1
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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2
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Mohanty L, Mishra C, Pradhan SK, Mishra SR, Nayak G. Identification of novel polymorphism and in silico analysis of caprine DNAJB3 gene. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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3
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Houndonougbo Y, Pugh B, VanWormer K, April C, Burgis N. Structural dynamics of inosine triphosphate pyrophosphatase (ITPA) protein and two clinically relevant mutants: molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:1236-1247. [PMID: 32129147 DOI: 10.1080/07391102.2020.1727363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The inosine triphosphate pyrophosphatase (ITPA) protein is responsible for removing noncanonical purine nucleoside triphosphates from intracellular nucleotide pools. Absence of ITPA results in genomic instability and increased levels of inosine in DNA and RNA. The proline to threonine substitution at position 32 (P32T) affects roughly 15% of the global population and can modulate treatment outcomes for cancer, lupus, and hepatitis C patients. The substitution of arginine with cysteine at position 178 (R178C) is extremely uncommon and has only been reported in a small cohort of early infantile encephalopathy patients suggesting that a functional ITPA protein is required for life in humans. Here we present molecular dynamic simulations that describe the structure and dynamics of the wild-type ITPA homodimer and two of its clinically relevant mutants, P32T and R178C. The simulation results indicate that both the P32T and R178C mutations alter the structure and dynamic properties of the protein and provide a possible explanation of the experimentally observed effect of the mutations on ITPA activity. Specifically, the mutations increased the overall flexibility of the protein and changed the dominant collective motions of the top lobe as well as the helix 2 of the lower lobe. Moreover, we have identified key active-site residues that are classified as essential or intermediate for inosine triphosphate (ITP) hydrolyzing activity based on their hydrogen bond occupancy. Here we also present biochemical data indicating that the R178C mutant has very low ITP hydrolyzing activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yao Houndonougbo
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Bethany Pugh
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Kandise VanWormer
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Caitlin April
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Nicholas Burgis
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
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4
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Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
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Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
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5
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Abstract
This article presents a review of the field of molecular modeling of peptides. The main focus is on atomistic modeling with molecular mechanics potentials. The description of peptide conformations and solvation through potentials is discussed. Several important computer simulation methods are briefly introduced, including molecular dynamics, accelerated sampling approaches such as replica-exchange and metadynamics, free energy simulations and kinetic network models like Milestoning. Examples of recent applications for predictions of structure, kinetics, and interactions of peptides with complex environments are described. The reliability of current simulation methods is analyzed by comparison of computational predictions obtained using different models with each other and with experimental data. A brief discussion of coarse-grained modeling and future directions is also presented.
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Affiliation(s)
- Krzysztof Kuczera
- Departments of Chemistry and Molecular Biosciences, University of Kansas, 1251 Wescoe Hall Drive, Room 5090, Lawrence, KS, 66045, USA,
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6
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Sayadi M, Feig M. Role of conformational sampling of Ser16 and Thr17-phosphorylated phospholamban in interactions with SERCA. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:577-85. [PMID: 22959711 DOI: 10.1016/j.bbamem.2012.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 08/18/2012] [Accepted: 08/21/2012] [Indexed: 11/17/2022]
Abstract
Phosphorylation of phospholamban (PLB) at Ser16 and/ or Thr17 is believed to release its inhibitory effect on sarcoplasmic reticulum calcium ATPase. Ser16 phosphorylation of PLB has been suggested to cause a conformational change that alters the interaction between the enzyme and protein. Using computer simulations, the conformational sampling of Ser16 phosphorylated PLB in implicit membrane environment is compared here with the unphosphorylated PLB system to investigate these conformational changes. The results suggest that conformational changes in the cytoplasmic domain of PLB upon phosphorylation at Ser16 increase the likelihood of unfavorable interactions with SERCA in the E2 state prompting a conformational switch of SERCA from E2 to E1. Phosphorylation of PLB at Thr17 on the other hand does not appear to affect interactions with SERCA significantly suggesting that the mechanism of releasing the inhibitory effect is different between Thr17 phosphorylated and Ser16 phosphorylated PLB.
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Affiliation(s)
- Maryam Sayadi
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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7
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Lian P, Wei DQ, Wang JF, Chou KC. An allosteric mechanism inferred from molecular dynamics simulations on phospholamban pentamer in lipid membranes. PLoS One 2011; 6:e18587. [PMID: 21525996 PMCID: PMC3078132 DOI: 10.1371/journal.pone.0018587] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Accepted: 03/10/2011] [Indexed: 11/18/2022] Open
Abstract
Phospholamban functions as a regulator of Ca(2+) concentration of cardiac muscle cells by triggering the bioactivity of sarcoplasmic reticulum Ca(2+)-ATPase. In order to understand its dynamic mechanism in the environment of bilayer surroundings, we performed long time-scale molecular dynamic simulations based on the high-resolution NMR structure of phospholamban pentamer. It was observed from the molecular dynamics trajectory analyses that the conformational transitions between the "bellflower" and "pinwheel" modes were detected for phospholamban. Particularly, the two modes became quite similar to each other after phospholamban was phosphorylated at Ser16. Based on these findings, an allosteric mechanism was proposed to elucidate the dynamic process of phospholamban interacting with Ca(2+)-ATPase.
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Affiliation(s)
- Peng Lian
- College of Life Science and Biotechnology and Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- College of Life Science and Biotechnology and Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail: (DQW); (JFW)
| | - Jing-Fang Wang
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Center for Bioinformation and Technology, Shanghai, China
- * E-mail: (DQW); (JFW)
| | - Kuo-Chen Chou
- Gordon Life Science Institute, San Diego, California, United States of America
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8
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Manna M, Mukhopadhyay C. Cholesterol driven alteration of the conformation and dynamics of phospholamban in model membranes. Phys Chem Chem Phys 2011; 13:20188-98. [DOI: 10.1039/c1cp21793c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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9
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10
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Sayadi M, Tanizaki S, Feig M. Effect of membrane thickness on conformational sampling of phospholamban from computer simulations. Biophys J 2010; 98:805-14. [PMID: 20197034 DOI: 10.1016/j.bpj.2009.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 10/31/2009] [Accepted: 11/09/2009] [Indexed: 10/19/2022] Open
Abstract
The conformational sampling of monomeric, membrane-bound phospholamban is described from computer simulations. Phospholamban (PLB) plays a key role as a regulator of sarcoplasmic reticulum calcium ATPase. An implicit membrane model is used in conjunction with replica exchange molecular dynamics simulations to reach mus-ms timescales. The implicit membrane model was also used to study the effect of different membrane thicknesses by scaling the low-dielectric region. The conformational sampling with the membrane model mimicking dipalmitoylphosphatidylcholine bilayers is in good agreement overall with experimental measurements, but consists of a wide variety of different conformations including structures not described previously. The conformational ensemble shifts significantly in the presence of thinner or thicker membranes. This has implications for the structure and dynamics of PLB in physiological membranes and offers what we believe to be a new interpretation of previous experimental measurements of PLB in detergents and microsomal membrane.
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Affiliation(s)
- Maryam Sayadi
- Department of Chemistry, Michigan State University, East Lansing, USA
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11
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Chu S, Abu-Baker S, Lu J, Lorigan GA. (15)N Solid-state NMR spectroscopic studies on phospholamban at its phosphorylated form at ser-16 in aligned phospholipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:312-7. [PMID: 20044975 DOI: 10.1016/j.bbamem.2009.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 12/18/2009] [Accepted: 12/22/2009] [Indexed: 11/17/2022]
Abstract
Wild-type phospholamban (WT-PLB) is a pentameric transmembrane protein that regulates the cardiac cycle (contraction and relaxation). From a physiological prospective, unphosphorylated WT-PLB inhibits sarcoplasmic reticulum ATPase activity; whereas, its phosphorylated form relieves the inhibition in a mechanism that is not completely understood. In this study, site-specifically (15)N-Ala-11- and (15)N-Leu-7-labeled WT-PLB and the corresponding phosphorylated forms (P-PLB) were incorporated into 1,2-dioleoyl-sn-glycero-3-phosphocholine/2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPC/DOPE) mechanically oriented lipid bilayers. The aligned (15)N-labeled Ala-11 and Leu-7 WT-PLB samples show (15)N resonance peaks at approximately 71ppm and 75ppm, respectively, while the corresponding phosphorylated forms P-PLB show (15)N peaks at 92ppm and 99ppm, respectively. These (15)N chemical shift changes upon phosphorylation are significant and in agreement with previous reports, which indicate that phosphorylation of WT-PLB at Ser-16 alters the structural properties of the cytoplasmic domain with respect to the lipid bilayers.
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Affiliation(s)
- Shidong Chu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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12
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Maffeo C, Aksimentiev A. Structure, dynamics, and ion conductance of the phospholamban pentamer. Biophys J 2009; 96:4853-65. [PMID: 19527644 DOI: 10.1016/j.bpj.2009.03.053] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 03/12/2009] [Accepted: 03/20/2009] [Indexed: 11/19/2022] Open
Abstract
A 52-residue membrane protein, phospholamban (PLN) is an inhibitor of an adenosine-5'-triphosphate-driven calcium pump, the Ca2+-ATPase. Although the inhibition of Ca2+-ATPase involves PLN monomers, in a lipid bilayer membrane, PLN monomers form stable pentamers of unknown biological function. The recent NMR structure of a PLN pentamer depicts cytoplasmic helices extending normal to the bilayer in what is known as the bellflower conformation. The structure shows transmembrane helices forming a hydrophobic pore 4 A in diameter, which is reminiscent of earlier reports of possible ion conductance through PLN pentamers. However, recent FRET measurements suggested an alternative structure for the PLN pentamer, known as the pinwheel model, which features a narrower transmembrane pore and cytoplasmic helices that lie against the bilayer. Here, we report on structural dynamics and conductance properties of the PLN pentamers from all-atom (AA) and coarse-grained (CG) molecular dynamics simulations. Our AA simulations of the bellflower model demonstrate that in a lipid bilayer membrane or a detergent micelle, the cytoplasmic helices undergo large structural fluctuations, whereas the transmembrane pore shrinks and becomes asymmetric. Similar asymmetry of the transmembrane region was observed in the AA simulations of the pinwheel model; the cytoplasmic helices remained in contact with the bilayer. Using the CG approach, structural dynamics of both models were investigated on a microsecond timescale. The cytoplasmic helices of the CG bellflower model were observed to fall against the bilayer, whereas in the CG pinwheel model the conformation of the cytoplasmic helices remained stable. Using steered molecular dynamics simulations, we investigated the feasibility of ion conductance through the pore of the bellflower model. The resulting approximate potentials of mean force indicate that the PLN pentamer is unlikely to function as an ion channel.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
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13
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Kim T, Lee J, Im W. Molecular dynamics studies on structure and dynamics of phospholamban monomer and pentamer in membranes. Proteins 2009; 76:86-98. [DOI: 10.1002/prot.22322] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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14
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Houndonougbo Y, Kuczera K, Jas GS. Effects of CMAP and Electrostatic Cutoffs on the Dynamics of an Integral Membrane Protein: The Phospholamban Study. J Biomol Struct Dyn 2008; 26:17-34. [DOI: 10.1080/07391102.2008.10507220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Thaning J, Högberg CJ, Stevensson B, Lyubartsev AP, Maliniak A. Molecular Conformations in a Phospholipid Bilayer Extracted from Dipolar Couplings: A Computer Simulation Study. J Phys Chem B 2007; 111:13638-44. [DOI: 10.1021/jp075278t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johan Thaning
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Carl-Johan Högberg
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Baltzar Stevensson
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Alexander P. Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Arnold Maliniak
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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16
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Abu-Baker S, Lu JX, Chu S, Brinn CC, Makaroff CA, Lorigan GA. Side chain and backbone dynamics of phospholamban in phospholipid bilayers utilizing 2H and 15N solid-state NMR spectroscopy. Biochemistry 2007; 46:11695-706. [PMID: 17910421 PMCID: PMC2756648 DOI: 10.1021/bi700749q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2H and 15N solid-state NMR spectroscopic techniques were used to investigate both the side chain and backbone dynamics of wild-type phospholamban (WT-PLB) and its phosphorylated form (P-PLB) incorporated into 1-palmitoyl-2-oleoyl-sn-glycerophosphocholine (POPC) phospholipid bilayers. 2H NMR spectra of site-specific CD3-labeled WT-PLB (at Leu51, Ala24, and Ala15) in POPC bilayers were similar under frozen conditions (-25 degrees C). However, significant differences in the line shapes of the 2H NMR spectra were observed in the liquid crystalline phase at and above 0 degrees C. The 2H NMR spectra indicate that Leu51, located toward the lower end of the transmembrane (TM) helix, shows restricted side chain motion, implying that it is embedded inside the POPC lipid bilayer. Additionally, the line shape of the 2H NMR spectrum of CD3-Ala24 reveals more side chain dynamics, indicating that this residue (located in the upper end of the TM helix) has additional backbone and internal side chain motions. 2H NMR spectra of both WT-PLB and P-PLB with CD3-Ala15 exhibit strong isotropic spectral line shapes. The dynamic isotropic nature of the 2H peak can be attributed to side chain and backbone motions to residues located in an aqueous environment outside the membrane. Also, the spectra of 15N-labeled amide WT-PLB at Leu51 and Leu42 residues showed only a single powder pattern component indicating that these two 15N-labeled residues located in the TM helix are motionally restricted at 25 degrees C. Conversely, 15N-labeled amide WT-PLB at Ala11 located in the cytoplasmic domain showed both powder and isotropic components at 25 degrees C. Upon phosphorylation, the mobile component contribution increases at Ala11. The 2H and 15N NMR data indicate significant backbone motion for the cytoplasmic domain of WT-PLB when compared to the transmembrane section.
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Affiliation(s)
- Shadi Abu-Baker
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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17
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Pantano S, Carafoli E. The role of phosphorylation on the structure and dynamics of phospholamban: a model from molecular simulations. Proteins 2007; 66:930-40. [PMID: 17154419 DOI: 10.1002/prot.21239] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Phospholamban (PLB) is a small membrane protein that regulates the activity of the calcium ATP-ase in the cardiac, slow-twitch, and smooth muscle sarcoplasmic reticulum through the reversible phosphorylation of Ser16. We present here a comparative molecular dynamics study of unmodified and phosphorylated PLB immersed in a phospholipid membrane. The study has been performed under different ionic strength conditions, using the NMR structures of two PLB variants determined in mixed organic solvent and dodecylphosphocholine micelles. The simulations indicate that all PLB forms studied display a highly dynamic behavior of the N-terminal cytoplasmic moiety, with a decrease of its helical content in the phosphorylated forms. The cytoplasmic domain undergoes large collective motions sampling conformations parallel as well as perpendicular to the membrane surface in all the simulations. The transmembrane domain retains a tightly folded helical conformation with a small tilt with respect to the membrane plane probably induced by the presence of Asn30 and Asn34 within the hydrophobic environment. Furthermore, the phosphoric group on Ser16 establishes transient electrostatic interactions with the phospholipid heads. We propose a model in which phosphorylation diminishes the probability of interactions of PLB with residues near Lys400 in the SERCA pump, thus relieving its inhibition.
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Affiliation(s)
- Sergio Pantano
- Venetian Institute of Molecular Medicine (VIMM),Via Orus 2, 35129, Padova, Italy
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18
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Unruh JR, Liyanage MR, Johnson CK. Tyrosyl rotamer interconversion rates and the fluorescence decays of N-acetyltyrosinamide and short tyrosyl peptides. J Phys Chem B 2007; 111:5494-502. [PMID: 17455970 DOI: 10.1021/jp0645059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It has long been recognized that the fluorescence lifetimes of amino acid residues such as tyrosine and tryptophan depend on the rotameric configuration of the aromatic side chain, but estimates of the rate of interchange of rotameric states have varied widely. We report measurements of the rotameric populations and interchange rates for tyrosine in N-acetyltyrosinamide (NATyrA), the tripeptide Tyr-Gly-Gly (YGG), and the pentapeptide Leu-enkephalin (YGGFL). The fluorescence lifetimes were analyzed to determine the rotameric interchange rates in the context of a model incorporating exchange among three rotameric states. Maximum entropy method analysis verified the presence of three fluorescence decay components for YGGFL and two for YGG and NATyrA. Rotameric exchange between the gauche(-) and trans states occurred on the nanosecond time scale, whereas exchange with the gauche(+) state occurred on a longer time scale. Good agreement was obtained with rotameric populations and exchange rates from molecular dynamics simulations. Quenching by iodide was used to vary the intrinsic fluorescence lifetimes, providing additional constraints on the determined interchange rates. The temperature dependence was measured to determine barriers to exchange of the two most populated rotamers of 3, 5, and 7 kcal/mol for NATyrA, YGG, and YGGFL, respectively.
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Affiliation(s)
- Jay R Unruh
- Department of Chemistry, University of Kansas, 1251 Wescoe Drive, Lawrence, Kansas 66044, USA
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19
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Abu-Baker S, Lorigan GA. Phospholamban and its phosphorylated form interact differently with lipid bilayers: a 31P, 2H, and 13C solid-state NMR spectroscopic study. Biochemistry 2006; 45:13312-22. [PMID: 17073452 PMCID: PMC2586141 DOI: 10.1021/bi0614028] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phospholamban (PLB) is a 52-amino acid integral membrane protein that helps to regulate the flow of Ca(2+) ions in cardiac muscle cells. Recent structural studies on the PLB pentamer and the functionally active monomer (AFA-PLB) debate whether its cytoplasmic domain, in either the phosphorylated or dephosphorylated states, is alpha-helical in structure as well as whether it associates with the lipid head groups (Oxenoid, K. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 10870-10875; Karim, C. B. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 14437-14442; Andronesi, C.A. (2005) J. Am. Chem. Soc. 127, 12965-12974; Li, J. (2003) Biochemistry 42, 10674-10682; Metcalfe, E. E. (2005) Biochemistry 44, 4386-4396: Clayton, J. C. (2005) Biochemistry 44, 17016-17026). Comparing the secondary structure of the PLB pentamer and its phosphorylated form (P-PLB) as well as their interaction with the lipid bilayer is crucial in order to understand its regulatory function. Therefore, in this study, the full-length wild-type (WT) PLB and P-PLB were incorporated into 1-palmitoyl-2-oleoyl-sn-glycero-phosphocholine (POPC) phospholipid bilayers and studied utilizing solid-state NMR spectroscopy. The analysis of the (2)H and (31)P solid-state NMR data of PLB and P-PLB in POPC multilamellar vesicles (MLVs) indicates that a direct interaction takes place between both proteins and the phospholipid head groups. However, the interaction of P-PLB with POPC bilayers was less significant compared that with PLB. Moreover, the secondary structure using (13)C=O site-specific isotopically labeled Ala15-PLB and Ala15-P-PLB in POPC bilayers suggests that this residue, located in the cytoplasmic domain, is a part of an alpha-helical structure for both PLB and P-PLB.
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Affiliation(s)
- Shadi Abu-Baker
- Department of Chemistry and Biochemistry Miami University, Oxford, Ohio 45056
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry Miami University, Oxford, Ohio 45056
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Abstract
Phospholamban (PLB) is a 52 amino acid transmembrane protein found in the sarcoplasmic reticulum of cardiac myocytes, where it regulates the transport of calcium ions by SERCA (sarcoplasmic/endoplasmic reticulum Ca2+-ATPase). This work has shown that the cytoplasmic domain of PLB associates with phospholipid vesicles, possibly with the lipid polar head groups, and, in doing so, undergoes a transition from a random coil to a more helical conformation. These findings support a recent hypothesis that the cytoplasmic domain of PLB acts as a conformational switch, alternating between an orientation that lies across the membrane surface and an upright orientation that associates with the regulatory site of SERCA.
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