1
|
Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
Collapse
Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
| |
Collapse
|
2
|
Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
Collapse
Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| |
Collapse
|
3
|
Picard LP, Prosser RS. Advances in the study of GPCRs by 19F NMR. Curr Opin Struct Biol 2021; 69:169-176. [PMID: 34130235 DOI: 10.1016/j.sbi.2021.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/18/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023]
Abstract
Crystallography and cryo-electron microscopy have advanced atomic resolution perspectives of inactive and active states of G protein-coupled receptors (GPCRs), alone and in complex with G proteins or arrestin. 19F NMR can play a role in ascertaining activation mechanisms and understanding the complete energy landscape associated with signal transduction. Fluorinated reporters are introduced biosynthetically via fluorinated amino acid analogs or chemically, via thiol-specific fluorinated reporters. The chemical shift sensitivity of these reporters makes it possible to discern details of conformational ensembles. In addition to spectroscopic details, paramagnetic species can be incorporated through orthogonal techniques to obtain distance information on fluorinated reporters, while T2-and T1-based relaxation experiments provide details on exchange kinetics in addition to fluctuations within a given state.
Collapse
|
4
|
Anandan A, Vrielink A. Structure and function of lipid A-modifying enzymes. Ann N Y Acad Sci 2019; 1459:19-37. [PMID: 31553069 DOI: 10.1111/nyas.14244] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/26/2019] [Accepted: 09/05/2019] [Indexed: 12/30/2022]
Abstract
Lipopolysaccharides are complex molecules found in the cell envelop of many Gram-negative bacteria. The toxic activity of these molecules has led to the terminology of endotoxins. They provide bacteria with structural integrity and protection from external environmental conditions, and they interact with host signaling receptors to induce host immune responses. Bacteria have evolved enzymes that act to modify lipopolysaccharides, particularly the lipid A region of the molecule, to enable the circumvention of host immune system responses. These modifications include changes to lipopolysaccharide by the addition of positively charged sugars, such as N-Ara4N, and phosphoethanolamine (pEtN). Other modifications include hydroxylation, acylation, and deacylation of fatty acyl chains. We review the two-component regulatory mechanisms for enzymes that carry out these modifications and provide details of the structures of four enzymes (PagP, PagL, pEtN transferases, and ArnT) that modify the lipid A portion of lipopolysaccharides. We focus largely on the three-dimensional structures of these enzymes, which provide an understanding of how their substrate binding and catalytic activities are mediated. A structure-function-based understanding of these enzymes provides a platform for the development of novel therapeutics to treat antibiotic resistance.
Collapse
Affiliation(s)
- Anandhi Anandan
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia
| |
Collapse
|
5
|
da Silva Xavier A, da Silva FP, Vidigal PMP, Lima TTM, de Souza FO, Alfenas-Zerbini P. Genomic and biological characterization of a new member of the genus Phikmvvirus infecting phytopathogenic Ralstonia bacteria. Arch Virol 2018; 163:3275-3290. [DOI: 10.1007/s00705-018-4006-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/10/2018] [Indexed: 02/07/2023]
|
6
|
Iyer BR, Zadafiya P, Vetal PV, Mahalakshmi R. Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein. J Biol Chem 2017; 292:12351-12365. [PMID: 28592485 PMCID: PMC5519381 DOI: 10.1074/jbc.m117.789446] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/02/2017] [Indexed: 01/07/2023] Open
Abstract
The free energy of water-to-interface amino acid partitioning is a major contributing factor in membrane protein folding and stability. The interface residues at the C terminus of transmembrane β-barrels form the β-signal motif required for assisted β-barrel assembly in vivo but are believed to be less important for β-barrel assembly in vitro. Here, we experimentally measured the thermodynamic contribution of all 20 amino acids at the β-signal motif to the unassisted folding of the model β-barrel protein PagP. We obtained the partitioning free energy for all 20 amino acids at the lipid-facing interface (ΔΔG0w,i(φ)) and the protein-facing interface (ΔΔG0w,i(π)) residues and found that hydrophobic amino acids are most favorably transferred to the lipid-facing interface, whereas charged and polar groups display the highest partitioning energy. Furthermore, the change in non-polar surface area correlated directly with the partitioning free energy for the lipid-facing residue and inversely with the protein-facing residue. We also demonstrate that the interface residues of the β-signal motif are vital for in vitro barrel assembly, because they exhibit a side chain–specific energetic contribution determined by the change in nonpolar accessible surface. We further establish that folding cooperativity and hydrophobic collapse are balanced at the membrane interface for optimal stability of the PagP β-barrel scaffold. We conclude that the PagP C-terminal β-signal motif influences the folding cooperativity and stability of the folded β-barrel and that the thermodynamic contributions of the lipid- and protein-facing residues in the transmembrane protein β-signal motif depend on the nature of the amino acid side chain.
Collapse
Affiliation(s)
- Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhauri, Bhopal 462066, India
| | - Punit Zadafiya
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhauri, Bhopal 462066, India
| | - Pallavi Vijay Vetal
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhauri, Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhauri, Bhopal 462066, India.
| |
Collapse
|
7
|
Javanainen M, Vattulainen I, Monticelli L. On Atomistic Models for Molecular Oxygen. J Phys Chem B 2017; 121:518-528. [PMID: 28004930 DOI: 10.1021/acs.jpcb.6b11183] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Molecular oxygen (O2) is key to all life on earth, as it is constantly cycled via photosynthesis and cellular respiration. Substantial scientific effort has been devoted to understanding every part of this cycle. Classical molecular dynamics (MD) simulations have been used to study some of the key processes involved in cellular respiration: O2 permeation through alveolar monolayers and cellular membranes, its binding to hemoglobin during transport in the bloodstream, as well as its transport along optimal pathways toward its reduction sites in proteins. Moreover, MD simulations can help interpret the results of several imaging techniques in which O2 is used because of its paramagnetic nature. However, despite the widespread use of computational models for the O2 molecule, their performances have never been systematically evaluated. In this paper, we assess the performances of 14 different models of O2 available in the literature by calculating four thermodynamic properties: density, heat of vaporization, free energy of hydration, and free energy of solvation in hexadecane. For each property, reliable experimental data are available. Most models perform reasonably well in predicting the correct trends, but they fail to reproduce the experimental data quantitatively. We then develop new models for O2, with and without a quadrupole moment, and compare their behavior with the behavior of previously published models. The new models show significant improvement in terms of density, heat of vaporization, and free energy of hydration. However, quantitative agreement with water-oil partitioning is not reached due to discrepancies between the calculated and measured free energies of solvation in hexadecane. We suggest that classical pairwise-additive models may be inadequate to properly describe the thermodynamics of solvation of apolar species, such as O2, in apolar solvents.
Collapse
Affiliation(s)
- Matti Javanainen
- Department of Physics, Tampere University of Technology , 33720 Tampere, Finland.,Department of Physics, University of Helsinki , 00100 Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology , 33720 Tampere, Finland.,Department of Physics, University of Helsinki , 00100 Helsinki, Finland.,MEMPHYS - Centre for Biomembrane Physics, University of Southern Denmark , 5230 Odense, Denmark
| | - Luca Monticelli
- University of Lyon, CNRS, UMR 5086 MMSB , 69367 Lyon, France
| |
Collapse
|
8
|
Schmidt T, Situ AJ, Ulmer TS. Direct Evaluation of Protein-Lipid Contacts Reveals Protein Membrane Immersion and Isotropic Bicelle Structure. J Phys Chem Lett 2016; 7:4420-4426. [PMID: 27776216 PMCID: PMC11027914 DOI: 10.1021/acs.jpclett.6b02159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The solvation of membrane proteins by both lipids and water makes their membrane immersion difficult to predict and the choice of a membrane mimic challenging. To characterize protein-lipid contacts and bicelle membrane mimics, we examined protein-lipid cross-relaxation of integrin αIIb and β3(A711P) transmembrane helices in isotropic phospholipid bicelles (q = 0.5 and 0.7). Long-chain bicelle lipids dominated contacts with central helix segments, whereas both short- and long-chain lipids contacted the terminal turns of each helix in corroboration of the mixed bicelle model. The saturation transfer profiles from long-chain lipids directly established helix midpoints in the lipid bilayer. Lipid headgroups and water molecules engaged the side chains of buried serine and threonine in competition with intrahelical hydrogen bonding, illustrating that polar side chains seek the most favorable electrostatic contacts.
Collapse
Affiliation(s)
- Thomas Schmidt
- Department of Biochemistry & Molecular Medicine and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
- Present address: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan J. Situ
- Department of Biochemistry & Molecular Medicine and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
| | - Tobias S. Ulmer
- Department of Biochemistry & Molecular Medicine and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA
| |
Collapse
|
9
|
Iyer BR, Mahalakshmi R. Distinct Structural Elements Govern the Folding, Stability, and Catalysis in the Outer Membrane Enzyme PagP. Biochemistry 2016; 55:4960-70. [PMID: 27525547 DOI: 10.1021/acs.biochem.6b00678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The outer membrane enzyme PagP is indispensable for lipid A palmitoylation in Gram-negative bacteria and has been implicated in resistance to host immune defenses. PagP possesses an unusual structure for an integral membrane protein, with a highly dynamic barrel domain that is tilted with respect to the membrane normal. In addition, it contains an N-terminal amphipathic helix. Recent functional and structural studies have shown that these molecular factors are critical for PagP to carry out its function in the challenging environment of the bacterial outer membrane. However, the precise contributions of the N-helix to folding and stability and residues that can influence catalytic rates remain to be addressed. Here, we identify a sequence-dependent stabilizing role for the N-terminal helix of PagP in the measured thermodynamic stability of the barrel. Using chimeric barrel sequences, we show that the Escherichia coli PagP N-terminal helix confers 2-fold greater stability to the Salmonella typhimurium barrel. Further, we find that the W78F substitution in S. typhimurium causes a nearly 20-fold increase in the specific activity in vitro for the phospholipase reaction, compared to that of E. coli PagP. Here, phenylalanine serves as a key regulator of catalysis, possibly by increasing the reaction rate. Through coevolution analysis, we detect an interaction network between seemingly unrelated segments of this membrane protein. Exchanging the structural and functional features between homologous PagP enzymes from E. coli and S. typhimurium has provided us with an understanding of the molecular factors governing PagP stability and function.
Collapse
Affiliation(s)
- Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research , Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research , Bhopal 462066, India
| |
Collapse
|
10
|
Iyer BR, Mahalakshmi R. Residue-Dependent Thermodynamic Cost and Barrel Plasticity Balances Activity in the PhoPQ-Activated Enzyme PagP of Salmonella typhimurium. Biochemistry 2015; 54:5712-22. [PMID: 26334694 DOI: 10.1021/acs.biochem.5b00543] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PagP is an eight-stranded transmembrane β-barrel enzyme indispensable for lipid A palmitoylation in Gram-negative bacteria. The severity of infection by pathogens, including Salmonella, Legionella, and Bordetella, and resistance to antimicrobial peptides, relies on lipid A remodeling by PagP, rendering PagP a sought-after drug target. Despite a conserved sequence, more robust palmitoylation of lipid A is observed in Salmonella typhimurium compared to Escherichia coli, a possible consequence of the differential regulation of PagP expression and/or specific activity. Work here identifies molecular signatures that demarcate thermodynamic stability and variances in catalytic efficiency between S. typhimurium (PagP-St) and E. coli (PagP-Ec) transmembrane PagP barrel variants. We demonstrate that Salmonella PagP displays a 2-fold destabilization of the barrel, while achieving 15-20 magnitude higher lipase efficiency, through subtle alterations of lipid-facing residues distal from the active site. We find that catalytic properties of these homologues are retained across different lipid environments such as micelles, vesicles, and natural extracts. By comparing thermodynamic stability with activity of selectively designed mutants, we conclude that activity-stability trade-offs can be influenced by factors secluded from the catalytic region. Our results provide a compelling correlation of the primary protein structure with enzymatic activity, barrel thermodynamic stability, and scaffold plasticity. Our analysis can open avenues for the development of potent pharmaceuticals against salmonellosis.
Collapse
Affiliation(s)
- Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research , Bhopal 462023, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research , Bhopal 462023, India
| |
Collapse
|
11
|
Tian Y, Schwieters CD, Opella SJ, Marassi FM. A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins. Biophys J 2015; 109:574-85. [PMID: 26244739 PMCID: PMC4572468 DOI: 10.1016/j.bpj.2015.06.047] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/18/2015] [Accepted: 06/23/2015] [Indexed: 01/22/2023] Open
Abstract
The highly anisotropic environment of the lipid bilayer membrane imposes significant constraints on the structures and functions of membrane proteins. However, NMR structure calculations typically use a simple repulsive potential that neglects the effects of solvation and electrostatics, because explicit atomic representation of the solvent and lipid molecules is computationally expensive and impractical for routine NMR-restrained calculations that start from completely extended polypeptide templates. Here, we describe the extension of a previously described implicit solvation potential, eefxPot, to include a membrane model for NMR-restrained calculations of membrane protein structures in XPLOR-NIH. The key components of eefxPot are an energy term for solvation free energy that works together with other nonbonded energy functions, a dedicated force field for conformational and nonbonded protein interaction parameters, and a membrane function that modulates the solvation free energy and dielectric screening as a function of the atomic distance from the membrane center, relative to the membrane thickness. Initial results obtained for membrane proteins with structures determined experimentally in lipid bilayer membranes show that eefxPot affords significant improvements in structural quality, accuracy, and precision. Calculations with eefxPot are straightforward to implement and can be used to both fold and refine structures, as well as to run unrestrained molecular-dynamics simulations. The potential is entirely compatible with the full range of experimental restraints measured by various techniques. Overall, it provides a useful and practical way to calculate membrane protein structures in a physically realistic environment.
Collapse
Affiliation(s)
- Ye Tian
- Sanford-Burnham Medical Research Institute, La Jolla, California; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | | |
Collapse
|
12
|
Afri M, Alexenberg C, Aped P, Bodner E, Cohen S, Ejgenburg M, Eliyahu S, Gilinsky-Sharon P, Harel Y, Naqqash ME, Porat H, Ranz A, Frimer AA. NMR-based molecular ruler for determining the depth of intercalants within the lipid bilayer. Chem Phys Lipids 2014; 184:105-18. [DOI: 10.1016/j.chemphyslip.2014.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 07/10/2014] [Accepted: 07/21/2014] [Indexed: 01/20/2023]
|
13
|
|
14
|
Alvares R, Gupta S, Macdonald PM, Prosser RS. Temperature and Pressure Based NMR Studies of Detergent Micelle Phase Equilibria. J Phys Chem B 2014; 118:5698-706. [DOI: 10.1021/jp500139p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Rohan Alvares
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
| | - Shaan Gupta
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
| | - Peter M. Macdonald
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
| | - R. Scott Prosser
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
- Department
of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| |
Collapse
|
15
|
|
16
|
Hocking HG, Zangger K, Madl T. Studying the structure and dynamics of biomolecules by using soluble paramagnetic probes. Chemphyschem 2013; 14:3082-94. [PMID: 23836693 PMCID: PMC4171756 DOI: 10.1002/cphc.201300219] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 12/20/2022]
Abstract
Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes.
Collapse
Affiliation(s)
- Henry G Hocking
- Chair of Biomolecular NMR, Department Chemie, Technische Universität München, 85747 Garching (Germany); Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg (Germany)
| | | | | |
Collapse
|
17
|
Solution NMR studies on the orientation of membrane-bound peptides and proteins by paramagnetic probes. Molecules 2013; 18:7407-35. [PMID: 23799448 PMCID: PMC6269851 DOI: 10.3390/molecules18077407] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/13/2013] [Accepted: 06/20/2013] [Indexed: 12/24/2022] Open
Abstract
Many peptides and proteins are attached to or immersed in a biological membrane. In order to understand their function not only the structure but also their topology in the membrane is important. Solution NMR spectroscopy is one of the most often used approaches to determine the orientation and localization of membrane-bound peptides and proteins. Here we give an application-oriented overview on the use of paramagnetic probes for the investigation of membrane-bound peptides and proteins. The examples discussed range from the large pool of antimicrobial peptides, bacterial toxins, cell penetrating peptides to domains of larger proteins or the calcium regulating protein phospholamban. Topological information is obtained in all these examples by the use of either attached or freely mobile paramagnetic tags. For some examples information obtained from the paramagnetic probes was included in the structure determination.
Collapse
|
18
|
Abstract
Long-chain-length hydrophobic acyl residues play a vital role in a multitude of essential biological structures and processes. They build the inner hydrophobic layers of biological membranes, are converted to intracellular storage compounds, and are used to modify protein properties or function as membrane anchors, to name only a few functions. Acyl thioesters are transferred by acyltransferases or transacylases to a variety of different substrates or are polymerized to lipophilic storage compounds. Lipases represent another important enzyme class dealing with fatty acyl chains; however, they cannot be regarded as acyltransferases in the strict sense. This review provides a detailed survey of the wide spectrum of bacterial acyltransferases and compares different enzyme families in regard to their catalytic mechanisms. On the basis of their studied or assumed mechanisms, most of the acyl-transferring enzymes can be divided into two groups. The majority of enzymes discussed in this review employ a conserved acyltransferase motif with an invariant histidine residue, followed by an acidic amino acid residue, and their catalytic mechanism is characterized by a noncovalent transition state. In contrast to that, lipases rely on completely different mechanism which employs a catalytic triad and functions via the formation of covalent intermediates. This is, for example, similar to the mechanism which has been suggested for polyester synthases. Consequently, although the presented enzyme types neither share homology nor have a common three-dimensional structure, and although they deal with greatly varying molecule structures, this variety is not reflected in their mechanisms, all of which rely on a catalytically active histidine residue.
Collapse
Affiliation(s)
- Annika Röttig
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
19
|
Alvares RD, Tulumello DV, Macdonald PM, Deber CM, Prosser RS. Effects of a polar amino acid substitution on helix formation and aggregate size along the detergent-induced peptide folding pathway. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:373-81. [DOI: 10.1016/j.bbamem.2012.09.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 09/06/2012] [Accepted: 09/24/2012] [Indexed: 12/15/2022]
|
20
|
Naveed H, Jimenez-Morales D, Tian J, Pasupuleti V, Kenney LJ, Liang J. Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding. J Mol Biol 2012; 419:89-101. [PMID: 22391420 DOI: 10.1016/j.jmb.2012.02.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 02/24/2012] [Accepted: 02/25/2012] [Indexed: 12/14/2022]
Abstract
Biogenesis of β-barrel membrane proteins is a complex, multistep, and as yet incompletely characterized process. The bacterial porin family is perhaps the best-studied protein family among β-barrel membrane proteins that allows diffusion of small solutes across the bacterial outer membrane. In this study, we have identified residues that contribute significantly to the protein-protein interaction (PPI) interface between the chains of outer membrane protein F (OmpF), a trimeric porin, using an empirical energy function in conjunction with an evolutionary analysis. By replacing these residues through site-directed mutagenesis either with energetically favorable residues or substitutions that do not occur in natural bacterial outer membrane proteins, we succeeded in engineering OmpF mutants with dimeric and monomeric oligomerization states instead of a trimeric oligomerization state. Moreover, our results suggest that the oligomerization of OmpF proceeds through a series of interactions involving two distinct regions of the extensive PPI interface: two monomers interact to form a dimer through the PPI interface near G19. This dimer then interacts with another monomer through the PPI interface near G135 to form a trimer. We have found that perturbing the PPI interface near G19 results in the formation of the monomeric OmpF only. Thermal denaturation of the designed dimeric OmpF mutant suggests that oligomer dissociation can be separated from the process of protein unfolding. Furthermore, the conserved site near G57 and G59 is important for the PPI interface and might provide the essential scaffold for PPIs.
Collapse
Affiliation(s)
- Hammad Naveed
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | | | | | | | | |
Collapse
|
21
|
Afri M, Naqqash ME, Frimer AA. Using fluorescence to locate intercalants within the lipid bilayer of liposomes, bioliposomes and erythrocyte ghosts. Chem Phys Lipids 2011; 164:759-65. [PMID: 21939642 DOI: 10.1016/j.chemphyslip.2011.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 08/15/2011] [Accepted: 09/06/2011] [Indexed: 11/15/2022]
Abstract
In previous work, we have shown the utility of the "NMR technique" in locating intercalants within the lipid bilayer. We describe herein the development of a more sensitive and complementary "fluorescence technique" for this purpose and its application to liposomes, bioliposomes and erythrocyte ghosts. This technique is based on the observation in selected compounds of an excellent correlation between the emission wavelength (λ(em)) and Dimroth-Reichardt E(T)(30) polarity parameter for the solvent in which the fluorescence emission spectrum was obtained.
Collapse
Affiliation(s)
- Michal Afri
- Department of Chemistry, Bar Ilan University, Ramat Gan, Israel.
| | | | | |
Collapse
|
22
|
Al-Abdul-Wahid MS, Verardi R, Veglia G, Prosser RS. Topology and immersion depth of an integral membrane protein by paramagnetic rates from dissolved oxygen. JOURNAL OF BIOMOLECULAR NMR 2011; 51:173-183. [PMID: 21947925 DOI: 10.1007/s10858-011-9551-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Accepted: 06/30/2011] [Indexed: 05/31/2023]
Abstract
In studies of membrane proteins, knowledge of protein topology can provide useful insight into both structure and function. In this work, we present a solution NMR method for the measurement the tilt angle and average immersion depth of alpha helices in membrane proteins, from analysis of the paramagnetic relaxation rate enhancements arising from dissolved oxygen. No modification to the micelle or protein is necessary, and the topology of both transmembrane and amphipathic helices are readily determined. We apply this method to the measure the topology of a monomeric mutant of phospholamban (AFA-PLN), a 52-residue membrane protein containing both an amphipathic and a transmembrane alpha helix. In dodecylphosphocholine micelles, the amphipathic helix of AFA-PLN was found to have a tilt angle of 87° ± 1° and an average immersion depth of 13.2 Å. The transmembrane helix was found to have an average immersion depth of 5.4 Å, indicating residues 41 and 42 are closest to the micelle centre. The resolution of paramagnetic relaxation rate enhancements from dissolved oxygen compares favourably to those from Ni (II), a hydrophilic paramagnetic species.
Collapse
|
23
|
Kang C, Li Q. Solution NMR study of integral membrane proteins. Curr Opin Chem Biol 2011; 15:560-9. [DOI: 10.1016/j.cbpa.2011.05.025] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 05/12/2011] [Accepted: 05/23/2011] [Indexed: 11/29/2022]
|
24
|
Gessmann D, Mager F, Naveed H, Arnold T, Weirich S, Linke D, Liang J, Nussberger S. Improving the resistance of a eukaryotic β-barrel protein to thermal and chemical perturbations. J Mol Biol 2011; 413:150-61. [PMID: 21835183 DOI: 10.1016/j.jmb.2011.07.054] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 07/22/2011] [Accepted: 07/23/2011] [Indexed: 10/17/2022]
Abstract
β-Barrel membrane proteins have regular structures with extensive hydrogen-bond networks between their transmembrane (TM) β-strands, which stabilize their protein fold. Nevertheless, weakly stable TM regions, which are important for the protein function and interaction with other proteins, exist. Here, we report on the apparent stability of human Tom40A, a member of the "mitochondrial porin family" and main constituent of the mitochondrial protein-conducting channel TOM (translocase of the outer membrane). Using a physical interaction model, TmSIP, for β-barrel membrane proteins, we have identified three unfavorable β-strands in the TM domain of the protein. Substitution of key residues inside these strands with hydrophobic amino acids results in a decreased sensitivity of the protein to chemical and/or thermal denaturation. The apparent melting temperature observed when denatured at a rate of 1 °C per minute is shifted from 73 to 84 °C. Moreover, the sensitivity of the protein to denaturant agents is significantly lowered. Further, we find a reduced tendency for the mutated protein to form dimers. We propose that the identified weakly stable β-strands 1, 2 and 9 of human Tom40A play an important role in quaternary protein-protein interactions within the mammalian TOM machinery. Our results show that the use of empirical energy functions to model the apparent stability of β-barrel membrane proteins may be a useful tool in the field of nanopore bioengineering.
Collapse
Affiliation(s)
- Dennis Gessmann
- Biophysics Department, Institute of Biology, University of Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Cuesta-Seijo JA, Neale C, Khan MA, Moktar J, Tran CD, Bishop RE, Pomès R, Privé GG. PagP crystallized from SDS/cosolvent reveals the route for phospholipid access to the hydrocarbon ruler. Structure 2011; 18:1210-9. [PMID: 20826347 DOI: 10.1016/j.str.2010.06.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 05/31/2010] [Accepted: 06/07/2010] [Indexed: 12/25/2022]
Abstract
Enzymatic reactions involving bilayer lipids occur in an environment with strict physical and topological constraints. The integral membrane enzyme PagP transfers a palmitoyl group from a phospholipid to lipid A in order to assist Escherichia coli in evading host immune defenses during infection. PagP measures the palmitoyl group with an internal hydrocarbon ruler that is formed in the interior of the eight-stranded antiparallel β barrel. The access and egress of the palmitoyl group is thought to take a lateral route from the bilayer phase to the barrel interior. Molecular dynamics, mutagenesis, and a 1.4 A crystal structure of PagP in an SDS / 2-methyl-2,4-pentanediol (MPD) cosolvent system reveal that phospholipid access occurs at the crenel present between strands F and G of PagP. In this way, the phospholipid head group can remain exposed to the cell exterior while the lipid acyl chain remains in a predominantly hydrophobic environment as it translocates to the protein interior.
Collapse
Affiliation(s)
- Jose Antonio Cuesta-Seijo
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute and Campbell Family Cancer Research Institute, 101 College Street, Toronto, ON M5G 1L7, Canada
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Khan MA, Moktar J, Mott PJ, Vu M, McKie AH, Pinter T, Hof F, Bishop RE. Inscribing the perimeter of the PagP hydrocarbon ruler by site-specific chemical alkylation. Biochemistry 2010; 49:9046-57. [PMID: 20853818 DOI: 10.1021/bi1011496] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The Escherichia coli outer membrane phospholipid:lipid A palmitoyltransferase PagP selects palmitate chains using its β-barrel-interior hydrocarbon ruler and interrogates phospholipid donors by gating them laterally through an aperture known as the crenel. Lipid A palmitoylation provides antimicrobial peptide resistance and modulates inflammation signaled through the host TLR4/MD2 pathway. Gly88 substitutions can raise the PagP hydrocarbon ruler floor to correspondingly shorten the selected acyl chain. To explore the limits of hydrocarbon ruler acyl chain selectivity, we have modified the single Gly88Cys sulfhydryl group with linear alkyl units and identified C10 as the shortest acyl chain to be efficiently utilized. Gly88Cys-S-ethyl, S-n-propyl, and S-n-butyl PagP were all highly specific for C12, C11, and C10 acyl chains, respectively, and longer aliphatic or aminoalkyl substitutions could not extend acyl chain selectivity any further. The donor chain length limit of C10 coincides with the phosphatidylcholine transition from displaying bilayer to micellar properties in water, but the detergent inhibitor lauryldimethylamine N-oxide also gradually became ineffective in a micellar assay as the selected acyl chains were shortened to C10. The Gly88Cys-S-ethyl and norleucine substitutions exhibited superior C12 acyl chain specificity compared to that of Gly88Met PagP, thus revealing detection by the hydrocarbon ruler of the Met side chain tolerance for terminal methyl group gauche conformers. Although norleucine substitution was benign, selenomethionine substitution at Met72 was highly destabilizing to PagP. Within the hydrophobic and van der Waals-contacted environment of the PagP hydrocarbon ruler, side chain flexibility, combined with localized thioether-aromatic dispersion attraction, likely influences the specificity of acyl chain selection.
Collapse
Affiliation(s)
- M Adil Khan
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada L8N 3Z5
| | | | | | | | | | | | | | | |
Collapse
|
27
|
O'Daniel PI, Zajicek J, Zhang W, Shi Q, Fisher JF, Mobashery S. Elucidation of the structure of the membrane anchor of penicillin-binding protein 5 of Escherichia coli. J Am Chem Soc 2010; 132:4110-8. [PMID: 20192190 DOI: 10.1021/ja9094445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Penicillin-binding protein 5 (PBP 5) of Escherichia coli is a membrane-bound cell wall dd-carboxypeptidase, localized in the outer leaflet of the cytosolic membrane of this Gram-negative bacterium. Not only is it the most abundant PBP of E. coli, but it is as well a target for penicillins and is the most studied of the PBP enzymes. PBP 5, as a representative peripheral membrane protein, is anchored to the cytoplasmic membrane by the 21 amino acids of its C-terminus. Although the importance of this terminus as a membrane anchor is well recognized, the structure of this anchor was previously unknown. Using natural isotope abundance NMR, the structure of the PBP 5 anchor peptide within a micelle was determined. The structure conforms to a helix-bend-helix-turn-helix motif and reveals that the anchor enters the membrane so as to form an amphiphilic structure within the interface of the hydrophilic/hydrophobic boundary regions near the lipid head groups. The bend and the turn within the motif allow the C-terminus to exit from the same side of the membrane that is penetrated. The PBP anchor sequences represent extraordinary diversity, encompassing both N-terminal and C-terminal anchoring domains. This study establishes a surface adherence mechanism for the PBP 5 C-terminus anchor peptide, as the structural basis for further study toward understanding the role of these domains in selecting membrane environments and in the assembly of the multienzyme hyperstructures of bacterial cell wall biosynthesis.
Collapse
Affiliation(s)
- Peter I O'Daniel
- Department of Chemistry and Biochemistry, 423 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | | | | | | | | | |
Collapse
|
28
|
Mahalakshmi R, Marassi FM. Orientation of the Escherichia coli outer membrane protein OmpX in phospholipid bilayer membranes determined by solid-State NMR. Biochemistry 2010; 47:6531-8. [PMID: 18512961 DOI: 10.1021/bi800362b] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solid-state NMR orientation-dependent frequencies measured for membrane proteins in macroscopically oriented lipid bilayers provide precise orientation restraints for structure determination in membranes. Here we show that this information can also be used to supplement crystallographic structural data to establish the orientation of a membrane protein in the membrane. This is achieved by incorporating a few orientation restraints, measured for the Escherichia coli outer membrane protein OmpX in magnetically oriented lipid bilayers (bicelles), in a simulated annealing calculation with the coordinates of the OmpX crystal structure. The (1)H-(15)N dipolar couplings measured for the seven Phe residues of OmpX in oriented bilayers can be assigned by back-calculation of the NMR spectrum from the crystal structure and are sufficient to establish the three-dimensional orientation of the protein in the membrane, while the (15)N chemical shifts provide a measure of cross-validation for the analysis. In C14 lipid bilayers, OmpX adopts a transmembrane orientation with a 7 degrees tilt of its beta-barrel axis relative to the membrane normal, matching the hydrophobic thickness of the barrel with that of the membrane.
Collapse
Affiliation(s)
- Radhakrishnan Mahalakshmi
- Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | | |
Collapse
|
29
|
Kim HJ, Howell SC, Van Horn WD, Jeon YH, Sanders CR. Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 55:335-360. [PMID: 20161395 PMCID: PMC2782866 DOI: 10.1016/j.pnmrs.2009.07.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Hak Jun Kim
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, 406-840, Korea
| | - Stanley C. Howell
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Wade D. Van Horn
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Young Ho Jeon
- Center for Magnetic Resonance, Korea Basic Research Institute, Daejon, 305-333, Korea
| | - Charles R. Sanders
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
- Corresponding Author: ; phone: 615-936-3756; fax: 615-936-2211
| |
Collapse
|
30
|
Franzmann M, Otzen D, Wimmer R. Quantitative Use of Paramagnetic Relaxation Enhancements for Determining Orientations and Insertion Depths of Peptides in Micelles. Chembiochem 2009; 10:2339-47. [DOI: 10.1002/cbic.200900347] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
31
|
Al-Abdul-Wahid MS, Neale C, Pomès R, Prosser RS. A solution NMR approach to the measurement of amphiphile immersion depth and orientation in membrane model systems. J Am Chem Soc 2009; 131:6452-9. [PMID: 19415935 DOI: 10.1021/ja808964e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxygen and Ni(II) are ideal paramagnetic species for NMR studies of immersion depth since they establish prominent concentration gradients across the membrane-water interface of either bilayers or micelles. Corresponding gradients of paramagnetic shifts and relaxation rates are observed by NMR for membrane embedded amphiphiles. Specifically, upon dissolution of oxygen at a partial pressure of 20 bar or more, (13)C NMR spectra of membrane embedded amphiphiles reveal chemical shift perturbations which depend sensitively on average immersion depth in the membrane. Similarly, depth-dependent enhancements of spin-lattice relaxation rates can be detected by (1)H NMR. Generally, such paramagnetic effects depend both on steric or accessibility factors and on the local concentration of the paramagnet. The steric terms can be factored out by combining paramagnetic rates arising from O(2) and Ni, in the form of a ratio, R(1P)(O(2))/R(1P)(Ni). The natural logarithm of this ratio is shown to depend linearly on immersion depth in a micelle. The analysis is verified using molecular dynamics simulations of dodecylphosphocholine in a detergent micelle, while thorough consideration of the paramagnetic rate data also allows for the determination of the orientation of imipramine in the micelle. Thus, a complete picture of topology arises from this approach which is readily applicable to studies of drugs and amphiphiles in fast-tumbling bicelles, small unilamellar vesicles, and micelles.
Collapse
Affiliation(s)
- M Sameer Al-Abdul-Wahid
- Department of Chemistry, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, Canada, L5L 1C6
| | | | | | | |
Collapse
|
32
|
Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins. Proc Natl Acad Sci U S A 2009; 106:12735-40. [PMID: 19622743 DOI: 10.1073/pnas.0902169106] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Although the structures of many beta-barrel membrane proteins are available, our knowledge of the principles that govern their energetics and oligomerization states is incomplete. Here we describe a computational method to study the transmembrane (TM) domains of beta-barrel membrane proteins. Our method is based on a physical interaction model, a simplified conformational space for efficient enumeration, and an empirical potential function from a detailed combinatorial analysis. Using this method, we can identify weakly stable regions in the TM domain, which are found to be important structural determinants for beta-barrel membrane proteins. By calculating the melting temperatures of the TM strands, our method can also assess the stability of beta-barrel membrane proteins. Predictions on membrane enzyme PagP are consistent with recent experimental NMR and mutant studies. We have also discovered that out-clamps, in-plugs, and oligomerization are 3 general mechanisms for stabilizing weakly stable TM regions. In addition, we have found that extended and contiguous weakly stable regions often signal the existence of an oligomer and that strands located in the interfaces of protein-protein interactions are considerably less stable. Based on these observations, we can predict oligomerization states and can identify the interfaces of protein-protein interactions for beta-barrel membrane proteins by using either structure or sequence information. In a set of 25 nonhomologous proteins with known structures, our method successfully predicted whether a protein forms a monomer or an oligomer with 91% accuracy; in addition, our method identified with 82% accuracy the protein-protein interaction interfaces by using sequence information only when correct strands are given.
Collapse
|
33
|
Li X, Rinkevicius Z, Tu Y, Tian H, Ågren H. Paramagnetic Perturbation of the 19F NMR Chemical Shift in Fluorinated Cysteine by O2: A Theoretical Study. J Phys Chem B 2009; 113:10916-22. [DOI: 10.1021/jp902659s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xin Li
- Department of Theoretical Chemistry, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden, Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, People’s Republic of China, and Biophysical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden, Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, People’s Republic of China, and Biophysical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Yaoquan Tu
- Department of Theoretical Chemistry, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden, Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, People’s Republic of China, and Biophysical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - He Tian
- Department of Theoretical Chemistry, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden, Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, People’s Republic of China, and Biophysical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden, Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, People’s Republic of China, and Biophysical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| |
Collapse
|
34
|
Bishop RE. Structural biology of membrane-intrinsic beta-barrel enzymes: sentinels of the bacterial outer membrane. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1778:1881-96. [PMID: 17880914 PMCID: PMC5007122 DOI: 10.1016/j.bbamem.2007.07.021] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 06/28/2007] [Accepted: 07/24/2007] [Indexed: 02/06/2023]
Abstract
The outer membranes of Gram-negative bacteria are replete with integral membrane proteins that exhibit antiparallel beta-barrel structures, but very few of these proteins function as enzymes. In Escherichia coli, only three beta-barrel enzymes are known to exist in the outer membrane; these are the phospholipase OMPLA, the protease OmpT, and the phospholipidColon, two colonslipid A palmitoyltransferase PagP, all of which have been characterized at the structural level. Structural details have also emerged for the outer membrane beta-barrel enzyme PagL, a lipid A 3-O-deacylase from Pseudomonas aeruginosa. Lipid A can be further modified in the outer membrane by two beta-barrel enzymes of unknown structure; namely, the Salmonella enterica 3'-acyloxyacyl hydrolase LpxR, and the Rhizobium leguminosarum oxidase LpxQ, which employs O(2) to convert the proximal glucosamine unit of lipid A into 2-aminogluconate. Structural biology now indicates how beta-barrel enzymes can function as sentinels that remain dormant when the outer membrane permeability barrier is intact. Host immune defenses and antibiotics that perturb this barrier can directly trigger beta-barrel enzymes in the outer membrane. The ensuing adaptive responses occur instantaneously and rapidly outpace other signal transduction mechanisms that similarly function to restore the outer membrane permeability barrier.
Collapse
Affiliation(s)
- Russell E Bishop
- Department of Biochemistry and Biomedical Sciences, 1200 Main Street West, Health Sciences Centre 4H19, McMaster University, Hamilton, ON, Canada L8N 3Z5.
| |
Collapse
|
35
|
Prosser RS, Evanics F, Kitevski JL, Patel S. The measurement of immersion depth and topology of membrane proteins by solution state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3044-51. [DOI: 10.1016/j.bbamem.2007.09.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 09/19/2007] [Accepted: 09/20/2007] [Indexed: 01/22/2023]
|
36
|
Huysmans GH, Radford SE, Brockwell DJ, Baldwin SA. The N-terminal helix is a post-assembly clamp in the bacterial outer membrane protein PagP. J Mol Biol 2007; 373:529-40. [PMID: 17868697 PMCID: PMC2887491 DOI: 10.1016/j.jmb.2007.07.072] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 07/23/2007] [Accepted: 07/29/2007] [Indexed: 12/04/2022]
Abstract
The Escherichia coli outer membrane beta-barrel enzyme PagP and its homologues are unique in that the eight-stranded barrel is tilted by about 25 degrees with respect to the membrane normal and is preceded by a 19-residue amphipathic alpha-helix. To investigate the role of this helix in the folding and stability of PagP, mutants were generated in which the helix was deleted (Delta(1-19)), or in which residues predicted to be involved in helix-barrel interactions were altered (W17A or R59L). The ability of the variants to insert into detergent micelles or liposomes was studied in vitro using circular dichroism, fluorescence, Fourier transform infrared spectroscopy, electrophoretic mobility and gain of enzyme activity. The data show that PagP, initially unfolded in 5% (w/v) perfluoro-octanoic acid or 6 M guanidinium chloride, inserts spontaneously and folds quantitatively to an active conformation into detergent micelles of cyclofos-7 or into large vesicles of diC(12:0)-phosphatidylcholine (diC(12:0)PC), respectively, the latter in the presence of 7 M urea. Successful refolding of all variants into both micelles and liposomes ruled out an essential role for the helix or helix-barrel interactions in folding and membrane insertion. Measurements of thermal stability indicated that the variants R59L, W17A/R59L and Delta(1-19) were destabilised substantially compared with wild-type PagP. However, in contrast to the other variants, destabilisation of the W17A variant relative to wild-type PagP was much greater in liposomes than in micelles. Analysis of the kinetics of folding and unfolding of all variants in diC(12:0)PC liposomes suggested that this destabilisation arises predominantly from an increased dissociation of the refolded variant proteins from the lipid-inserted state. The data support the view that the helix of PagP is not required for folding and assembly, but instead acts as a clamp, stabilising membrane-inserted PagP after folding and docking with the membrane are complete.
Collapse
Affiliation(s)
- Gerard H.M. Huysmans
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Institute of Membrane and Systems Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Stephen A. Baldwin
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Institute of Membrane and Systems Biology, University of Leeds, Leeds, LS2 9JT, UK
| |
Collapse
|
37
|
Mahalakshmi R, Franzin CM, Choi J, Marassi FM. NMR structural studies of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3216-24. [PMID: 17916325 DOI: 10.1016/j.bbamem.2007.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/01/2007] [Accepted: 08/02/2007] [Indexed: 10/22/2022]
Abstract
The beta-barrels found in the outer membranes of prokaryotic and eukaryotic organisms constitute an important functional class of proteins. Here we present solid-state NMR spectra of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. We show that OmpX is folded in both glass-supported oriented lipid bilayers and in lipid bicelles that can be magnetically oriented with the membrane plane parallel or perpendicular to the direction of the magnetic field. The presence of resolved peaks in these spectra demonstrates that OmpX undergoes rotational diffusion around an axis perpendicular to the membrane surface. A tightly hydrogen-bonded domain of OmpX resists exchange with D2O for days and is assigned to the transmembrane beta-barrel, while peaks at isotropic resonance frequencies that disappear rapidly in D2O are assigned to the extracellular and periplasmic loops. The two-dimensional 1H/15N separated local field spectra of OmpX have several resolved peaks, and agree well with the spectra calculated from the crystal structure of OmpX rotated with the barrel axis nearly parallel (5 degrees tilt) to the direction of the magnetic field. The data indicate that it will be possible to obtain site-specific resonance assignments and to determine the structure, tilt, and rotation of OmpX in membranes using the solid-state NMR methods that are currently being applied to alpha-helical membrane proteins.
Collapse
|
38
|
Respondek M, Madl T, Göbl C, Golser R, Zangger K. Mapping the orientation of helices in micelle-bound peptides by paramagnetic relaxation waves. J Am Chem Soc 2007; 129:5228-34. [PMID: 17397158 DOI: 10.1021/ja069004f] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many antimicrobial peptides form alpha-helices when bound to a membrane. In addition, around 80% of residues in membrane-bound proteins are found in alpha-helical regions. The orientation and location of such helical peptides and proteins in the membrane are key factors determining their function and activity. Here we present a new solution state NMR method for obtaining the orientation of helical peptides in a membrane-mimetic environment (micelle-bound) without any chemical perturbation of the peptide-micelle system. By monitoring proton longitudinal relaxation rates upon addition of the freely water-soluble and inert paramagnetic probe Gd(DTPA-BMA) to an alpha-helical peptide, a wavelike pattern with a periodicity of 3.6 residues per turn is observed. The tilt and azimuth (rotation) angle of the helix determine the shape of this paramagnetic relaxation wave and can be obtained by least-square fitting of measured relaxation enhancements. Results are presented for the 15-residue antimicrobial peptide CM15 which forms an amphipathic helix almost parallel to the surface of the micelle. Thus, a few fast experiments enable the identification of helical regions and determination of the helix orientation within the micelle without the need for covalent modification, isotopic labeling, or sophisticated equipment. This approach opens a path toward the topology determination of alpha-helical membrane-proteins without the need for a complete NOE-based structure determination.
Collapse
Affiliation(s)
- Michal Respondek
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | | | | | | | | |
Collapse
|
39
|
Dvinskikh SV, Dürr UHN, Yamamoto K, Ramamoorthy A. High-resolution 2D NMR spectroscopy of bicelles to measure the membrane interaction of ligands. J Am Chem Soc 2007; 129:794-802. [PMID: 17243815 PMCID: PMC2527737 DOI: 10.1021/ja065536k] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Magnetically aligned bicelles are increasingly being used as model membranes in solution- and solid-state NMR studies of the structure, dynamics, topology, and interaction of membrane-associated peptides and proteins. These studies commonly utilize the PISEMA pulse sequence to measure dipolar coupling and chemical shift, the two key parameters used in subsequent structural analysis. In the present study, we demonstrate that the PISEMA and other rotating-frame pulse sequences are not suitable for the measurement of long-range heteronuclear dipolar couplings, and that they provide inaccurate values when multiple protons are coupled to a 13C nucleus. Furthermore, we demonstrate that a laboratory-frame separated-local-field experiment is capable of overcoming these difficulties in magnetically aligned bicelles. An extension of this approach to accurately measure 13C-31P and 1H-31P couplings from phospholipids, which are useful to understand the interaction of molecules with the membrane, is also described. In these 2D experiments, natural abundance 13C was observed from bicelles containing DMPC and DHPC lipid molecules. As a first application, these solid-state NMR approaches were utilized to probe the membrane interaction of an antidepressant molecule, desipramine, and its location in the membrane.
Collapse
Affiliation(s)
| | - Ulrich H. N. Dürr
- Biophysics Research Division and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, U.S.A
| | - Kazutoshi Yamamoto
- Biophysics Research Division and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, U.S.A
| | - Ayyalusamy Ramamoorthy
- Biophysics Research Division and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, U.S.A
| |
Collapse
|
40
|
Bezsonova I, Evanics F, Marsh JA, Forman-Kay JD, Prosser RS. Oxygen as a Paramagnetic Probe of Clustering and Solvent Exposure in Folded and Unfolded States of an SH3 Domain. J Am Chem Soc 2007; 129:1826-35. [PMID: 17253684 DOI: 10.1021/ja065173o] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The N-terminal SH3 domain of the Drosophila modular protein Drk undergoes slow exchange between a folded (Fexch) and highly populated unfolded (Uexch) state under nondenaturing buffer conditions, enabling both Fexch and Uexch states to be simultaneously monitored. The addition of dissolved oxygen, equilibrated to a partial pressure of either 30 atm or 60 atm, provides the means to study solvent exposure with atomic resolution via 13C NMR paramagnetic shifts in 1H,13C HSQC (heteronuclear single quantum coherence) spectra. Absolute differences in these paramagnetic shifts between the Fexch and Uexch states allow the discrimination of regions of the protein which undergo change in solvent exposure upon unfolding. Contact with dissolved oxygen for both the Fexch and Uexch states could also be assessed through 13C paramagnetic shifts which were normalized based on the corresponding paramagnetic shifts seen in the free amino acids. In the Fexch state, the 13C nuclei belonging to the hydrophobic core of the protein exhibited very weak normalized paramagnetic shifts while those with greater solvent accessible surface area exhibited significantly larger normalized shifts. The Uexch state displayed less varied 13C paramagnetic shifts although distinct regions of protection from solvent exposure could be identified by a lack of such shifts. These regions, which included Phe9, Thr12, Ala13, Lys21, Thr22, Ile24, Ile27, and Arg38, overlapped with those found to have residual nativelike and non-native structures in previous studies and in some cases provided novel information. Thus, the paramagnetic shifts from dissolved oxygen are highly useful in the study of a transient structure or clustering in disordered systems, where conventional NMR measurements (couplings, chemical shift deviations from random coil values, and NOEs) may give little information.
Collapse
Affiliation(s)
- Irina Bezsonova
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 1A8
| | | | | | | | | |
Collapse
|
41
|
Mittag T, Forman-Kay JD. Atomic-level characterization of disordered protein ensembles. Curr Opin Struct Biol 2007; 17:3-14. [PMID: 17250999 DOI: 10.1016/j.sbi.2007.01.009] [Citation(s) in RCA: 339] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 12/21/2006] [Accepted: 01/15/2007] [Indexed: 11/25/2022]
Abstract
The roles of unfolded states of proteins in normal folding and in diseases involving aggregation, as well as the prevalence and regulatory functions of intrinsically disordered proteins, have become increasingly recognized. The structural representation of these disordered states as ensembles of interconverting conformers can therefore provide critical insights. Experimental methods can be used to probe ensemble-averaged structural properties of disordered states and computational approaches generate representative ensembles of conformers using experimental restraints. In particular, NMR and small-angle X-ray scattering provide quantitative data that can readily be incorporated into calculations. These techniques have gleaned structural information about denatured, unfolded and intrinsically disordered proteins. The use of experimental data in different computational approaches, including ensemble molecular dynamics simulations and algorithms that assign populations to pregenerated conformers, has highlighted the presence of both local and long-range structure, and the occurrence of native-like and non-native interactions in unfolded and denatured states. Analysis of the resulting ensembles has suggested important implications of this fluctuating structure for folding, aggregation and binding.
Collapse
Affiliation(s)
- Tanja Mittag
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 1X8 and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | |
Collapse
|
42
|
Abstract
The lipid A moiety of lipopolysaccharide forms the outer monolayer of the outer membrane of most gram-negative bacteria. Escherichia coli lipid A is synthesized on the cytoplasmic surface of the inner membrane by a conserved pathway of nine constitutive enzymes. Following attachment of the core oligosaccharide, nascent core-lipid A is flipped to the outer surface of the inner membrane by the ABC transporter MsbA, where the O-antigen polymer is attached. Diverse covalent modifications of the lipid A moiety may occur during its transit from the outer surface of the inner membrane to the outer membrane. Lipid A modification enzymes are reporters for lipopolysaccharide trafficking within the bacterial envelope. Modification systems are variable and often regulated by environmental conditions. Although not required for growth, the modification enzymes modulate virulence of some gram-negative pathogens. Heterologous expression of lipid A modification enzymes may enable the development of new vaccines.
Collapse
Affiliation(s)
- Christian R H Raetz
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.
| | | | | | | |
Collapse
|
43
|
Evanics F, Bezsonova I, Marsh J, Kitevski JL, Forman-Kay JD, Prosser RS. Tryptophan Solvent Exposure in Folded and Unfolded States of an SH3 Domain by 19F and 1H NMR. Biochemistry 2006; 45:14120-8. [PMID: 17115707 DOI: 10.1021/bi061389r] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The isolated N-terminal SH3 domain of the Drosophila signal transduction protein Drk (drkN SH3) is a useful model for the study of residual structure and fluctuating structure in disordered proteins since it exists in slow exchange between a folded (Fexch) and compact unfolded (Uexch) state in roughly equal proportions under nondenaturing conditions. The single tryptophan residue, Trp36, is believed to play a key role in forming a non-native hydrophobic cluster in the Uexch state, with a number of long-range nuclear Overhauser contacts (NOEs) observed primarily to the indole proton. Substitution of Trp36 for 5-fluoro-Trp36 resulted in a substantial shift in the equilibrium to favor the Fexch state. A variety of 19F NMR measurements were performed to investigate the degree of solvent exposure and hydrophobicity associated with the 5-fluoro position in both the Fexch and Uexch states. Ambient T1 measurements and H2O/D2O solvent isotope effects indicated extensive protein contacts to the 5-fluoro position in the Fexch state and greater solvent exposure in the Uexch state. This was corroborated by the measurements of paramagnetic effects (chemical shift perturbations and T1 relaxation enhancement) from dissolved oxygen at a partial pressure of 20 atm. In contrast, paramagnetic effects from dissolved oxygen revealed less solvent exposure to the indole proton of Trp36 in the Uexch state than that observed for the Fexch state, consistent with the model in which Trp36 indole belongs to a non-native cluster. Thus, although the Uexch state may be described as a dynamically interconverting ensemble of conformers, there appears to be significant asymmetry in the environment of the indole group and the six-membered ring or backbone of Trp36. This implied lack of averaging of a side chain position is in contrast to the general view of fluctuating side chains within disordered states.
Collapse
Affiliation(s)
- Ferenc Evanics
- Department of Chemistry, University of Toronto, Toronto, Canada
| | | | | | | | | | | |
Collapse
|