic Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Equipe de Bioinformatique Génomique et Moléculaire INSERM UMR-S 726, Université Paris-Diderot-Paris 7, Case Courrier 7113, 2, place Jussieu, 75251 Paris Cedex 05, France
| | - Catherine Etchebest
- Contribution from the Department of Chemical Biology and Organic Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Equipe de Bioinformatique Génomique et Moléculaire INSERM UMR-S 726, Université Paris-Diderot-Paris 7, Case Courrier 7113, 2, place Jussieu, 75251 Paris Cedex 05, France
| | - J. Antoinette Killian
- Contribution from the Department of Chemical Biology and Organic Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Equipe de Bioinformatique Génomique et Moléculaire INSERM UMR-S 726, Université Paris-Diderot-Paris 7, Case Courrier 7113, 2, place Jussieu, 75251 Paris Cedex 05, France
| | - Patrick F. J. Fuchs
- Contribution from the Department of Chemical Biology and Organic Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Equipe de Bioinformatique Génomique et Moléculaire INSERM UMR-S 726, Université Paris-Diderot-Paris 7, Case Courrier 7113, 2, place Jussieu, 75251 Paris Cedex 05, France
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Le Gall T, Romero PR, Cortese MS, Uversky VN, Dunker AK. Intrinsic disorder in the Protein Data Bank. J Biomol Struct Dyn 2007; 24:325-42. [PMID: 17206849 DOI: 10.1080/07391102.2007.10507123] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The Protein Data Bank (PDB) is the preeminent source of protein structural information. PDB contains over 32,500 experimentally determined 3-D structures solved using X-ray crystallography or nuclear magnetic resonance spectroscopy. Intrinsically disordered regions fail to form a fixed 3-D structure under physiological conditions. In this study, we compare the amino-acid sequences of proteins whose structures are determined by X-ray crystallography with the corresponding sequences from the Swiss-Prot database. The analyzed dataset includes 16,370 structures, which represent 18,101 PDB chains and 5,434 different proteins from 910 different organisms (2,793 eukaryotic, 2,109 bacterial, 288 viral, and 244 archaeal). In this dataset, on average, each Swiss-Prot protein is represented by 7 PDB chains with 76% of the crystallized regions being represented by more than one structure. Intriguingly, the complete sequences of only approximately 7% of proteins are observed in the corresponding PDB structures, and only approximately 25% of the total dataset have >95% of their lengths observed in the corresponding PDB structures. This suggests that the vast majority of PDB proteins is shorter than their corresponding Swiss-Prot sequences and/or contain numerous residues, which are not observed in maps of electron density. To determine the prevalence of disordered regions in PDB, the residues in the Swiss-Prot sequences were grouped into four general categories, "Observed" (which correspond to structured regions), "Not observed" (regions with missing electron density, potentially disordered), "Uncharacterized," and "Ambiguous," depending on their appearance in the corresponding PDB entries. This non-redundant set of residues can be viewed as a 'fragment' or empirical domain database that contains a set of experimentally determined structured regions or domains and a set of experimentally verified disordered regions or domains. We studied the propensities and properties of residues in these four categories and analyzed their relations to the predictions of disorder using several algorithms. "Non-observed," "Ambiguous," and "Uncharacterized" regions were shown to possess the amino acid compositional biases typical of intrinsically disordered proteins. The application of four different disorder predictors (PONDR(R) VL-XT, VL3-BA, VSL1P, and IUPred) revealed that the vast majority of residues in the "Observed" dataset are ordered, and that the "Not observed" regions are mostly disordered. The "Uncharacterized" regions possess some tendency toward order, whereas the predictions for the short "Ambiguous" regions are really ambiguous. Long "Ambiguous" regions (>70 amino acid residues) are mostly predicted to be ordered, suggesting that they are likely to be "wobbly" domains. Overall, we showed that completely ordered proteins are not highly abundant in PDB and many PDB sequences have disordered regions. In fact, in the analyzed dataset approximately 10% of the PDB proteins contain regions of consecutive missing or ambiguous residues longer than 30 amino-acids and approximately 40% of the proteins possess short regions (> or =10 and < 30 amino-acid long) of missing and ambiguous residues.
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Affiliation(s)
- Tanguy Le Gall
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Stopar D, Spruijt RB, Hemminga MA. Anchoring mechanisms of membrane-associated M13 major coat protein. Chem Phys Lipids 2006; 141:83-93. [PMID: 16620800 DOI: 10.1016/j.chemphyslip.2006.02.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 02/16/2006] [Accepted: 02/20/2006] [Indexed: 11/17/2022]
Abstract
Bacteriophage M13 major coat protein is extensively used as a biophysical, biochemical, and molecular biology reference system for studying membrane proteins. The protein has several elements that control its position and orientation in a lipid bilayer. The N-terminus is dominated by the presence of negatively charged amino acid residues (Glu2, Asp4, and Asp5), which will always try to extend into the aqueous phase and therefore act as a hydrophilic anchor. The amphipathic and the hydrophobic transmembrane part contain the most important hydrophobic anchoring elements. In addition there are specific aromatic and charged amino acid residues in these domains (Phe 11, Tyr21, Tyr24, Trp26, Phe42, Phe45, Lys40, Lys43, and Lys44) that fine-tune the association of the protein to the lipid bilayer. The interfacial Tyr residues are important recognition elements for precise protein positioning, a function that cannot be performed optimally by residues with an aliphatic character. The Trp26 anchor is not very strong: depending on the context, the tryptophan residue may move in or out of the membrane. On the other hand, Lys residues and Phe residues at the C-terminus of the protein act in a unique concerted action to strongly anchor the protein in the lipid bilayer.
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Affiliation(s)
- David Stopar
- University of Ljubljana, Biotechnical Faculty, Slovenia
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14
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Ma J, Yoshimura M, Yamashita E, Nakagawa A, Ito A, Tsukihara T. Structure of rat monoamine oxidase A and its specific recognitions for substrates and inhibitors. J Mol Biol 2004; 338:103-14. [PMID: 15050826 DOI: 10.1016/j.jmb.2004.02.032] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2003] [Revised: 02/05/2004] [Accepted: 02/12/2004] [Indexed: 11/20/2022]
Abstract
Monoamine oxidase (MAO), a mitochondrial outer membrane enzyme, catalyzes the degradation of neurotransmitters in the central nervous system and is the target for anti-depression drug design. Two subtypes of MAO, MAOA and MAOB, are similar in primary sequences but have unique substrate and inhibitor specificities. The structures of human MAOB complexed with various inhibitors were reported early. To understand the mechanisms of specific substrate and inhibitor recognitions of MAOA and MAOB, we have determined the crystal structure of rat MAOA complexed with the specific inhibitor, clorgyline, at 3.2A resolution. The comparison of the structures between MAOA and MAOB clearly explains the specificity of clorgyline for MAOA inhibition. The fitting of serotonin into the binding pockets of MAOs demonstrates that MAOB Tyr326 would block access of the 5-hydroxy group of serotonin into the enzyme. These results will lead to further understanding of the MAOA function and to new anti-depression drug design. This study also presents that MAOA has a transmembrane helix at the C-terminal region. This is the first crystal structure of membrane protein with an isolated transmembrane helix.
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Affiliation(s)
- Jichun Ma
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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15
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Bracey MH, Cravatt BF, Stevens RC. Structural commonalities among integral membrane enzymes. FEBS Lett 2004; 567:159-65. [PMID: 15178315 DOI: 10.1016/j.febslet.2004.04.084] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2004] [Revised: 04/15/2004] [Accepted: 04/26/2004] [Indexed: 11/26/2022]
Abstract
The X-ray crystal structures of five distinct enzymes (prostaglandin H(2) synthase, squalene cyclase, fatty acid amide hydrolase, microsomal cytochrome P450, and estrone sulfatase) challenge contemporary descriptions of integral membrane proteins. This structurally divergent group represents an important component of the integral membrane proteome that lies at the bilayer's aqueous interface. We summarize here what is collectively understood about the membrane insertion of these proteins, what roles they may play in lipid biology, and their relationship to soluble structural homologs.
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Affiliation(s)
- Michael H Bracey
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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16
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de Planque MRR, Bonev BB, Demmers JAA, Greathouse DV, Koeppe RE, Separovic F, Watts A, Killian JA. Interfacial anchor properties of tryptophan residues in transmembrane peptides can dominate over hydrophobic matching effects in peptide-lipid interactions. Biochemistry 2003; 42:5341-8. [PMID: 12731875 DOI: 10.1021/bi027000r] [Citation(s) in RCA: 218] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane model systems consisting of phosphatidylcholines and hydrophobic alpha-helical peptides with tryptophan flanking residues, a characteristic motif for transmembrane protein segments, were used to investigate the contribution of tryptophans to peptide-lipid interactions. Peptides of different lengths and with the flanking tryptophans at different positions in the sequence were incorporated in relatively thick or thin lipid bilayers. The organization of the systems was assessed by NMR methods and by hydrogen/deuterium exchange in combination with mass spectrometry. Previously, it was found that relatively short peptides induce nonlamellar phases and that relatively long analogues order the lipid acyl chains in response to peptide-bilayer mismatch. Here it is shown that these effects do not correlate with the total hydrophobic peptide length, but instead with the length of the stretch between the flanking tryptophan residues. The tryptophan indole ring was consistently found to be positioned near the lipid carbonyl moieties, regardless of the peptide-lipid combination, as indicated by magic angle spinning NMR measurements. These observations suggest that the lipid adaptations are not primarily directed to avoid a peptide-lipid hydrophobic mismatch, but instead to prevent displacement of the tryptophan side chains from the polar-apolar interface. In contrast, long lysine-flanked analogues fully associate with a bilayer without significant lipid adaptations, and hydrogen/deuterium exchange experiments indicate that this is achieved by simply exposing more (hydrophobic) residues to the lipid headgroup region. The results highlight the specific properties that are imposed on transmembrane protein segments by flanking tryptophan residues.
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Affiliation(s)
- Maurits R R de Planque
- Department of Biochemistry of Membranes, Center for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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17
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de Planque MRR, Boots JWP, Rijkers DTS, Liskamp RMJ, Greathouse DV, Killian JA. The effects of hydrophobic mismatch between phosphatidylcholine bilayers and transmembrane alpha-helical peptides depend on the nature of interfacially exposed aromatic and charged residues. Biochemistry 2002; 41:8396-404. [PMID: 12081488 DOI: 10.1021/bi0257686] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we investigated the extent to which different aromatic and positively charged side chains, which often flank transmembrane segments of proteins, can influence lipid-peptide interactions. Model systems consisting of phosphatidylcholine and hydrophobic alpha-helical peptides with different flanking residues were investigated. The peptides were incorporated in relatively thick and in relatively thin lipid bilayers to create a peptide-bilayer hydrophobic mismatch, and the compensating effects on lipid structure were analyzed. When relatively long with respect to the thickness of the bilayer, the peptides that are flanked by the aromatic side chains, Trp, Tyr, and Phe, all induce a significant ordering of the lipid acyl chains, while the peptides flanked by the charged residues Lys, Arg, and His do not. However, when the peptides are relatively short with respect to the thickness of the bilayer, their effect on lipid organization does not depend primarily on their aromatic or charged character. Peptides flanked by Trp, Tyr, Lys, or (at low pH) His residues are effective in inducing mismatch-relieving cubic and inverted hexagonal phases, while analogues flanked by Phe, Arg, or (at neutral pH) His residues cannot induce an inverted hexagonal phase. The different responses to mismatch might reflect the different interfacial affinities of the residues that were investigated.
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Affiliation(s)
- Maurits R R de Planque
- Center for Biomembranes and Lipid Enzymology, Institute of Biomembranes, Department of Biochemistry of Membranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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18
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Abstract
It has been shown previously that some membrane proteins have a conserved core of amino acid residues. This idea not only serves to orient helices during model building exercises but may also provide insight into the structural role of residues mediating helix-helix interactions. Using experimentally determined high-resolution structures of alpha-helical transmembrane proteins we show that, of the residues within the hydrophobic transmembrane spans, the residues at lipid and subunit interfaces are more evolutionarily variable than those within the lipid-inaccessible core of a polypeptide's transmembrane domain. This supports the idea that helix-helix interactions within the same polypeptide chain and those at the interface between different polypeptide chains may arise in distinct ways. To show this, we use a new method to estimate the substitution rate of an amino acid residue given an alignment and phylogenetic tree of closely related proteins. This method gives better sensitivity in the otherwise-conserved transmembrane domains than a conventional similarity analysis and is relatively insensitive to the sequences used.
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Affiliation(s)
- T J Stevens
- Cambridge Center for Molecular Recognition, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
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19
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Harrop SJ, DeMaere MZ, Fairlie WD, Reztsova T, Valenzuela SM, Mazzanti M, Tonini R, Qiu MR, Jankova L, Warton K, Bauskin AR, Wu WM, Pankhurst S, Campbell TJ, Breit SN, Curmi PM. Crystal structure of a soluble form of the intracellular chloride ion channel CLIC1 (NCC27) at 1.4-A resolution. J Biol Chem 2001; 276:44993-5000. [PMID: 11551966 DOI: 10.1074/jbc.m107804200] [Citation(s) in RCA: 166] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CLIC1 (NCC27) is a member of the highly conserved class of chloride ion channels that exists in both soluble and integral membrane forms. Purified CLIC1 can integrate into synthetic lipid bilayers forming a chloride channel with similar properties to those observed in vivo. The structure of the soluble form of CLIC1 has been determined at 1.4-A resolution. The protein is monomeric and structurally homologous to the glutathione S-transferase superfamily, and it has a redox-active site resembling glutaredoxin. The structure of the complex of CLIC1 with glutathione shows that glutathione occupies the redox-active site, which is adjacent to an open, elongated slot lined by basic residues. Integration of CLIC1 into the membrane is likely to require a major structural rearrangement, probably of the N-domain (residues 1-90), with the putative transmembrane helix arising from residues in the vicinity of the redox-active site. The structure indicates that CLIC1 is likely to be controlled by redox-dependent processes.
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Affiliation(s)
- S J Harrop
- Initiative for Biomolecular Structure, School of Physics and the Department of Medicine, University of New South Wales, New South Wales 2052, Australia
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20
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Batista CV, Scaloni A, Rigden DJ, Silva LR, Rodrigues Romero A, Dukor R, Sebben A, Talamo F, Bloch C. A novel heterodimeric antimicrobial peptide from the tree-frog Phyllomedusa distincta. FEBS Lett 2001; 494:85-9. [PMID: 11297740 DOI: 10.1016/s0014-5793(01)02324-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We present here the purification and the analysis of the structural and functional properties of distinctin, a 5.4 kDa heterodimeric peptide with antimicrobial activity from the tree-frog Phyllomedusa distincta. This peptide was isolated from the crude extract of skin granular glands by different chromatographic steps. Its minimal inhibitory concentration was determined against pathogenic Escherichia coli, Staphylococcus aureus, Enterococcus faecalis and Pseudomonas aeruginosa strains. Amino acid sequencing and mass spectrometric investigations demonstrated that distinctin is constituted of two different polypeptide chains connected by an intermolecular disulphide bridge. Circular dichroism and Fourier-transformed infrared spectroscopy studies showed that this molecule adopts, in water, a structure containing a significant percentage of anti-parallel beta-sheet. A conformational variation was observed under experimental conditions mimicking a membrane-like environment. Database searches did not show sequence similarities with any known antimicrobial peptides. In the light of these results, we can consider distinctin as the first example of a new class of antimicrobial heterodimeric peptides from frog skin.
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Affiliation(s)
- C V Batista
- Institute of Biology, University of Brasilia, Brazil
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21
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Abstract
Helical membrane protein folding and oligomerization can be usefully conceptualized as involving two energetically distinct stages-the formation and subsequent side-to-side association of independently stable transbilayer helices. The interactions of helices with the bilayer, with prosthetic groups, and with each other are examined in the context of recent evidence. We conclude that the two-stage concept remains useful as an approach to simplifying discussions of stability, as a framework for folding concepts, and as a basis for understanding membrane protein evolution.
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Affiliation(s)
- J L Popot
- Laboratoire de Physicochimie Moléculaire des Membranes Biologiques, Centre National de la Recherche Scientifique UPR 9052, Institut de Biologie Physico-Chimique, F-75005 Paris, France.
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22
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Appleyard AN, Herbert RB, Henderson PJ, Watts A, Spooner PJ. Selective NMR observation of inhibitor and sugar binding to the galactose-H(+) symport protein GalP, of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1509:55-64. [PMID: 11118517 DOI: 10.1016/s0304-4157(00)00017-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The binding of the transport inhibitor forskolin, synthetically labelled with (13)C, to the galactose-H(+) symport protein GalP, overexpressed in its native inner membranes from Escherichia coli, was studied using cross-polarization magic angle spinning (13)C NMR. (13)C-Labelled D-galactose and D-glucose were displaced from GalP with the singly labelled [7-OCO(13)CH(3)]forskolin and were not bound to any alternative site within the protein, demonstrating that any multiple sugar binding sites are not simultaneously accessible to these sugars and the inhibitor within GalP. The observation of singly (13)C-labelled forskolin was hampered by interference from natural abundance (13)C in the membranes and so the effectiveness of double-quantum filtration was assessed for the exclusive detection of (13)C spin pairs in sugar (D-[1,2-(13)C(2)]glucose) and inhibitor ([7-O(13)CO(13)CH(3)]forskolin) bound to the GalP protein. The solid state NMR methodology was not effective in creating double-quantum selection of ligand bound with membranes in the 'fluid' state (approx. 2 degrees C) but could be applied in a straightforward way to systems that were kept frozen. At -35 degrees C, double-quantum filtration detected unbound sugar that was incorporated into ice structure within the sample, and was not distinguished from protein-bound sugar. However, the method detected doubly labelled forskolin that is selectively bound only to the transport system under these conditions and provided very effective suppression of interference from natural abundance (13)C background. These results indicate that solid state NMR methods can be used to resolve selectively the interactions of more hydrophobic ligands in the binding sites of target proteins.
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Affiliation(s)
- A N Appleyard
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, UK
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23
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le Maire M, Champeil P, Moller JV. Interaction of membrane proteins and lipids with solubilizing detergents. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1508:86-111. [PMID: 11090820 DOI: 10.1016/s0304-4157(00)00010-1] [Citation(s) in RCA: 722] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Detergents are indispensable in the isolation of integral membrane proteins from biological membranes to study their intrinsic structural and functional properties. Solubilization involves a number of intermediary states that can be studied by a variety of physicochemical and kinetic methods; it usually starts by destabilization of the lipid component of the membranes, a process that is accompanied by a transition of detergent binding by the membrane from a noncooperative to a cooperative interaction already below the critical micellar concentration (CMC). This leads to the formation of membrane fragments of proteins and lipids with detergent-shielded edges. In the final stage of solubilization membrane proteins are present as protomers, with the membrane inserted sectors covered by detergent. We consider in detail the nature of this interaction and conclude that in general binding as a monolayer ring, rather than as a micelle, is the most probable mechanism. This mode of interaction is supported by neutron diffraction investigations on the disposition of detergent in 3-D crystals of membrane proteins. Finally, we briefly discuss the use of techniques such as analytical ultracentrifugation, size exclusion chromatography, and mass spectrometry relevant for the structural investigation of detergent solubilized membrane proteins.
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Affiliation(s)
- M le Maire
- Unite de recherche Associée 2096 (Centre National de la Recherche Scientifique et Commissariat a l'Energie Atomique), Cedex, France.
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24
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Abstract
We have applied 25 different detergents to the PNS myelin membrane. The extracts produced were analyzed regarding the total amount of protein solubilized, and which myelin glycoproteins were solubilized. The degree of protein extraction was correlated with the critical micelle concentration. For some detergents the protein extraction ability depends clearly on critical micelle concentration. These detergents are more potent if critical micelle concentration is small. The other type of extraction is independent on the critical micelle concentration, but extractability of proteins is low. The best detergents for solubilization of myelin proteins are neutral of the alkyl chain length n =9-11, as follows: dodecyl-beta-D-maltopyranoside, decyl-beta-D-maltopyranoside, n-dodecylsulfobetaine. We expect that these detergents will also be suitable for crystallization of P0 and PASII/PMP22 glycoproteins.
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Affiliation(s)
- J Sedzik
- Institute for Protein Research, Osaka University, Japan
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25
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Saier MH. A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol Mol Biol Rev 2000; 64:354-411. [PMID: 10839820 PMCID: PMC98997 DOI: 10.1128/mmbr.64.2.354-411.2000] [Citation(s) in RCA: 567] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the International Union of Biochemistry and Molecular Biology. This system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. Almost all of the more than 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters, and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Transport mode and energy coupling prove to be relatively immutable characteristics and therefore provide primary bases for classification. Phylogenetic grouping reflects structure, function, mechanism, and often substrate specificity and therefore provides a reliable secondary basis for classification. Substrate specificity and polarity of transport prove to be more readily altered during evolutionary history and therefore provide a tertiary basis for classification. With very few exceptions, a phylogenetic family of transporters includes members that function by a single transport mode and energy coupling mechanism, although a variety of substrates may be transported, sometimes with either inwardly or outwardly directed polarity. In this review, I provide cross-referencing of well-characterized constituent transporters according to (i) transport mode, (ii) energy coupling mechanism, (iii) phylogenetic grouping, and (iv) substrates transported. The structural features and distribution of recognized family members throughout the living world are also evaluated. The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects.
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Affiliation(s)
- M H Saier
- Department of Biology, University of California at San Diego, La Jolla, California 92093-0116, USA.
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26
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Kasahara T, Kasahara M. Interaction between the critical aromatic amino acid residues Tyr(352) and Phe(504) in the yeast Gal2 transporter. FEBS Lett 2000; 471:103-7. [PMID: 10760522 DOI: 10.1016/s0014-5793(00)01371-5] [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: 11/24/2022]
Abstract
Three critical aromatic sites have been identified in the yeast galactose transporter Gal2: Tyr(352) at the extracellular boundary of putative transmembrane segment (TM) 7, Tyr(446) in the middle of TM10 and Phe(504) in the middle of TM12. The relationship between these sites was investigated by random mutagenesis of each combination of two of the three residues. Galactose transport-positive clones selected by plate assays encoded Tyr(446) and specific combinations of aromatic residues at sites 352 and 504. Double-site mutants containing aromatic residues at these latter two positions showed either essentially full galactose transport activity (Phe(352)Trp(504) and Trp(352)Trp(504)) or no significant activity (Phe(352)Tyr(504) and Trp(352)Tyr(504)), whereas single-site mutants showed markedly reduced activity. These results are indicative of a specific interaction between sites 352 and 504 of Gal2.
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Affiliation(s)
- T Kasahara
- Laboratory of Biophysics, School of Medicine, Teikyo University, Hachioji, Tokyo, Japan
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27
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Degrip W, Rothschild K. Chapter 1 Structure and mechanism of vertebrate visual pigments. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1383-8121(00)80004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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28
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Saier MH. Genome archeology leading to the characterization and classification of transport proteins. Curr Opin Microbiol 1999; 2:555-61. [PMID: 10508720 DOI: 10.1016/s1369-5274(99)00016-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In the study of transmembrane transport, molecular phylogeny provides a reliable guide to protein structure, catalytic and noncatalytic transport mechanisms, mode of energy coupling and substrate specificity. It also allows prediction of the evolutionary history of a transporter family, leading to estimations of its age, source, and route of appearance. Phylogenetic analyses, therefore, provide a rational basis for the characterization and classification of transporters. A universal classification system has been described, based on both function and phylogeny, which has been designed to be applicable to all currently recognized and yet-to-be discovered transport proteins found in living organisms on Earth.
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Affiliation(s)
- M H Saier
- Department of Biology University of California at San Diego La Jolla, CA 92093-0116, USA.
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29
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Villoutreix BO, Blom AM, Dahlbäck B. Structural prediction and analysis of endothelial cell protein C/activated protein C receptor. PROTEIN ENGINEERING 1999; 12:833-40. [PMID: 10556243 DOI: 10.1093/protein/12.10.833] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The endothelial cell receptor (EPCR) for protein C (PC)/activated protein C (APC) is a 221 amino-acid residues long transmembrane glycoprotein with unclear physiological function. To facilitate future studies and to rationalize recently reported experimental data about this protein, we have constructed three-dimensional models of human, bovine and mouse EPCR using threading and comparative model building. EPCR is homologous to CD1/MHC class I molecules. It consists of two domains, which are similar to the alpha1 and alpha2 domains of MHC class I molecules, whereas the alpha3 domain of MHC is replaced in EPCR by a transmembrane region followed by a short cytosolic tail. The alpha1 and alpha2 domains of CD1/MHC proteins form a groove, which binds short peptides. These domains are composed of an eight-stranded antiparallel beta-pleated sheet with two long antiparallel alpha-helices. The distance between the helical segments dictates the width of the groove. The cleft in EPCR appears to be relatively narrow and it is lined with hydrophobic/aromatic and polar residues with a few charged amino acids. Analysis of the human EPCR model predicts that (a) the protein does not contain any calcium binding pockets; (b) C101 and C169 form a buried disulphide bridge, while C97 is free, and buried in the core of the molecule; and (c) four potential glycosylation sites are solvent exposed.
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Affiliation(s)
- B O Villoutreix
- Lund University, The Wallenberg Laboratory, Department of Clinical Chemistry, University Hospital Malmö, S-205 02 Malmö, Sweden
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30
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Kotra LP, Golemi D, Amro NA, Liu GY, Mobashery S. Dynamics of the Lipopolysaccharide Assembly on the Surface ofEscherichiacoli. J Am Chem Soc 1999. [DOI: 10.1021/ja991374z] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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