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Duart G, Graña-Montes R, Pastor-Cantizano N, Mingarro I. Experimental and computational approaches for membrane protein insertion and topology determination. Methods 2024; 226:102-119. [PMID: 38604415 DOI: 10.1016/j.ymeth.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Membrane proteins play pivotal roles in a wide array of cellular processes and constitute approximately a quarter of the protein-coding genes across all organisms. Despite their ubiquity and biological significance, our understanding of these proteins remains notably less comprehensive compared to their soluble counterparts. This disparity in knowledge can be attributed, in part, to the inherent challenges associated with employing specialized techniques for the investigation of membrane protein insertion and topology. This review will center on a discussion of molecular biology methodologies and computational prediction tools designed to elucidate the insertion and topology of helical membrane proteins.
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Affiliation(s)
- Gerard Duart
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ricardo Graña-Montes
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Noelia Pastor-Cantizano
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain.
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2
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Yang X, Zhang Z, Wu L, Yang M, Li S, Gao J. Conserved Residues Lys64 and Glu78 at the Subunit Surface of Tau Glutathione Transferase in Rice Affect Structure and Enzymatic Properties. Int J Mol Sci 2023; 25:398. [PMID: 38203568 PMCID: PMC10778600 DOI: 10.3390/ijms25010398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Glutathione transferases (GSTs) are a superfamily of dimeric proteins associated with the detoxification of various reactive electrophiles and responsive to a multitude of stressors. We individually substituted Lys64 and Glu78 with Ala using site-directed mutagenesis to understand the role of subunit interactions in the structure and enzymatic properties of a rice GST (OsGSTU17). The wild-type OsGSTU17 lost the conserved hydrogen bond between subunits in tau class GSTs due to conserved Tyr92 replaced with Phe92, but still exhibited high substrate activities, and thermal stability remained in its dimeric structure. The significant decrease in thermal stability and obvious changes in the structure of mutant K64A implied that conserved Lys64 might play an essential role in the structural stability of tau class GSTs. The mutant E78A, supposed to be deprived of hydrogen and salt bonds between subunits, appeared in the soluble form of dimers, even though its tertiary structure altered and stability declined dramatically. These results suggest that the hydrogen and ionic bonds provided by conserved residues are not as important for OsGSTU17 dimerization and enzymatic properties. These results further supplement our understanding of the relationship between the structure and function of GSTs and provide a theoretical basis for improving crop resistance through targeted modification of GSTs.
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Affiliation(s)
- Xue Yang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.Y.); (Z.Z.); (L.W.)
| | - Zhe Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.Y.); (Z.Z.); (L.W.)
| | - Lei Wu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.Y.); (Z.Z.); (L.W.)
| | - Meiying Yang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.Y.); (Z.Z.); (L.W.)
| | - Siyuan Li
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.Y.); (Z.Z.); (L.W.)
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
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3
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Almeida PF. In Search of a Molecular View of Peptide-Lipid Interactions in Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37478368 DOI: 10.1021/acs.langmuir.3c00538] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Lipid bilayer membranes are often represented as a continuous nonpolar slab with a certain thickness bounded by two more polar interfaces. Phenomena such as peptide binding to the membrane surface, folding, insertion, translocation, and diffusion are typically interpreted on the basis of this view. In this Perspective, I argue that this membrane representation as a hydrophobic continuum solvent is not adequate to understand peptide-lipid interactions. Lipids are not small compared to membrane-active peptides: their sizes are similar. Therefore, peptide diffusion needs to be understood in terms of free volume, not classical continuum mechanics; peptide solubility or partitioning in membranes cannot be interpreted in terms of hydrophobic mismatch between membrane thickness and peptide length; peptide folding and translocation, often involving cationic peptides, can only be understood if realizing that lipids adapt to the presence of peptides and the membrane may undergo considerable lipid redistribution in the process. In all of those instances, the detailed molecular interactions between the peptide residues and the lipid components are essential to understand the mechanisms involved.
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Affiliation(s)
- Paulo F Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
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4
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Dunleavy KM, Oi C, Li T, Secunda A, Jaufer AM, Zhu Y, Friedman L, Kim A, Fanucci GE. Hydrogen Bonding Compensation on the Convex Solvent-Exposed Helical Face of IA 3, an Intrinsically Disordered Protein. Biochemistry 2023. [PMID: 37198000 DOI: 10.1021/acs.biochem.3c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Saccharomyces cerevisiae IA3 is a 68 amino acid peptide inhibitor of yeast proteinase A (YPRA) characterized as a random coil when in solution, folding into an N-terminal amphipathic alpha helix for residues 2-32 when bound to YPRA, with residues 33-68 unresolved in the crystal complex. Circular dichroism (CD) spectroscopy results show that amino acid substitutions that remove hydrogen-bonding interactions observed within the hydrophilic face of the N-terminal domain (NTD) of IA3-YPRA crystal complex reduce the 2,2,2-trifluoroethanol (TFE)-induced helical transition in solution. Although nearly all substitutions decreased TFE-induced helicity compared to wild-type (WT), each construct did retain helical character in the presence of 30% (v/v) TFE and retained disorder in the absence of TFE. The NTDs of 8 different Saccharomyces species have nearly identical amino acid sequences, indicating that the NTD of IA3 may be highly evolved to adopt a helical fold when bound to YPRA and in the presence of TFE but remain unstructured in solution. Only one natural amino acid substitution explored within the solvent-exposed face of the NTD of IA3 induced TFE-helicity greater than the WT sequence. However, chemical modification of a cysteine by a nitroxide spin label that contains an acetamide side chain did enhance TFE-induced helicity. This finding suggests that non-natural amino acids that can increase hydrogen bonding or alter hydration through side-chain interactions may be important to consider when rationally designing intrinsically disordered proteins (IDPs) with varied biotechnological applications.
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Affiliation(s)
- Katie M Dunleavy
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Collin Oi
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Tianyan Li
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Andrew Secunda
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Afnan M Jaufer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Yinlu Zhu
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Lee Friedman
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Alexander Kim
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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5
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White SH. Fifty Years of Biophysics at the Membrane Frontier. Annu Rev Biophys 2023; 52:21-67. [PMID: 36791747 DOI: 10.1146/annurev-biophys-051622-112341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The author first describes his childhood in the South and the ways in which it fostered the values he has espoused throughout his life, his development of a keen fascination with science, and the influences that supported his progress toward higher education. His experiences in ROTC as a student, followed by two years in the US Army during the Vietnam War, honed his leadership skills. The bulk of the autobiography is a chronological journey through his scientific career, beginning with arrival at the University of California, Irvine in 1972, with an emphasis on the postdoctoral students and colleagues who have contributed substantially to each phase of his lab's progress. White's fundamental findings played a key role in the development of membrane biophysics, helping establish it as fertile ground for research. A story gradually unfolds that reveals the deeply collaborative and painstakingly executed work necessary for a successful career in science.
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Affiliation(s)
- Stephen H White
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California, USA;
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6
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Zimmerberg J, Soubias O, Pastor RW. Special issue for Klaus Gawrisch. Biophys J 2023; 122:E1-E8. [PMID: 36921597 PMCID: PMC10111273 DOI: 10.1016/j.bpj.2023.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/17/2023] Open
Affiliation(s)
- Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Olivier Soubias
- Macromolecular NMR Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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7
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Brady R, Harris NJ, Pellowe GA, Gulaidi Breen S, Booth PJ. How lipids affect the energetics of co-translational alpha helical membrane protein folding. Biochem Soc Trans 2022; 50:555-567. [PMID: 35212365 PMCID: PMC9022994 DOI: 10.1042/bst20201063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 11/23/2022]
Abstract
Membrane proteins need to fold with precision in order to function correctly, with misfolding potentially leading to disease. The proteins reside within a hydrophobic lipid membrane and must insert into the membrane and fold correctly, generally whilst they are being translated by the ribosome. Favourable and unfavourable free energy contributions are present throughout each stage of insertion and folding. The unfavourable energy cost of transferring peptide bonds into the hydrophobic membrane interior is compensated for by the favourable hydrophobic effect of partitioning a hydrophobic transmembrane alpha-helix into the membrane. Native membranes are composed of many different types of lipids, but how these different lipids influence folding and the associated free energies is not well understood. Altering the lipids in the bilayer is known to affect the probability of transmembrane helix insertion into the membrane, and lipids also affect protein stability and can promote successful folding. This review will summarise the free energy contributions associated with insertion and folding of alpha helical membrane proteins, as well as how lipids can make these processes more or less favourable. We will also discuss the implications of this work for the free energy landscape during the co-translational folding of alpha helical membrane proteins.
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Affiliation(s)
- Ryan Brady
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Nicola J. Harris
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Grant A. Pellowe
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Samuel Gulaidi Breen
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Paula J. Booth
- King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
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8
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Hong H, Choi HK, Yoon TY. Untangling the complexity of membrane protein folding. Curr Opin Struct Biol 2022; 72:237-247. [PMID: 34995926 DOI: 10.1016/j.sbi.2021.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/15/2022]
Abstract
Delineating the folding steps of helical-bundle membrane proteins has been a challenging task. Many questions remain unanswered, including the conformation and stability of the states populated during folding, the shape of the energy barriers between the states, and the role of lipids as a solvent in mediating the folding. Recently, theoretical frames have matured to a point that permits detailed dissection of the folding steps, and advances in experimental techniques at both single-molecule and ensemble levels enable selective modulation of specific steps for quantitative determination of the folding energy landscapes. We also discuss how lipid molecules would play an active role in shaping the folding energy landscape of membrane proteins, and how folding of multi-domain membrane proteins can be understood based on our current knowledge. We conclude this review by offering an outlook for emerging questions in the study of membrane protein folding.
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Affiliation(s)
- Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA.
| | - Hyun-Kyu Choi
- Wallace H. Coulter Department of Biomedical Engineering and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Tae-Young Yoon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea.
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9
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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10
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Ghosh G, Panicker L. Protein-nanoparticle interactions and a new insight. SOFT MATTER 2021; 17:3855-3875. [PMID: 33885450 DOI: 10.1039/d0sm02050h] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The study of protein-nanoparticle interactions provides knowledge about the bio-reactivity of nanoparticles, and creates a database of nanoparticles for applications in nanomedicine, nanodiagnosis, and nanotherapy. The problem arises when nanoparticles come in contact with physiological fluids such as plasma or serum, wherein they interact with the proteins (or other biomolecules). This interaction leads to the coating of proteins on the nanoparticle surface, mostly due to the electrostatic interaction, called 'corona'. These proteins are usually partially unfolded. The protein corona can deter nanoparticles from their targeted functionalities, such as drug/DNA delivery at the site and fluorescence tagging of diseased tissues. The protein corona also has many repercussions on cellular intake, inflammation, accumulation, degradation, and clearance of the nanoparticles from the body depending on the exposed part of the proteins. Hence, the protein-nanoparticle interaction and the configuration of the bound-proteins on the nanosurface need thorough investigation and understanding. Several techniques such as DLS and zeta potential measurement, UV-vis spectroscopy, fluorescence spectroscopy, circular dichroism, FTIR, and DSC provide valuable information in the protein-nanoparticle interaction study. Besides, theoretical simulations also provide additional understanding. Despite a lot of research publications, the fundamental question remained unresolved. Can we aim for the application of functional nanoparticles in medicine? A new insight, given by us, in this article assumes a reasonable solution to this crucial question.
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Affiliation(s)
- Goutam Ghosh
- UGC-DAE Consortium for Scientific Research, Mumbai Centre, Mumbai 400 085, India.
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11
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Shabane PS, Onufriev AV. Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure. J Mol Biol 2020; 433:166683. [PMID: 33096105 DOI: 10.1016/j.jmb.2020.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/30/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
The intrinsically disordered, positively charged H4 histone tail is important for chromatin structure and function. We have explored conformational ensembles of human H4 tail in solution, with varying levels of charge neutralization via acetylation or amino-acid substitutions such as K→Q. We have employed an explicit water model shown recently to be well suited for simulations of intrinsically disordered proteins. Upon progressive neutralization of the H4, its radius of gyration decreases linearly with the tail charge q, the trend is explained using a simple polymer model. While the wild type state (q=+8) is essentially a random coil, hyper-acetylated H4 (q=+3) is virtually as compact and stable as a globular protein of the same number of amino-acids. Conformational ensembles of acetylated H4 match the corresponding K→X substitutions only approximately: based on the ensemble similarity, we propose K→M as a possible alternative to the commonly used K→Q. Possible effects of the H4 tail compaction on chromatin structure are discussed within a qualitative model in which the chromatin is highly heterogeneous, easily inter-converting between various structural forms. We predict that upon progressive charge neutralization of the H4 tail, the least compact sub-states of chromatin de-condense first, followed by de-condensation of more compact structures, e.g. those that harbor a high fraction of stacked di-nucleosomes. The predicted hierarchy of DNA accessibility increase upon progressive acetylation of H4 might be utilized by the cell for selective DNA accessibility control.
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Affiliation(s)
| | - Alexey V Onufriev
- Departments of Computer Science, Virginia Tech, Blacksburg, VA 24060, United States; Department of Physics, Virginia Tech, Blacksburg, VA 24060, United States; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA.
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12
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Catunda R, Rekhi U, Clark D, Levin L, Febbraio M. Downregulation von Loricrin und epitheliale Erkrankungen: ein systematischer Überblick. J Dtsch Dermatol Ges 2019; 17:1227-1238. [PMID: 31885179 DOI: 10.1111/ddg.14001_g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/19/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Raisa Catunda
- School of Dentistry, Faculty of Medecine and Dentistry, University of Alberta
| | - Umar Rekhi
- School of Dentistry, Faculty of Medecine and Dentistry, University of Alberta
| | - Danielle Clark
- School of Dentistry, Faculty of Medecine and Dentistry, University of Alberta
| | - Liran Levin
- School of Dentistry, Division of Periodontology, Faculty of Medecine and Dentistry, University of Alberta
| | - Maria Febbraio
- School of Dentistry, Faculty of Medecine and Dentistry, University of Alberta
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13
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Catunda R, Rekhi U, Clark D, Levin L, Febbraio M. Loricrin downregulation and epithelial-related disorders: a systematic review. J Dtsch Dermatol Ges 2019; 17:1227-1238. [PMID: 31846220 DOI: 10.1111/ddg.14001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/19/2019] [Indexed: 12/15/2022]
Abstract
Loricrin downregulation has been associated with age-related changes as well as inherited and inflammatory skin diseases. We hypothesize that changes in loricrin could be more related to altered barrier function and consequently disorders that affect epithelial cells, such as psoriasis, atopic dermatitis (AD), erythrokeratoderma, loricrin keratoderma (LK) and periodontitis. The aim of this review is to summarize what is known about the association between loricrin downregulation and epithelial-related disorders (ERDs). A search was performed on the following databases: Medline, Cochrane Library, PubMed, EMBASE, Lilacs, Scopus and Google Scholar, resulting in 16 included articles. Loricrin keratoderma was the ERD most frequently associated with loricrin mutations (730insG, 709insC and 578insG; 5/7 cases - 71.44 %). Atopic dermatitis was the ERD most frequently associated with loricrin downregulation (2/7 cases - 28.6 %). Mutilating palmoplantar keratoderma, progressive symmetrical erythrokeratoderma and a new type of erythrokeratoderma were not associated with any mutations. At the gene level, periodontitis patients showed the highest decrease (-6.89x), followed by AD (-6.5x) and psoriasis patients (-0.5x). In summary, loricrin mutation and downregulation were associated with several ERDs. The diversity in disease presentation is likely related to whether there is a total loss of loricrin, mislocalization and/or if the mutant form of loricrin causes dysfunction of other proteins and/or changes in cornification.
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Affiliation(s)
- Raisa Catunda
- School of Dentistry, Faculty of Medecine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Umar Rekhi
- School of Dentistry, Faculty of Medecine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Danielle Clark
- School of Dentistry, Faculty of Medecine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liran Levin
- School of Dentistry, Division of Periodontology, Faculty of Medecine and Dentistry, University of Alberta
| | - Maria Febbraio
- School of Dentistry, Faculty of Medecine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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14
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Cui Y, Yang K, Tabang DN, Huang J, Tang W, Li L. Finding the Sweet Spot in ERLIC Mobile Phase for Simultaneous Enrichment of N-Glyco and Phosphopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2491-2501. [PMID: 31286442 PMCID: PMC6917886 DOI: 10.1007/s13361-019-02230-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/10/2019] [Accepted: 04/13/2019] [Indexed: 05/30/2023]
Abstract
Simultaneous enrichment of glyco- and phosphopeptides will benefit the studies of biological processes regulated by these posttranslational modifications (PTMs). It will also reveal potential crosstalk between these two ubiquitous PTMs. Unlike custom-designed multifunctional solid phase extraction (SPE) materials, operating strong anion exchange (SAX) resin in electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) mode provides a readily available strategy to analytical labs for enrichment of these PTMs for subsequent mass spectrometry (MS)-based characterization. However, the choice of mobile phase has largely relied on empirical rules from hydrophilic interaction chromatography (HILIC) or ion-exchange chromatography (IEX) without further optimization and adjustments. In this study, ten mobile phase compositions of ERLIC were systematically compared; the impact of multiple factors including organic phase proportion, ion pairing reagent, pH, and salt on the retention of glycosylated and phosphorylated peptides was evaluated. This study demonstrated good enrichment of glyco- and phosphopeptides from the nonmodified peptides in a complex tryptic digest. Moreover, the enriched glyco- and phosphopeptides elute in different fractions by orthogonal retention mechanisms of hydrophilic interaction and electrostatic interaction in ERLIC, maximizing the LC-MS identification of each PTM. The optimized mobile phase can be adapted to the ERLIC HPLC system, where the high resolution in separating multiple PTMs will benefit large-scale MS-based PTM profiling and in-depth characterization.
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Affiliation(s)
- Yusi Cui
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Ka Yang
- School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705, USA
| | | | - Junfeng Huang
- School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705, USA
| | - Weiping Tang
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
- School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705, USA.
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15
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Zamora WJ, Campanera JM, Luque FJ. Development of a Structure-Based, pH-Dependent Lipophilicity Scale of Amino Acids from Continuum Solvation Calculations. J Phys Chem Lett 2019; 10:883-889. [PMID: 30741551 DOI: 10.1021/acs.jpclett.9b00028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lipophilicity is a fundamental property to characterize the structure and function of proteins, motivating the development of lipophilicity scales. We report a versatile strategy to derive a pH-adapted scale that relies on theoretical estimates of distribution coefficients from conformational ensembles of amino acids. This is accomplished by using an accurately parametrized version of the IEFPCM/MST continuum solvation model as an effective way to describe the partitioning between n-octanol and water, in conjunction with a formalism that combines partition coefficients of neutral and ionic species of residues and the corresponding p Ka values of ionizable groups. Two weighting schemes are considered to derive solvent-like and protein-like scales, which have been calibrated by comparison with other experimental scales developed in different chemical/biological environments and pH conditions as well as by examining properties such as the retention time of small peptides and the recognition of antigenic peptides. A straightforward extension to nonstandard residues is enabled by this efficient methodological strategy.
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Affiliation(s)
- William J Zamora
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), Campus Torribera , University of Barcelona , 08921 Santa Coloma de Gramenet , Spain
| | - Josep M Campanera
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), Campus Torribera , University of Barcelona , 08921 Santa Coloma de Gramenet , Spain
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), Campus Torribera , University of Barcelona , 08921 Santa Coloma de Gramenet , Spain
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16
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Fast Amide Bond Cleavage Assisted by a Secondary Amino and a Carboxyl Group-A Model for yet Unknown Peptidases? Molecules 2019; 24:molecules24030572. [PMID: 30764512 PMCID: PMC6384577 DOI: 10.3390/molecules24030572] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
Unconstrained amides that undergo fast hydrolysis under mild conditions are valuable sources of information about how amide bonds may be activated in enzymatic transformations. We report a compound possessing an unconstrained amide bond surrounded by an amino and a carboxyl group, each mounted in close proximity on a bicyclic scaffold. Fast amide hydrolysis of this model compound was found to depend on the presence of both the amino and carboxyl functions, and to involve a proton transfer in the rate-limiting step. Possible mechanisms for the hydrolytic cleavage and their relevance to peptide bond cleavage catalyzed by natural enzymes are discussed. Experimental observations suggest that the most probable mechanisms of the model compound hydrolysis might include a twisted amide intermediate and a rate-determining proton transfer.
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17
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Ma Q, Fite K, New CP, Dabney‐Smith C. Thylakoid-integrated recombinant Hcf106 participates in the chloroplast twin arginine transport system. PLANT DIRECT 2018; 2:e00090. [PMID: 31245690 PMCID: PMC6508782 DOI: 10.1002/pld3.90] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 06/09/2023]
Abstract
The chloroplast twin arginine transport (cpTat) system distinguishes itself as a protein transport pathway by translocating fully folded proteins, using the proton-motive force (PMF) as the sole source of energy. The cpTat pathway is evolutionarily conserved with the Tat pathway found in the plasma membrane of many prokaryotes. The cpTat (Escherichia coli) system uses three proteins, Tha4 (TatA), Hcf106 (TatB), and cpTatC (TatC), to form a transient translocase allowing the passage of precursor proteins. Briefly, cpTatC and Hcf106, with Tha4, form the initial receptor complex responsible for precursor protein recognition and binding in an energy-independent manner, while a separate pool of Tha4 assembles with the precursor-bound receptor complex in the presence the PMF. Analysis by blue-native polyacrylamide gel electrophoresis (BN-PAGE) shows that the receptor complex, in the absence of precursor, migrates near 700 kDa and contains cpTatC and Hcf106 with little Tha4 remaining after detergent solubilization. To investigate the role that Hcf106 may play in receptor complex oligomerization and/or stability, systematic cysteine substitutions were made in positions from the N-terminal transmembrane domain to the end of the predicted amphipathic helix of the protein. BN-PAGE analysis allowed us to identify the locations of amino acids in Hcf106 that were critical for interacting with cpTatC. Oxidative cross-linking allowed us to map interactions of the transmembrane domain and amphipathic helix region of Hcf106. In addition, we showed that in vitro expressed, integrated Hcf106 can interact with the precursor signal peptide domain and imported cpTatC, strongly suggesting that a subpopulation of the integrated Hcf106 is participating in competent cpTat complexes.
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Affiliation(s)
- Qianqian Ma
- Graduate Program in Cell, Molecular, and Structural BiologyMiami UniversityOxfordOhio
- Present address:
Johns Hopkins University School of MedicineBaltimoreMaryland
| | - Kristen Fite
- Department of Chemistry and BiochemistryMiami UniversityOxfordOhio
- Present address:
Boonshoft School of MedicineWright State UniversityDaytonOhio
| | - Christopher Paul New
- Graduate Program in Cell, Molecular, and Structural BiologyMiami UniversityOxfordOhio
| | - Carole Dabney‐Smith
- Graduate Program in Cell, Molecular, and Structural BiologyMiami UniversityOxfordOhio
- Department of Chemistry and BiochemistryMiami UniversityOxfordOhio
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18
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Rogers L, Obasa AE, Jacobs GB, Sarafianos SG, Sönnerborg A, Neogi U, Singh K. Structural Implications of Genotypic Variations in HIV-1 Integrase From Diverse Subtypes. Front Microbiol 2018; 9:1754. [PMID: 30116231 PMCID: PMC6083056 DOI: 10.3389/fmicb.2018.01754] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/13/2018] [Indexed: 01/02/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) integrase (IN) integrates viral DNA into the host genome using its 3′-end processing and strand-transfer activities. Due to the importance of HIV-1 IN, it is targeted by the newest class of approved drugs known as integrase strand transfer inhibitors (INSTIs). INSTIs are efficient in maintaining low viral load; however, as with other approved antivirals, resistance mutations emerge in patients receiving INSTI-containing therapy. As INSTIs are becoming increasingly accessible worldwide, it is important to understand the mechanism(s) of INSTI susceptibility. There is strong evidence suggesting differences in the patterns and mechanisms of drug resistance between HIV-1 subtype B, which dominates in United States, Western Europe and Australia, and non-B infections that are most prevalent in countries of Africa and Asia. IN polymorphisms and other genetic differences among diverse subtypes are likely responsible for these different patterns, but lack of a full-length high-resolution structure of HIV-1 IN has been a roadblock in understanding the molecular mechanisms of INSTI resistance and the impact of polymorphisms on therapy outcome. A recently reported full-length medium-resolution cryoEM structure of HIV-1 IN provides insights into understanding the mechanism of integrase function and the impact of genetic variation on the effectiveness of INSTIs. Here we use molecular modeling to explore the structural impact of IN polymorphisms on the IN reaction mechanism and INSTI susceptibility.
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Affiliation(s)
- Leonard Rogers
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Adetayo E Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Graeme B Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Kamalendra Singh
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
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19
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Vasquez-Montes V, Gerhart J, King KE, Thévenin D, Ladokhin AS. Comparison of lipid-dependent bilayer insertion of pHLIP and its P20G variant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:534-543. [PMID: 29138065 DOI: 10.1016/j.bbamem.2017.11.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/18/2017] [Accepted: 11/10/2017] [Indexed: 02/07/2023]
Abstract
The ability of the pH-Low Insertion Peptide (pHLIP) to insert into lipid membranes in a transbilayer conformation makes it an important tool for targeting acidic diseased tissues. pHLIP can also serve as a model template for thermodynamic studies of membrane insertion. We use intrinsic fluorescence and circular dichroism spectroscopy to examine the effect of replacing pHLIP's central proline on the pH-triggered lipid-dependent conformational switching of the peptide. We find that the P20G variant (pHLIP-P20G) has a higher helical propensity than the native pHLIP (pHLIP-WT), in both water:organic solvent mixtures and in the presence of lipid bilayers. Spectral shifts of tryptophan fluorescence reveal that with both pHLIP-WT and pHLIP-P20G, the deeply penetrating interfacial form (traditionally called State II) is populated only in pure phosphocholine bilayers. The presence of either anionic lipids or phosphatidylethanolamine leads to a much shallower penetration of the peptide (referred to here as State IIS, for "shallow"). This novel state can be differentiated from soluble state by a reduction in accessibility of tryptophans to acrylamide and by FRET to vesicles doped with Dansyl-PE, but not by a spectral shift in fluorescence emission. FRET experiments indicate free energies for interfacial partitioning range from 6.2 to 6.8kcal/mol and are marginally more favorable for pHLIP-P20G. The effective pKa for the insertion of both peptides depends on the lipid composition, but is always higher for pHLIP-P20G than for pHLIP-WT by approximately one pH unit, which corresponds to a difference of 1.3kcal/mol in free energy of protonation favoring insertion of pHLIP-P20G.
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Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, United States
| | - Janessa Gerhart
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Kelly E King
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, United States.
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20
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Peck MT, Ortega G, De Luca-Johnson JN, Schlessman JL, Robinson AC, García-Moreno E B. Local Backbone Flexibility as a Determinant of the Apparent pKa Values of Buried Ionizable Groups in Proteins. Biochemistry 2017; 56:5338-5346. [DOI: 10.1021/acs.biochem.7b00678] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Meredith T. Peck
- Department
of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gabriel Ortega
- Structural
Biology Unit, CIC bioGUNE, Bizkaia Technology Park Ed. 800, 48160 Derio, Spain
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | | | - Jamie L. Schlessman
- Chemistry
Department, U.S. Naval Academy, Annapolis, Maryland 21402, United States
| | - Aaron C. Robinson
- Department
of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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21
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Potassium and sodium ions enhance the activity and thermostability of 1,4-α-glucan branching enzyme from Geobacillus thermoglucosidasius in the presence of glycerol. Int J Biol Macromol 2017; 102:712-717. [DOI: 10.1016/j.ijbiomac.2017.04.061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/14/2017] [Accepted: 04/14/2017] [Indexed: 11/22/2022]
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22
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Ablan FDO, Spaller BL, Abdo KI, Almeida PF. Charge Distribution Fine-Tunes the Translocation of α-Helical Amphipathic Peptides across Membranes. Biophys J 2017; 111:1738-1749. [PMID: 27760360 DOI: 10.1016/j.bpj.2016.08.047] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/09/2016] [Accepted: 08/30/2016] [Indexed: 11/29/2022] Open
Abstract
Hundreds of cationic antimicrobial and cell-penetrating peptides (CPPs) form amphipathic α-helices when bound to lipid membranes. Here, we test two hypotheses for the differences in the ability of these peptides to translocate across membranes. The first, which we now call the hydrophobicity hypothesis, is that peptide translocation is determined by the Gibbs energy of insertion into the bilayer from the membrane interface. The second, which we call the charge-distribution hypothesis, is that translocation is determined by whether the distribution of cationic residues in the peptide can transiently stabilize a high-energy inserted intermediate by forming salt bridges to the phosphates of lipid headgroups. To test these hypotheses, we measured translocation of two series of peptide variants. The first series was based on TP10W, a peptide derived from the amphipathic CPP transportan 10; the second was based on DL1a, a synthetic peptide derived from staphylococcal δ-lysin. The peptides in those two series had small sequence changes relative to TP10W and DL1a: either single-residue substitutions or two-residue switches, which were designed to increase or decrease translocation differently according to the two hypotheses. We found that with regard to the changes introduced in the sequences, five out of six peptide variants translocated in agreement with the charge-distribution hypothesis, whereas none showed agreement with the hydrophobicity hypothesis. We conclude that large effects on translocation are probably determined by hydrophobicity, but the fine tuning appears to arise from the distribution of cationic residues along the peptide sequence.
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Affiliation(s)
- Francis D O Ablan
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina
| | - B Logan Spaller
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina
| | - Kaitlyn I Abdo
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina
| | - Paulo F Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina.
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23
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Xie NZ, Du QS, Li JX, Huang RB. Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design. PLoS One 2015; 10:e0137113. [PMID: 26339784 PMCID: PMC4560430 DOI: 10.1371/journal.pone.0137113] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/12/2015] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. METHODS Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. RESULTS The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. CONCLUSION (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.
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Affiliation(s)
- Neng-Zhong Xie
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
| | - Qi-Shi Du
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA, 02478, United States of America
| | - Jian-Xiu Li
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
| | - Ri-Bo Huang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
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24
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Wu H, Zeng H, Lam R, Tempel W, Kerr ID, Min J. Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome. Acta Crystallogr F Struct Biol Commun 2015; 71:981-5. [PMID: 26249686 PMCID: PMC4528928 DOI: 10.1107/s2053230x15010183] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/26/2015] [Indexed: 02/25/2023] Open
Abstract
Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson-Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. The structure shares a high degree of similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more accurate platform for the classification of MLH1 variants.
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Affiliation(s)
- Hong Wu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Robert Lam
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Iain D. Kerr
- Myriad Genetic Laboratories Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5G 1L7, Canada
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25
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Listowski MA, Leluk J, Kraszewski S, Sikorski AF. Cholesterol Interaction with the MAGUK Protein Family Member, MPP1, via CRAC and CRAC-Like Motifs: An In Silico Docking Analysis. PLoS One 2015; 10:e0133141. [PMID: 26186446 PMCID: PMC4505867 DOI: 10.1371/journal.pone.0133141] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 06/24/2015] [Indexed: 12/22/2022] Open
Abstract
Cholesterol is essential for the proper organization of the biological membrane. Therefore, predicting which proteins can bind cholesterol is important in understanding how proteins participate in lateral membrane organization. In this study, a simple bioinformatics approach was used to establish whether MPP1, a member of the MAGUK protein family, is capable of binding cholesterol. Modelled and experimentally-validated fragment structures were mined from online resources and searched for CRAC and CRAC-like motifs. Several of these motifs were found in the primary structure of MPP1, and these were structurally visualized to see whether they localized to the protein surface. Since all of the CRAC and CRAC-like motifs were found at the surface of MPP1 domains, in silico docking experiments were performed to assess the possibility of interaction between CRAC motifs and cholesterol. The results obtained show that MPP1 can bind cholesterol via CRAC and CRAC-like motifs with moderate to high affinity (KI in the nano- to micro-molar range). It was also found that palmitoylation-mimicking mutations (C/F or C/M) did not affect the affinity of MPP1 towards cholesterol. Data presented here may help to understand at least one of the molecular mechanisms via which MPP1 affects lateral organization of the membrane.
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Affiliation(s)
- Marcin A. Listowski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Jacek Leluk
- Department of Molecular Biology, University of Zielona Góra, Zielona Góra, Poland
| | - Sebastian Kraszewski
- Department of Biomedical Engineering, Wrocław University of Technology, Wrocław, Poland
| | - Aleksander F. Sikorski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
- Department of Molecular Biology, University of Zielona Góra, Zielona Góra, Poland
- * E-mail:
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26
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Vener MV, Odinokov AV, Wehmeyer C, Sebastiani D. The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations. J Chem Phys 2015; 142:215106. [DOI: 10.1063/1.4922165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. V. Vener
- Mendeleev University of Chemical Technology, Moscow, Russia
| | - A. V. Odinokov
- Photochemistry Center of the Russian Academy of Sciences, Moscow, Russia
| | | | - D. Sebastiani
- Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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27
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Sun D, Forsman J, Woodward CE. Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol. J Chem Theory Comput 2015; 11:1775-91. [PMID: 26574387 DOI: 10.1021/ct501063a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol.
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Affiliation(s)
- Delin Sun
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra ACT 2600, Australia
| | - Jan Forsman
- Theoretical Chemistry, Chemical Centre, Lund University , P.O. Box 124, S-221 00 Lund, Sweden
| | - Clifford E Woodward
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra ACT 2600, Australia
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28
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Toward understanding driving forces in membrane protein folding. Arch Biochem Biophys 2014; 564:297-313. [DOI: 10.1016/j.abb.2014.07.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022]
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29
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Cherry MA, Higgins SK, Melroy H, Lee HS, Pokorny A. Peptides with the same composition, hydrophobicity, and hydrophobic moment bind to phospholipid bilayers with different affinities. J Phys Chem B 2014; 118:12462-70. [PMID: 25329983 PMCID: PMC4234449 DOI: 10.1021/jp507289w] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We investigated the dependence of membrane binding on amino acid
sequence for a series of amphipathic peptides derived from δ-lysin.
δ-Lysin is a 26 amino acid, N-terminally formylated, hemolytic
peptide that forms an amphipathic α-helix bound at membrane–water
interfaces. A shortened peptide, lysette, was derived from δ-lysin
by deletion of the four N-terminal amino acid residues. Five variants
of lysette were synthesized by altering the amino acid sequence such
that the overall hydrophobic moment remained essentially the same
for all peptides. Peptide–lipid equilibrium dissociation constants
and helicities of peptides bound to zwitterionic lipid vesicles were
determined by stopped-flow fluorescence and circular dichroism. We
found that binding to phosphatidylcholine bilayers was a function
of the helicity of the bound peptide alone and independent of the a priori hydrophobic moment or the ability to form intramolecular
salt bridges. Molecular dynamics (MD) simulations on two of the peptides
suggest that sequence determines the insertion depth into the bilayer.
The location of the two aspartate residues at the C-terminus of lysette-2
leads to a loss of helical content in the simulations, which correlates
with faster desorption from the bilayer as compared to lysette. We
also found a systematic deviation of the experimentally determined
dissociation constant and that predicted by the Wimley–White
interfacial hydrophobicity scale. The reason for the discrepancy remains
unresolved but appears to correlate with a predominance of isoleucine
over leucine residues in the lysette family of peptides.
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Affiliation(s)
- Melissa A Cherry
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington , Wilmington, North Carolina 28403, United States
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30
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Cymer F, von Heijne G, White SH. Mechanisms of integral membrane protein insertion and folding. J Mol Biol 2014; 427:999-1022. [PMID: 25277655 DOI: 10.1016/j.jmb.2014.09.014] [Citation(s) in RCA: 262] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/13/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022]
Abstract
The biogenesis, folding, and structure of α-helical membrane proteins (MPs) are important to understand because they underlie virtually all physiological processes in cells including key metabolic pathways, such as the respiratory chain and the photosystems, as well as the transport of solutes and signals across membranes. Nearly all MPs require translocons--often referred to as protein-conducting channels--for proper insertion into their target membrane. Remarkable progress toward understanding the structure and functioning of translocons has been made during the past decade. Here, we review and assess this progress critically. All available evidence indicates that MPs are equilibrium structures that achieve their final structural states by folding along thermodynamically controlled pathways. The main challenge for cells is the targeting and membrane insertion of highly hydrophobic amino acid sequences. Targeting and insertion are managed in cells principally by interactions between ribosomes and membrane-embedded translocons. Our review examines the biophysical and biological boundaries of MP insertion and the folding of polytopic MPs in vivo. A theme of the review is the under-appreciated role of basic thermodynamic principles in MP folding and assembly. Thermodynamics not only dictates the final folded structure but also is the driving force for the evolution of the ribosome-translocon system of assembly. We conclude the review with a perspective suggesting a new view of translocon-guided MP insertion.
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Affiliation(s)
- Florian Cymer
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm.,Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden
| | - Stephen H White
- Department of Physiology and Biophysics and the Center for Biomembrane Systems University of California, Irvine Irvine, CA 92697
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31
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Walther TH, Ulrich AS. Transmembrane helix assembly and the role of salt bridges. Curr Opin Struct Biol 2014; 27:63-8. [DOI: 10.1016/j.sbi.2014.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 10/25/2022]
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32
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Walther FJ, Waring AJ, Hernández-Juviel JM, Ruchala P, Wang Z, Notter RH, Gordon LM. Surfactant protein C peptides with salt-bridges ("ion-locks") promote high surfactant activities by mimicking the α-helix and membrane topography of the native protein. PeerJ 2014; 2:e485. [PMID: 25083348 PMCID: PMC4106191 DOI: 10.7717/peerj.485] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/23/2014] [Indexed: 11/20/2022] Open
Abstract
Background. Surfactant protein C (SP-C; 35 residues) in lungs has a cationic N-terminal domain with two cysteines covalently linked to palmitoyls and a C-terminal region enriched in Val, Leu and Ile. Native SP-C shows high surface activity, due to SP-C inserting in the bilayer with its cationic N-terminus binding to the polar headgroup and its hydrophobic C-terminus embedded as a tilted, transmembrane α-helix. The palmitoylcysteines in SP-C act as ‘helical adjuvants’ to maintain activity by overriding the β-sheet propensities of the native sequences. Objective. We studied SP-C peptides lacking palmitoyls, but containing glutamate and lysine at 4-residue intervals, to assess whether SP-C peptides with salt-bridges (“ion-locks”) promote surface activity by mimicking the α-helix and membrane topography of native SP-C. Methods. SP-C mimics were synthesized that reproduce native sequences, but without palmitoyls (i.e., SP-Css or SP-Cff, with serines or phenylalanines replacing the two cysteines). Ion-lock SP-C molecules were prepared by incorporating single or double Glu−–Lys+ into the parent SP-C’s. The secondary structures of SP-C mimics were studied with Fourier transform infrared (FTIR) spectroscopy and PASTA, an algorithm that predicts β-sheet propensities based on the energies of the various β-sheet pairings. The membrane topography of SP-C mimics was investigated with orientated and hydrogen/deuterium (H/D) exchange FTIR, and also Membrane Protein Explorer (MPEx) hydropathy analysis. In vitro surface activity was determined using adsorption surface pressure isotherms and captive bubble surfactometry, and in vivo surface activity from lung function measures in a rabbit model of surfactant deficiency. Results. PASTA calculations predicted that the SP-Css and SP-Cff peptides should each form parallel β-sheet aggregates, with FTIR spectroscopy confirming high parallel β-sheet with ‘amyloid-like’ properties. The enhanced β-sheet properties for SP-Css and SP-Cff are likely responsible for their low surfactant activities in the in vitro and in vivo assays. Although standard 12C-FTIR study showed that the α-helicity of these SP-C sequences in lipids was uniformly increased with Glu−–Lys+ insertions, elevated surfactant activity was only selectively observed. Additional results from oriented and H/D exchange FTIR experiments indicated that the high surfactant activities depend on the SP-C ion-locks recapitulating both the α-helicity and the membrane topography of native SP-C. SP-Css ion-lock 1, an SP-Css with a salt-bridge for a Glu−–Lys+ ion-pair predicted from MPEx hydropathy calculations, demonstrated enhanced surfactant activity and a transmembrane helix simulating those of native SP-C. Conclusion. Highly active SP-C mimics were developed that replace the palmitoyls of SP-C with intrapeptide salt-bridges and represent a new class of synthetic surfactants with therapeutic interest.
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Affiliation(s)
- Frans J Walther
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , United States of America ; Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles , Los Angeles, CA , United States of America
| | - Alan J Waring
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , United States of America ; Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles , Los Angeles, CA , United States of America ; Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles , Los Angeles, CA , United States of America ; Department of Physiology & Biophysics, School of Medicine, University of California , Irvine, CA , United States of America
| | - José M Hernández-Juviel
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , United States of America
| | - Piotr Ruchala
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles , Los Angeles, CA , United States of America
| | - Zhengdong Wang
- Department of Pediatrics, University of Rochester , Rochester, NY , United States of America
| | - Robert H Notter
- Department of Pediatrics, University of Rochester , Rochester, NY , United States of America
| | - Larry M Gordon
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, CA , United States of America
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Almeida PF. Membrane-active peptides: binding, translocation, and flux in lipid vesicles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2216-27. [PMID: 24769436 DOI: 10.1016/j.bbamem.2014.04.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/14/2014] [Accepted: 04/17/2014] [Indexed: 01/21/2023]
Abstract
Recently, new and improved methods have been developed to measure translocation of membrane-active peptides (antimicrobial, cytolytic, and amphipathic cell-penetrating peptides) across lipid bilayer membranes. The hypothesis that translocation of membrane-active peptides across a lipid bilayer is determined by the Gibbs energy of insertion of the peptide into the bilayer is re-examined in the light of new experimental tests. The original hypothesis and its motivation are first revisited, examining some of the specific predictions that it generated, followed by the results of the initial tests. Translocation is understood as requiring two previous steps: binding and insertion in the membrane. The problem of peptide binding to membranes, its prediction, measurement, and calculation are addressed. Particular attention is given to understanding the reason for the need for amphipathic structures in the function of membrane-active peptides. Insertion into the membrane is then examined. Hydrophobicity scales are compared, and their influence on calculations is discussed. The relation between translocation and graded or all-or-none peptide-induced flux from or into lipid vesicles is also considered. Finally, the most recent work on translocation is examined, both experimental and from molecular dynamics simulations. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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Affiliation(s)
- Paulo F Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA.
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Mechanism of μ-conotoxin PIIIA binding to the voltage-gated Na+ channel NaV1.4. PLoS One 2014; 9:e93267. [PMID: 24676211 PMCID: PMC3968119 DOI: 10.1371/journal.pone.0093267] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/03/2014] [Indexed: 12/19/2022] Open
Abstract
Several subtypes of voltage-gated Na+ (NaV) channels are important targets for pain management. μ-Conotoxins isolated from venoms of cone snails are potent and specific blockers of different NaV channel isoforms. The inhibitory effect of μ-conotoxins on NaV channels has been examined extensively, but the mechanism of toxin specificity has not been understood in detail. Here the known structure of μ-conotoxin PIIIA and a model of the skeletal muscle channel NaV1.4 are used to elucidate elements that contribute to the structural basis of μ-conotoxin binding and specificity. The model of NaV1.4 is constructed based on the crystal structure of the bacterial NaV channel, NaVAb. Six different binding modes, in which the side chain of each of the basic residues carried by the toxin protrudes into the selectivity filter of NaV1.4, are examined in atomic detail using molecular dynamics simulations with explicit solvent. The dissociation constants (Kd) computed for two selected binding modes in which Lys9 or Arg14 from the toxin protrudes into the filter of the channel are within 2 fold; both values in close proximity to those determined from dose response data for the block of NaV currents. To explore the mechanism of PIIIA specificity, a double mutant of NaV1.4 mimicking NaV channels resistant to μ-conotoxins and tetrodotoxin is constructed and the binding of PIIIA to this mutant channel examined. The double mutation causes the affinity of PIIIA to reduce by two orders of magnitude.
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35
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A membrane-translocating peptide penetrates into bilayers without significant bilayer perturbations. Biophys J 2014; 104:2419-28. [PMID: 23746514 DOI: 10.1016/j.bpj.2013.04.043] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 04/17/2013] [Accepted: 04/22/2013] [Indexed: 11/21/2022] Open
Abstract
Using a high throughput screen, we have identified a family of 12-residue long peptides that spontaneously translocate across membranes. These peptides function by a poorly understood mechanism that is very different from that of the well-known, highly cationic cell penetrating peptides such as the tat peptide from HIV. The newly discovered translocating peptides can carry polar cargoes across synthetic bilayers and across cellular membranes quickly and spontaneously without disrupting the membrane. Here we report on the biophysical characterization of a representative translocating peptide from the selected family, TP2, as well as a negative control peptide, ONEG, from the same library. We measured the binding of the two peptides to lipid bilayers, their secondary structure propensities, their dispositions in bilayers by neutron diffraction, and the response of the bilayer to the peptides. Compared to the negative control, TP2 has a greater propensity for membrane partitioning, although it still binds only weakly, and a higher propensity for secondary structure. Perhaps most revealing, TP2 has the ability to penetrate deep into the bilayer without causing significant bilayer perturbations, a property that may help explain its ability to translocate without bilayer permeabilization.
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36
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Blumenthal S, Tang Y, Yang W, Chen BY. Isolating influential regions of electrostatic focusing in protein and DNA structure. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:1188-1198. [PMID: 24384707 DOI: 10.1109/tcbb.2013.124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Electrostatic focusing is a general phenomenon that occurs in cavities and grooves on the molecular surface of biomolecules. Narrow surface features can partially shield charged atoms from the high-dielectric solvent, enhancing electrostatic potentials inside the cavity and projecting electric field lines outward into the solvent. This effect has been observed in many instances and is widely considered in the human examination of molecular structure, but it is rarely integrated into the digital representations used in protein structure comparison software. To create a computational representation of electrostatic focusing, that is compatible with structure comparison algorithms, this paper presents an approach that generates three-dimensional solids that approximate regions where focusing occurs. We verify the accuracy of this representation against instances of focusing in proteins and DNA. Noting that this representation also identifies thin focusing regions on the molecular surface that are unlikely to affect binding, we describe a second algorithm that conservatively isolates larger focusing regions. The resulting 3D solids can be compared with Boolean set operations, permitting a new range of analyses on the regions where electrostatic focusing occurs. They also represent a novel integration of molecular shape and electrostatic focusing into the same structure comparison framework.
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37
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Chen R, Chung SH. Complex structures between the N-type calcium channel (CaV2.2) and ω-conotoxin GVIA predicted via molecular dynamics. Biochemistry 2013; 52:3765-72. [PMID: 23651160 DOI: 10.1021/bi4003327] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The N-type voltage-gated Ca(2+) channel CaV2.2 is one of the important targets for pain management. ω-Conotoxins isolated from venoms of cone snails, which specifically inhibit CaV2.2, are promising scaffolds for novel analgesics. The inhibitory action of ω-conotoxins on CaV2.2 has been examined experimentally, but the modes of binding of the toxins to this and other related subfamilies of Ca(2+) channels are not understood in detail. Here molecular dynamics simulations are used to construct models of ω-conotoxin GVIA in complex with a homology model of the pore domain of CaV2.2. Three different binding modes in which the side chain of Lys2, Arg17, or Lys24 from the toxin protrudes into the selectivity filter of CaV2.2 are considered. In all the modes, the toxin forms a salt bridge with an aspartate residue of subunit II just above the EEEE ring of the selectivity filter. Using the umbrella sampling technique and potential of mean force calculations, the half-maximal inhibitory concentration (IC50) values are calculated to be 1.5 and 0.7 nM for the modes in which Lys2 and Arg17 occlude the ion conduction pathway, respectively. Both IC50 values compare favorably with the values of 0.04-1.0 nM determined experimentally. The similar IC50 values calculated for the different binding modes demonstrate that GVIA can inhibit CaV2.2 with alternative binding modes. Such a multiple-binding mode mechanism may be common for ω-conotoxins.
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Affiliation(s)
- Rong Chen
- Research School of Biology, Australian National University , Canberra, ACT 0200, Australia
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38
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Pluhařová E, Marsalek O, Schmidt B, Jungwirth P. Peptide salt bridge stability: from gas phase via microhydration to bulk water simulations. J Chem Phys 2013; 137:185101. [PMID: 23163393 DOI: 10.1063/1.4765052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The salt bridge formation and stability in the terminated lysine-glutamate dipeptide is investigated in water clusters of increasing size up to the limit of bulk water. Proton transfer dynamics between the acidic and basic side chains is described by DFT-based Born-Oppenheimer molecular dynamics simulations. While the desolvated peptide prefers to be in its neutral state, already the addition of a single water molecule can trigger proton transfer from the glutamate side chain to the lysine side chain, leading to a zwitterionic salt bridge state. Upon adding more water molecules we find that stabilization of the zwitterionic state critically depends on the number of hydrogen bonds between side chain termini, the water molecules, and the peptidic backbone. Employing classical molecular dynamics simulations for larger clusters, we observed that the salt bridge is weakened upon additional hydration. Consequently, long-lived solvent shared ion pairs are observed for about 30 water molecules while solvent separated ion pairs are found when at least 40 or more water molecules hydrate the dipeptide. These results have implications for the formation and stability of salt bridges at partially dehydrated surfaces of aqueous proteins.
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Affiliation(s)
- Eva Pluhařová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, Prague 6, CZ-16610, Czech Republic.
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39
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Nordholm J, da Silva DV, Damjanovic J, Dou D, Daniels R. Polar residues and their positional context dictate the transmembrane domain interactions of influenza A neuraminidases. J Biol Chem 2013; 288:10652-60. [PMID: 23447533 DOI: 10.1074/jbc.m112.440230] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Interactions that facilitate transmembrane domain (TMD) dimerization have been identified mainly using synthetic TMDs. Here, we investigated how inherent properties within natural TMDs modulate their interaction strength by exploiting the sequence variation in the nine neuraminidase subtypes (N1-N9) and the prior knowledge that a N1 TMD oligomerizes. Initially, consensus TMDs were created from the influenza A virus database, and their interaction strengths were measured in a biological membrane system. The TMD interactions increased with respect to decreasing hydrophobicity across the subtypes (N1-N9) and within the human N1 subtype where the N1 TMDs from the pandemic H1N1 strain of swine origin were found to be significantly less hydrophobic. The hydrophobicity correlation was attributed to the conserved amphipathicity within the TMDs as the interactions were abolished by mutating residues on the polar faces that are unfavorably positioned in the membrane. Similarly, local changes enhanced the interactions only when a larger polar residue existed on the appropriate face in an unfavorable membrane position. Together, the analysis of this unique natural TMD data set demonstrates how polar-mediated TMD interactions from bitopic proteins depend on which polar residues are involved and their positioning with respect to the helix and the membrane bilayer.
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Affiliation(s)
- Johan Nordholm
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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40
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Hotiana HA, Haider MK. Structural modeling of HCV NS3/4A serine protease drug-resistance mutations using end-point continuum solvation and side-chain flexibility calculations. J Chem Inf Model 2013; 53:435-51. [PMID: 23305404 DOI: 10.1021/ci3004754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational methods of modeling protein-ligand interactions have gained widespread application in modern drug discovery. In continuum solvation-based methods of binding affinity estimation, limited description of solvent environment and protein flexibility is traded for a time scale that fits medicinal chemistry test cycles. The results of this speed-accuracy trade-off have been promising in terms of modeling structure-activity relationships of ligand series against protein targets. The potential of these approaches in recapitulating structural and energetic effects of resistance mutations, which involve large changes in binding affinity, remains relatively unexplored. We used continuum solvation binding affinity predictions and graph theory-based flexibility calculations to model thirteen drug resistance mutations in HCV NS3/4A serine protease, against three small-molecule inhibitors, with a 2-fold objective: quantitative assessment of binding energy predictions against experimental data and elucidation of structural/energetic determinants of resistance. The results show statistically significant correlation between predicted and experimental binding affinities, with R(2) and predictive index of up to 0.83 and 0.91, respectively. The level of accuracy was consistent with what has been reported for the inverse problem of binding affinity estimation of congeneric ligands against the same target. The quality of predictions was poor for mutations involving induced-fit effects, primarily, because of the lack of entropy terms. Flexibility analysis explained this discrepancy by indicating characteristic changes in side-chain mobility of a key binding site residue. The combined results from two approaches provide novel insights regarding the molecular mechanism of resistance. NS3/4A inhibitors, with large P2 substituents, derive high affinity with optimal van der Waals interactions in the S2 subsite, in order to overcome unfavorable desolvation and entropic cost of induced-fit effects. High-level resistance mutations tend to increase the desolvation and/or entropic barrier to ligand binding. The lead optimization strategies should, therefore, address the balance of these opposing energetic contributions in both the wild-type and mutant target.
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Affiliation(s)
- Hajira Ahmed Hotiana
- Undergraduate Program in Science, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
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41
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Valley CC, Cembran A, Perlmutter JD, Lewis AK, Labello NP, Gao J, Sachs JN. The methionine-aromatic motif plays a unique role in stabilizing protein structure. J Biol Chem 2012; 287:34979-34991. [PMID: 22859300 DOI: 10.1074/jbc.m112.374504] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Of the 20 amino acids, the precise function of methionine (Met) remains among the least well understood. To establish a determining characteristic of methionine that fundamentally differentiates it from purely hydrophobic residues, we have used in vitro cellular experiments, molecular simulations, quantum calculations, and a bioinformatics screen of the Protein Data Bank. We show that approximately one-third of all known protein structures contain an energetically stabilizing Met-aromatic motif and, remarkably, that greater than 10,000 structures contain this motif more than 10 times. Critically, we show that as compared with a purely hydrophobic interaction, the Met-aromatic motif yields an additional stabilization of 1-1.5 kcal/mol. To highlight its importance and to dissect the energetic underpinnings of this motif, we have studied two clinically relevant TNF ligand-receptor complexes, namely TRAIL-DR5 and LTα-TNFR1. In both cases, we show that the motif is necessary for high affinity ligand binding as well as function. Additionally, we highlight previously overlooked instances of the motif in several disease-related Met mutations. Our results strongly suggest that the Met-aromatic motif should be exploited in the rational design of therapeutics targeting a range of proteins.
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Affiliation(s)
- Christopher C Valley
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Alessandro Cembran
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jason D Perlmutter
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Andrew K Lewis
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Nicholas P Labello
- Department of Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455.
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42
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Abstract
Of great interest to the academic and pharmaceutical research communities, helical transmembrane proteins are characterized by their ability to dissolve and fold in lipid bilayers—properties conferred by polypeptide spans termed transmembrane domains (TMDs). The apolar nature of TMDs necessitates the use of membrane-mimetic solvents for many structure and folding studies. This review examines the relationship between TMD structure and solvent environment, focusing on principles elucidated largely in membrane-mimetic environments with single-TMD protein and peptide models. Following a brief description of TMD sequence and conformational characteristics gleaned from the structural database, we present an overview of the conceptual models used to study folding in vitro. The impact of sequence and solvent context on the incorporation of TMDs into membranes, and its role in measurements of TMD self-assembly strengths, is then described. We conclude with a discussion of the nonspecific effects of membrane components on TMD stability.
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Affiliation(s)
- Arianna Rath
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 1X8 Canada
| | - Charles M. Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, M5G 1X8 Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
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43
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Li E, Wimley WC, Hristova K. Transmembrane helix dimerization: beyond the search for sequence motifs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:183-93. [PMID: 21910966 DOI: 10.1016/j.bbamem.2011.08.031] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/25/2011] [Accepted: 08/26/2011] [Indexed: 01/07/2023]
Abstract
Studies of the dimerization of transmembrane (TM) helices have been ongoing for many years now, and have provided clues to the fundamental principles behind membrane protein (MP) folding. Our understanding of TM helix dimerization has been dominated by the idea that sequence motifs, simple recognizable amino acid sequences that drive lateral interaction, can be used to explain and predict the lateral interactions between TM helices in membrane proteins. But as more and more unique interacting helices are characterized, it is becoming clear that the sequence motif paradigm is incomplete. Experimental evidence suggests that the search for sequence motifs, as mediators of TM helix dimerization, cannot solve the membrane protein folding problem alone. Here we review the current understanding in the field, as it has evolved from the paradigm of sequence motifs into a view in which the interactions between TM helices are much more complex. This article is part of a Special Issue entitled: Membrane protein structure and function.
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Affiliation(s)
- Edwin Li
- Department of Biology, Saint Joseph's University, Philadelphia, PA 19131, USA
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44
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Clark KS, Svetlovics J, McKeown AN, Huskins L, Almeida PF. What determines the activity of antimicrobial and cytolytic peptides in model membranes. Biochemistry 2011; 50:7919-32. [PMID: 21870782 DOI: 10.1021/bi200873u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We previously proposed three hypotheses relating the mechanism of antimicrobial and cytolytic peptides in model membranes to the Gibbs free energies of binding and insertion into the membrane [Almeida, P. F., and Pokorny, A. (2009) Biochemistry 48, 8083-8093]. Two sets of peptides were designed to test those hypotheses, by mutating of the sequences of δ-lysin, cecropin A, and magainin 2. Peptide binding and activity were measured on phosphatidylcholine membranes. In the first set, the peptide charge was changed by mutating basic to acidic residues or vice versa, but the amino acid sequence was not altered much otherwise. The type of dye release changed from graded to all-or-none according to prediction. However, location of charged residues in the sequence with the correct spacing to form salt bridges failed to improve binding. In the second set, the charged and other key residues were kept in the same positions, whereas most of the sequence was significantly but conservatively simplified, maintaining the same hydrophobicity and amphipathicity. This set behaved completely different from predicted. The type of release, which was expected to be maintained, changed dramatically from all-or-none to graded in the mutants of cecropin and magainin. Finally, contrary to the hypotheses, the results indicate that the Gibbs energy of binding to the membrane, not the Gibbs energy of insertion, is the primary determinant of peptide activity.
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Affiliation(s)
- Kim S Clark
- Department of Chemistry and Biochemistry, University of North Carolina, Wilmington, North Carolina 28403, USA
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45
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Chung KM, Huang CH, Cheng JH, Tsai CH, Suen CS, Hwang MJ, Chen X. Proline in transmembrane domain of type II protein DPP-IV governs its translocation behavior through endoplasmic reticulum. Biochemistry 2011; 50:7909-18. [PMID: 21834515 DOI: 10.1021/bi200605h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A transmembrane domain (TMD) at the N-terminus of a membrane protein is a signal sequence that targets the protein to the endoplasmic reticulum (ER) membrane. Proline is found more frequently in TM helices compared to water-soluble helices. To investigate the effects of proline on protein translocation and integration in mammalian cells, we made proline substitutions throughout the TMD of dipeptidyl peptidase IV, a type II membrane protease with a single TMD at its N-terminus. The proteins were expressed and their capacities for targeting and integrating into the membrane were measured in both mammalian cells and in vitro translation systems. Three proline substitutions in the central region of the TMD resulted in various defects in membrane targeting and/or integration. The replacement of proline with other amino acids of similar hydrophobicity rescued both the translocation and anchoring defects of all three proline mutants, indicating that conformational change caused by proline is a determining factor. Increasing hydrophobicity of the TMD by replacing other residues with more hydrophobic residues also effectively reversed the translocation and integration defects. Intriguingly, increasing hydrophobicity at the C-terminal end of the TMD rescued much more effectively than it did at the N-terminal end. Thus, the effect of proline on translocation and integration of the TMD is not determined solely by its conformation and hydrophobicity, but also by the location of proline in the TMD, the location of highly hydrophobic residues, and the relative position of the proline to other proline residues in the TMD.
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Affiliation(s)
- Kuei-Min Chung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 350, Taiwan, ROC
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Rovó P, Farkas V, Hegyi O, Szolomájer-Csikós O, Tóth GK, Perczel A. Cooperativity network of Trp-cage miniproteins: probing salt-bridges. J Pept Sci 2011; 17:610-9. [DOI: 10.1002/psc.1377] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/18/2011] [Accepted: 03/24/2011] [Indexed: 11/06/2022]
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Packer LE, Song B, Raleigh DP, McKnight CJ. Competition between intradomain and interdomain interactions: a buried salt bridge is essential for villin headpiece folding and actin binding. Biochemistry 2011; 50:3706-12. [PMID: 21449557 PMCID: PMC3086997 DOI: 10.1021/bi1020343] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Villin-type headpiece domains are ∼70 residue motifs that reside at the C-terminus of a variety of actin-associated proteins. Villin headpiece (HP67) is a commonly used model system for both experimental and computational studies of protein folding. HP67 is made up of two subdomains that form a tightly packed interface. The isolated C-terminal subdomain of HP67 (HP35) is one of the smallest autonomously folding proteins known. The N-terminal subdomain requires the presence of the C-terminal subdomain to fold. In the structure of HP67, a conserved salt bridge connects N- and C-terminal subdomains. This buried salt bridge between residues E39 and K70 is unusual in a small protein domain. We used mutational analysis, monitored by CD and NMR, and functional assays to determine the role of this buried salt bridge. First, the two residues in the salt bridge were replaced with strictly hydrophobic amino acids, E39M/K70M. Second, the two residues in the salt bridge were swapped, E39K/K70E. Any change from the wild-type salt bridge residues results in unfolding of the N-terminal subdomain, even when the mutations were made in a stabilized variant of HP67. The C-terminal subdomain remains folded in all mutants and is stabilized by some of the mutations. Using actin sedimentation assays, we find that a folded N-terminal domain is essential for specific actin binding. Therefore, the buried salt bridge is required for the specific folding of the N-terminal domain which confers actin-binding activity to villin-type headpiece domains, even though the residues required for this specific interaction destabilize the C-terminal subdomain.
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Affiliation(s)
- Laura E Packer
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118, USA
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McKeown AN, Naro JL, Huskins LJ, Almeida PF. A thermodynamic approach to the mechanism of cell-penetrating peptides in model membranes. Biochemistry 2011; 50:654-62. [PMID: 21166473 PMCID: PMC3035854 DOI: 10.1021/bi1013358] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a first test of the hypothesis that the mechanism of antimicrobial, cytolytic, and amphipathic cell-penetrating peptides in model membranes is determined by the thermodynamics of insertion of the peptide into the lipid bilayer from the surface-associated state. Three peptides were designed with minimal mutations relative to the sequence of TP10W, the Y3W variant of transportan 10, which is a helical, amphipathic cell-penetrating peptide previously studied. Binding to 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) membranes and release of dye from those vesicles were assessed by stopped-flow fluorescence, and the secondary structure of the peptides on the membrane was determined by circular dichroism. The Gibbs energy of binding determined experimentally was in excellent agreement with that calculated using the Wimley-White interfacial hydrophobicity scale, taking into account the helical content of the membrane-associated peptide. Release of dye from POPC vesicles remained graded, as predicted by the hypothesis. More significantly, as the Gibbs energy of insertion into the bilayer became more unfavorable, which was estimated using the Wimley-White octanol hydrophobicity scale, dye release became slower, in quantitative agreement with the prediction.
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Affiliation(s)
- Alesia N. McKeown
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403
| | - Jeffrey L. Naro
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403
| | - Laura J. Huskins
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403
| | - Paulo F. Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403
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Huerta-Viga A, Shaw DJ, Woutersen S. pH Dependence of the Conformation of Small Peptides Investigated with Two-Dimensional Vibrational Spectroscopy. J Phys Chem B 2010; 114:15212-20. [DOI: 10.1021/jp105133r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Adriana Huerta-Viga
- Van’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Daniel J. Shaw
- Van’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Sander Woutersen
- Van’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
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Tandang-Silvas MRG, Fukuda T, Fukuda C, Prak K, Cabanos C, Kimura A, Itoh T, Mikami B, Utsumi S, Maruyama N. Conservation and divergence on plant seed 11S globulins based on crystal structures. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:1432-42. [PMID: 20215054 DOI: 10.1016/j.bbapap.2010.02.016] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 02/23/2010] [Accepted: 02/24/2010] [Indexed: 11/30/2022]
Abstract
The crystal structures of two pro-11S globulins namely: rapeseed procruciferin and pea prolegumin are presented here. We have extensively compared them with the other known structures of plant seed 11S and 7S globulins. In general, the disordered regions in the crystal structures among the 11S globulins correspond to their five variable regions. Variable region III of procruciferin is relatively short and is in a loop conformation. This region is highly disordered in other pro-11S globulin crystals. Local helical and strand variations also occur across the group despite general structure conservation. We showed how these variations may alter specific physicochemical, functional and physiological properties. Aliphatic hydrophobic residues on the molecular surface correlate well with Tm values of the globulins. We also considered other structural features that were reported to influence thermal stability but no definite conclusion was drawn since each factor has additive or subtractive effect. Comparison between proA3B4 and mature A3B4 revealed an increase in r.m.s.d. values near variable regions II and IV. Both regions are on the IE face. Secondary structure based alignment of 11S and 7S globulins revealed 16 identical residues. Based on proA3B4 sequence, Pro60, Gly128, Phe163, Phe208, Leu213, Leu227, Ile237, Pro382, Val404, Pro425 and Val 466 are involved in trimer formation and stabilization. Gly28, Gly74, Asp135, Gly349 and Gly397 are involved in correct globular folding.
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Affiliation(s)
- Mary Rose G Tandang-Silvas
- Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Kyoto 611-0011, Japan
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