101
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Kashtanov S, Borcherds W, Wu H, Daughdrill GW, Ytreberg FM. Using chemical shifts to assess transient secondary structure and generate ensemble structures of intrinsically disordered proteins. Methods Mol Biol 2012; 895:139-152. [PMID: 22760318 DOI: 10.1007/978-1-61779-927-3_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The chemical shifts of backbone atoms in polypeptides are sensitive to the dihedral angles phi and psi and can be used to estimate transient secondary structure and to generate structural ensembles of intrinsically disordered proteins (IDPs). In this chapter, several of the random coil reference databases used to estimate transient secondary structure are described, and the procedure is outlined for using these databases to estimate transient secondary structure. A new protocol is also presented for generating a diverse ensemble of structures for an IDP and reweighting these structures to optimize the fit between simulated and experimental chemical shift values.
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102
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Kleckner IR, Gollnick P, Foster MP. Mechanisms of allosteric gene regulation by NMR quantification of microsecond-millisecond protein dynamics. J Mol Biol 2011; 415:372-81. [PMID: 22115774 DOI: 10.1016/j.jmb.2011.11.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 10/17/2011] [Accepted: 11/08/2011] [Indexed: 11/17/2022]
Abstract
The trp RNA-binding attenuation protein (TRAP) is a paradigmatic allosteric protein that regulates the tryptophan biosynthetic genes associated with the trp operon in bacilli. The ring-shaped 11-mer TRAP is activated for recognition of a specific trp-mRNA target by binding up to 11 tryptophan molecules. To characterize the mechanisms of tryptophan-induced TRAP activation, we have performed methyl relaxation dispersion (MRD) nuclear magnetic resonance (NMR) experiments that probe the time-dependent structure of TRAP in the microsecond-to-millisecond "chemical exchange" time window. We find significant side chain flexibility localized to the RNA and tryptophan binding sites of the apo protein and that these dynamics are dramatically reduced upon ligand binding. Analysis of the MRD NMR data provides insights into the structural nature of transiently populated conformations sampled in solution by apo TRAP. The MRD data are inconsistent with global two-state exchange, indicating that conformational sampling in apo TRAP is asynchronous. These findings imply a temporally heterogeneous population of structures that are incompatible with RNA binding and substantiate the study of TRAP as a paradigm for probing and understanding essential dynamics in allosteric, regulatory proteins.
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Affiliation(s)
- Ian R Kleckner
- Biophysics Program, Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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103
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Assembly of the complex between archaeal RNase P proteins RPP30 and Pop5. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2011; 2011:891531. [PMID: 22162665 PMCID: PMC3227427 DOI: 10.1155/2011/891531] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 08/10/2011] [Accepted: 08/17/2011] [Indexed: 01/27/2023]
Abstract
RNase P is a highly conserved ribonucleoprotein enzyme that represents a model complex for understanding macromolecular RNA-protein interactions. Archaeal RNase P consists of one RNA and up to five proteins (Pop5, RPP30, RPP21, RPP29, and RPP38/L7Ae). Four of these proteins function in pairs (Pop5-RPP30 and RPP21–RPP29). We have used nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC) to characterize the interaction between Pop5 and RPP30 from the hyperthermophilic archaeon Pyrococcus furiosus (Pfu). NMR backbone resonance assignments of free RPP30 (25 kDa) indicate that the protein is well structured in solution, with a secondary structure matching that observed in a closely related crystal structure. Chemical shift perturbations upon the addition of Pop5 (14 kDa) reveal its binding surface on RPP30. ITC experiments confirm a net 1 : 1 stoichiometry for this tight protein-protein interaction and exhibit complex isotherms, indicative of higher-order binding. Indeed, light scattering and size exclusion chromatography data reveal the complex to exist as a 78 kDa heterotetramer with two copies each of Pop5 and RPP30. These results will inform future efforts to elucidate the functional role of the Pop5-RPP30 complex in RNase P assembly and catalysis.
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104
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Tang S, Case DA. Calculation of chemical shift anisotropy in proteins. JOURNAL OF BIOMOLECULAR NMR 2011; 51:303-12. [PMID: 21866436 PMCID: PMC3196061 DOI: 10.1007/s10858-011-9556-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 08/03/2011] [Indexed: 05/24/2023]
Abstract
Individual peptide groups in proteins must exhibit some variation in the chemical shift anisotropy (CSA) of their constituent atoms, but not much is known about the extent or origins of this dispersion. Direct spectroscopic measurement of CSA remains technically challenging, and theoretical methods can help to overcome these limitations by estimating shielding tensors for arbitrary structures. Here we use an automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach to compute (15)N, (13)C' and (1)H chemical shift tensors for human ubiquitin and the GB1 and GB3 fragments of staphylococcal protein G. The average and range of variation of the anisotropies is in good agreement with experimental estimates from solid-state NMR, and the variation among residues is somewhat smaller than that estimated from solution-state measurements. Hydrogen-bond effects account for much of the variation, both between helix and sheet regions, and within elements of secondary structure, but other effects (including variations in torsion angles) may play a role as well.
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Affiliation(s)
- Sishi Tang
- Department of Chemistry and Chemical Biology, BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA
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105
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Rao JN, Warren GZL, Estolt-Povedano S, Zammit VA, Ulmer TS. An environment-dependent structural switch underlies the regulation of carnitine palmitoyltransferase 1A. J Biol Chem 2011; 286:42545-42554. [PMID: 21990363 DOI: 10.1074/jbc.m111.306951] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The enzyme carnitine palmitoyltransferase 1 (CPT1), which is anchored in the outer mitochondrial membrane (OMM), controls the rate-limiting step in fatty acid β-oxidation in mammalian tissues. It is inhibited by malonyl-CoA, the first intermediate of fatty acid synthesis, and it responds to OMM curvature and lipid characteristics, which reflect long term nutrient/hormone availability. Here, we show that the N-terminal regulatory domain (N) of CPT1A can adopt two complex amphiphilic structural states, termed Nα and Nβ, that interchange in a switch-like manner in response to offered binding surface curvature. Structure-based site-directed mutageneses of native CPT1A suggest Nα to be inhibitory and Nβ to be noninhibitory, with the relative Nα/Nβ ratio setting the prevalent malonyl-CoA sensitivity of the enzyme. Based on the amphiphilic nature of N and molecular modeling, we propose malonyl-CoA sensitivity to be coupled to the properties of the OMM by Nα-OMM associations that alter the Nα/Nβ ratio. For enzymes residing at the membrane-water interface, this constitutes an integrative regulatory mechanism of exceptional sophistication.
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Affiliation(s)
- Jampani N Rao
- Department of Biochemistry and Molecular Biology and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - Gemma Z L Warren
- Metabolic and Vascular Health Division, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Sara Estolt-Povedano
- Metabolic and Vascular Health Division, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Victor A Zammit
- Metabolic and Vascular Health Division, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Tobias S Ulmer
- Department of Biochemistry and Molecular Biology and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033.
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106
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Kang L, Wu KP, Vendruscolo M, Baum J. The A53T mutation is key in defining the differences in the aggregation kinetics of human and mouse α-synuclein. J Am Chem Soc 2011; 133:13465-70. [PMID: 21721555 DOI: 10.1021/ja203979j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite a 95% sequence similarity, the aggregation of human and mouse α-synuclein is remarkably different, as the human form is slower than the mouse form in forming fibrils but is associated with Parkinson's disease in both humans and transgenic mice. Here, the amino acid code underlying these differences is investigated by comparing the lag times, growth rates, and secondary structure propensities of a systematic series of eight human-mouse chimeras. Fluorescence analysis of these variants shows that the A53T substitution dominates the growth kinetics, while the lag phase is affected by a combination of the A53T and S87N substitutions. The secondary structure propensities derived from an NMR chemical shift analysis of the monomeric forms of the human-mouse variants enable us to establish a link between the changes in the conformational properties in the region of position 53 upon mutation and the corresponding changes in growth rates. These results suggest that the presence of an alanine residue at position 53 may be an evolutionary adaptation to minimize Parkinson's disease in humans and indicates that effective drug development efforts may be directed to target this N-terminal region of the sequence.
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Affiliation(s)
- Lijuan Kang
- Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
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107
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Cohen LS, Arshava B, Neumoin A, Becker JM, Güntert P, Zerbe O, Naider F. Comparative NMR analysis of an 80-residue G protein-coupled receptor fragment in two membrane mimetic environments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2674-84. [PMID: 21791199 DOI: 10.1016/j.bbamem.2011.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/17/2011] [Accepted: 07/12/2011] [Indexed: 01/09/2023]
Abstract
Fragments of integral membrane proteins have been used to study the physical chemical properties of regions of transporters and receptors. Ste2p(G31-T110) is an 80-residue polypeptide which contains a portion of the N-terminal domain, transmembrane domain 1 (TM1), intracellular loop 1, TM2 and part of extracellular loop 1 of the α-factor receptor (Ste2p) from Saccharomyces cerevisiae. The structure of this peptide was previously determined to form a helical hairpin in lyso-palmitoylphosphatidyl-glycerol micelles (LPPG) [1]. Herein, we perform a systematic comparison of the structure of this protein fragment in micelles and trifluoroethanol (TFE):water in order to understand whether spectra recorded in organic:aqueous medium can facilitate the structure determination in a micellar environment. Using uniformly labeled peptide and peptide selectively protonated on Ile, Val and Leu methyl groups in a perdeuterated background and a broad set of 3D NMR experiments we assigned 89% of the observable atoms. NOEs and chemical shift analysis were used to define the helical regions of the fragment. Together with constraints from paramagnetic spin labeling, NOEs were used to calculate a transiently folded helical hairpin structure for this peptide in TFE:water. Correlation of chemical shifts was insufficient to transfer assignments from TFE:water to LPPG spectra in the absence of further information.
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Affiliation(s)
- L S Cohen
- Department of Chemistry, The College of Staten Island, City University of New York, Staten Island, NY 10314, USA
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108
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Korzhnev DM, Vernon RM, Religa TL, Hansen AL, Baker D, Fersht AR, Kay LE. Nonnative interactions in the FF domain folding pathway from an atomic resolution structure of a sparsely populated intermediate: an NMR relaxation dispersion study. J Am Chem Soc 2011; 133:10974-82. [PMID: 21639149 PMCID: PMC3705915 DOI: 10.1021/ja203686t] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several all-helical single-domain proteins have been shown to fold rapidly (microsecond time scale) to a compact intermediate state and subsequently rearrange more slowly to the native conformation. An understanding of this process has been hindered by difficulties in experimental studies of intermediates in cases where they are both low-populated and only transiently formed. One such example is provided by the on-pathway folding intermediate of the small four-helix bundle FF domain from HYPA/FBP11 that is populated at several percent with a millisecond lifetime at room temperature. Here we have studied the L24A mutant that has been shown previously to form nonnative interactions in the folding transition state. A suite of Carr-Purcell-Meiboom-Gill relaxation dispersion NMR experiments have been used to measure backbone chemical shifts and amide bond vector orientations of the invisible folding intermediate that form the input restraints in calculations of atomic resolution models of its structure. Despite the fact that the intermediate structure has many features that are similar to that of the native state, a set of nonnative contacts is observed that is even more extensive than noted previously for the wild-type (WT) folding intermediate. Such nonnative interactions, which must be broken prior to adoption of the native conformation, explain why the transition from the intermediate state to the native conformer (millisecond time scale) is significantly slower than from the unfolded ensemble to the intermediate and why the L24A mutant folds more slowly than the WT.
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Affiliation(s)
- Dmitry M. Korzhnev
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Robert M. Vernon
- Department of Biochemistry, University of Washington, Box 357350, 1705 NE Pacific Street, Seattle, Washington 98195-7350, United States
| | - Tomasz L. Religa
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Alexandar L. Hansen
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David Baker
- Department of Biochemistry, University of Washington, Box 357350, 1705 NE Pacific Street, Seattle, Washington 98195-7350, United States
| | - Alan R. Fersht
- Center for Protein Engineering, Medical Research Council, Cambridge, United Kingdom
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
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109
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Ndao M, Dutta K, Bromley KM, Lakshminarayanan R, Sun Z, Rewari G, Moradian-Oldak J, Evans JS. Probing the self-association, intermolecular contacts, and folding propensity of amelogenin. Protein Sci 2011; 20:724-34. [PMID: 21351181 DOI: 10.1002/pro.603] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Amelogenins are an intrinsically disordered protein family that plays a major role in the development of tooth enamel, one of the most highly mineralized materials in nature. Monomeric porcine amelogenin possesses random coil and residual secondary structures, but it is not known which sequence regions would be conformationally attractive to potential enamel matrix targets such as other amelogenins (self-assembly), other matrix proteins, cell surfaces, or biominerals. To address this further, we investigated recombinant porcine amelogenin (rP172) using "solvent engineering" techniques to simultaneously promote native-like structure and induce amelogenin oligomerization in a manner that allows identification of intermolecular contacts between amelogenin molecules. We discovered that in the presence of 2,2,2-trifluoroethanol (TFE) significant folding transitions and stabilization occurred primarily within the N- and C-termini, while the polyproline Type II central domain was largely resistant to conformational transitions. Seven Pro residues (P2, P127, P130, P139, P154, P157, P162) exhibited conformational response to TFE, and this indicates these Pro residues act as folding enhancers in rP172. The remaining Pro residues resisted TFE perturbations and thus act as conformational stabilizers. We also noted that TFE induced rP172 self-association via the formation of intermolecular contacts involving P4-H6, V19-P33, and E40-T58 regions of the N-terminus. Collectively, these results confirm that the N- and C-termini of amelogenin are conformationally responsive and represent potential interactive sites for amelogenin-target interactions during enamel matrix mineralization. Conversely, the Pro, Gln central domain is resistant to folding and this may have important functional significance for amelogenin.
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Affiliation(s)
- Moise Ndao
- Laboratory for Chemical Physics, New York University, New York, New York 10010, USA
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110
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Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion. Proc Natl Acad Sci U S A 2011; 108:9078-83. [PMID: 21562212 DOI: 10.1073/pnas.1105682108] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use (15)N, , and (13)CO NMR R(2) relaxation dispersion to investigate spontaneous unfolding and refolding events of native apomyoglobin. Above pH 5.0, dispersion is dominated by processes involving fluctuations of the F-helix region, which is invisible in NMR spectra. Measurements of R(2) dispersion for residues contacted by the F-helix region in the native (N) structure reveal a transient state formed by local unfolding of helix F and undocking from the protein core. A similar state was detected at pH 4.75-4.95 and determined to be an on-pathway intermediate (I1) in a linear three-state unfolding scheme (N&lrarr2;I1&lrarr2;MG) leading to a transiently populated molten globule (MG) state. The slowest steps in unfolding and refolding are N → I1 (36 s(-1)) and MG → I1 (26 s(-1)), respectively. Differences in chemical shift between N and I1 are very small, except in regions adjacent to helix F, showing that their core structures are similar. Chemical shift changes between the N and MG states, obtained from R(2) dispersion, reveal that the transient MG state is structurally similar to the equilibrium MG observed previously at high temperature and low pH. Analysis of MG state chemical shifts shows the location of residual helical structure in the transient intermediate and identifies regions that unfold or rearrange into nonnative structure during the N → MG transition. The experiments also identify regions of energetic frustration that "crack" during unfolding and impede the refolding process.
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111
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Bouvignies G, Vallurupalli P, Cordes MHJ, Hansen DF, Kay LE. Measuring 1HN temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2011; 50:13-8. [PMID: 21424227 PMCID: PMC3229278 DOI: 10.1007/s10858-011-9498-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 02/22/2011] [Indexed: 05/30/2023]
Abstract
A method based on the Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated 'invisible' protein states that exchange with a 'visible' ground state on the millisecond time-scale. The utility of the approach is demonstrated with an application to an I58D mutant of the Pfl6 Cro protein that undergoes exchange between the native, folded state and a cold denatured, unfolded conformational ensemble that is populated at a level of 6% at 2.5°C. A wide distribution of amide temperature coefficients is measured for the unfolded state. The distribution is centered about -5.6 ppb/K, consistent with an absence of intra-molecular hydrogen bonds, on average. However, the large range of values (standard deviation of 2.1 ppb/K) strongly supports the notion that the unfolded state of the protein is not a true random coil polypeptide chain.
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Affiliation(s)
- Guillaume Bouvignies
- Department of Molecular Genetics, The University of Toronto, Toronto, ON, Canada
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112
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Wood GPF, Rothlisberger U. Secondary Structure Assignment of Amyloid-β Peptide Using Chemical Shifts. J Chem Theory Comput 2011; 7:1552-63. [PMID: 26610144 DOI: 10.1021/ct200156e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The distinct conformational dependence of chemical shifts caused by α-helices and β-sheets renders NMR chemical shift analysis a powerful tool for the structural determination of proteins. However, the time scale of NMR experiments can make a secondary structure assignment of highly flexible peptides or proteins, which may be converting between conformational substates, problematic. For instance the amyloid-β monomer, according to NMR chemical shifts, adopts a predominately random coil structure in aqueous solution (with <3% α-helical content). Molecular dynamics simulations, on the other hand, suggest that α-helical content can be significant (10-25%). In this paper, we explore the possible reasons for this discrepancy and show that the different results from experiments and theory are not necessarily mutually exclusive but may reflect a general problem of secondary structure assignment of conformationally flexible biomolecules.
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Affiliation(s)
- Geoffrey P F Wood
- Laboratory of Computational Chemistry and Biochemistry, BCH 4107 EPF Lausanne, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, BCH 4107 EPF Lausanne, CH-1015 Lausanne, Switzerland
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113
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Wu KP, Baum J. Backbone assignment and dynamics of human α-synuclein in viscous 2 M glucose solution. BIOMOLECULAR NMR ASSIGNMENTS 2011; 5:43-6. [PMID: 20872101 PMCID: PMC3064444 DOI: 10.1007/s12104-010-9263-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 08/02/2010] [Indexed: 05/29/2023]
Abstract
We present (1)H(N), (15)N, (13)C(α), (13)C(β) and (13)C' assignments and (15)N transverse relaxation rates (R(2)) of a Parkinson's disease-related intrinsically disordered protein, α-synuclein, in the presence of 2 M (360 g/l) glucose solution.
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Affiliation(s)
- Kuen-Phon Wu
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
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114
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Abstract
Around half of all protein structures solved nowadays using solution-state nuclear magnetic resonance (NMR) spectroscopy have been because of automated data analysis. The pervasiveness of computational approaches in general hides, however, a more nuanced view in which the full variety and richness of the field appears. This review is structured around a comparison of methods associated with three NMR observables: classical nuclear Overhauser effect (NOE) constraint gathering in contrast with more recent chemical shift and residual dipole coupling (RDC) based protocols. In each case, the emphasis is placed on the latest research, covering mainly the past 5 years. By describing both general concepts and representative programs, the objective is to map out a field in which--through the very profusion of approaches--it is all too easy to lose one's bearings.
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115
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Wishart DS. Interpreting protein chemical shift data. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:62-87. [PMID: 21241884 DOI: 10.1016/j.pnmrs.2010.07.004] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 07/29/2010] [Indexed: 05/12/2023]
Affiliation(s)
- David S Wishart
- Department of Biological Sciences, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8.
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116
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Sivertsen AC, Bayro MJ, Belenky M, Griffin RG, Herzfeld J. Solid-state NMR characterization of gas vesicle structure. Biophys J 2011; 99:1932-9. [PMID: 20858439 DOI: 10.1016/j.bpj.2010.06.041] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 05/30/2010] [Accepted: 06/07/2010] [Indexed: 11/20/2022] Open
Abstract
Gas vesicles are gas-filled buoyancy organelles with walls that consist almost exclusively of gas vesicle protein A (GvpA). Intact, collapsed gas vesicles from the cyanobacterium Anabaena flos-aquae were studied by solid-state NMR spectroscopy, and most of the GvpA sequence was assigned. Chemical shift analysis indicates a coil-α-β-β-α-coil peptide backbone, consistent with secondary-structure-prediction algorithms, and complementary information about mobility and solvent exposure yields a picture of the overall topology of the vesicle subunit that is consistent with its role in stabilizing an air-water interface.
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Affiliation(s)
- Astrid C Sivertsen
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, USA
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117
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Tamiola K, Acar B, Mulder FAA. Sequence-Specific Random Coil Chemical Shifts of Intrinsically Disordered Proteins. J Am Chem Soc 2010; 132:18000-3. [DOI: 10.1021/ja105656t] [Citation(s) in RCA: 245] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kamil Tamiola
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9749 AG Groningen, The Netherlands
| | - Burçin Acar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9749 AG Groningen, The Netherlands
| | - Frans A. A. Mulder
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9749 AG Groningen, The Netherlands
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118
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Robustelli P, Kohlhoff K, Cavalli A, Vendruscolo M. Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins. Structure 2010; 18:923-33. [PMID: 20696393 DOI: 10.1016/j.str.2010.04.016] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Revised: 03/30/2010] [Accepted: 04/22/2010] [Indexed: 10/19/2022]
Abstract
We introduce a procedure to determine the structures of proteins by incorporating NMR chemical shifts as structural restraints in molecular dynamics simulations. In this approach, the chemical shifts are expressed as differentiable functions of the atomic coordinates and used to compute forces to generate trajectories that lead to the reduction of the differences between experimental and calculated chemical shifts. We show that this strategy enables the folding of a set of proteins with representative topologies starting from partially denatured initial conformations without the use of additional experimental information. This method also enables the straightforward combination of chemical shifts with other standard NMR restraints, including those derived from NOE, J-coupling, and residual dipolar coupling measurements. We illustrate this aspect by calculating the structure of a transiently populated excited state conformation from chemical shift and residual dipolar coupling data measured by relaxation dispersion NMR experiments.
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Affiliation(s)
- Paul Robustelli
- Department of Chemistry, University of Cambridge Lensfield Road, Cambridge CB2 1EW, UK
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119
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Kleckner IR, Foster MP. An introduction to NMR-based approaches for measuring protein dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:942-68. [PMID: 21059410 DOI: 10.1016/j.bbapap.2010.10.012] [Citation(s) in RCA: 346] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 01/15/2023]
Abstract
Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Ian R Kleckner
- The Ohio State University Biophysics Program, 484 West 12th Ave Room 776, Columbus, OH 43210, USA
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120
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Abstract
The public archives containing protein information in the form of NMR chemical shift data at the BioMagResBank (BMRB) and of 3D structure coordinates at the Protein Data Bank are continuously expanding. The quality of the data contained in these archives, however, varies. The main issue for chemical shift values is that they are determined relative to a reference frequency. When this reference frequency is set incorrectly, all related chemical shift values are systematically offset. Such wrongly referenced chemical shift values, as well as other problems such as chemical shift values that are assigned to the wrong atom, are not easily distinguished from correct values and effectively reduce the usefulness of the archive. We describe a new method to correct and validate protein chemical shift values in relation to their 3D structure coordinates. This method classifies atoms using two parameters: the per-atom solvent accessible surface area (as calculated from the coordinates) and the secondary structure of the parent amino acid. Through the use of Gaussian statistics based on a large database of 3220 BMRB entries, we obtain per-entry chemical shift corrections as well as Z scores for the individual chemical shift values. In addition, information on the error of the correction value itself is available, and the method can retain only dependable correction values. We provide an online resource with chemical shift, atom exposure, and secondary structure information for all relevant BMRB entries (http://www.ebi.ac.uk/pdbe/nmr/vasco) and hope this data will aid the development of new chemical shift-based methods in NMR. Proteins 2010. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Wolfgang Rieping
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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121
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Rao JN, Jao CC, Hegde BG, Langen R, Ulmer TS. A combinatorial NMR and EPR approach for evaluating the structural ensemble of partially folded proteins. J Am Chem Soc 2010; 132:8657-68. [PMID: 20524659 DOI: 10.1021/ja100646t] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Partially folded proteins, characterized as exhibiting secondary structure elements with loose or absent tertiary contacts, represent important intermediates in both physiological protein folding and pathological protein misfolding. To aid in the characterization of the structural state(s) of such proteins, a novel structure calculation scheme is presented that combines structural restraints derived from pulsed EPR and NMR spectroscopy. The methodology is established for the protein alpha-synuclein (alphaS), which exhibits characteristics of a partially folded protein when bound to a micelle of the detergent sodium lauroyl sarcosinate (SLAS). By combining 18 EPR-derived interelectron spin label distance distributions with NMR-based secondary structure definitions and bond vector restraints, interelectron distances were correlated and a set of theoretical ensemble basis populations was calculated. A minimal set of basis structures, representing the partially folded state of SLAS-bound alphaS, was subsequently derived by back-calculating correlated distance distributions. A surprising variety of well-defined protein-micelle interactions was thus revealed in which the micelle is engulfed by two differently arranged antiparallel alphaS helices. The methodology further provided the population ratios between dominant ensemble structural states, whereas limitation in obtainable structural resolution arose from spin label flexibility and residual uncertainties in secondary structure definitions. To advance the understanding of protein-micelle interactions, the present study concludes by showing that, in marked contrast to secondary structure stability, helix dynamics of SLAS-bound alphaS correlate with the degree of protein-induced departures from free micelle dimensions.
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Affiliation(s)
- Jampani Nageswara Rao
- Department of Biochemistry & Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, California 90033, USA
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122
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Dynamic interactions between clathrin and locally structured elements in a disordered protein mediate clathrin lattice assembly. J Mol Biol 2010; 404:274-90. [PMID: 20875424 DOI: 10.1016/j.jmb.2010.09.044] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 09/17/2010] [Accepted: 09/17/2010] [Indexed: 11/22/2022]
Abstract
Assembly of clathrin lattices is mediated by assembly/adaptor proteins that contain domains that bind lipids or membrane-bound cargo proteins and clathrin binding domains (CBDs) that recruit clathrin. Here, we characterize the interaction between clathrin and a large fragment of the CBD of the clathrin assembly protein AP180. Mutational, NMR chemical shift, and analytical ultracentrifugation analyses allowed us to precisely define two clathrin binding sites within this fragment, each of which is found to bind weakly to the N-terminal domain of the clathrin heavy chain (TD). The locations of the two clathrin binding sites are consistent with predictions from sequence alignments of previously identified clathrin binding elements and, by extension, indicate that the complete AP180 CBD contains ∼12 degenerate repeats, each containing a single clathrin binding site. Sequence and circular dichroism analyses have indicated that the AP180 CBD is predominantly unstructured and our NMR analyses confirm that this is largely the case for the AP180 fragment characterized here. Unexpectedly, unlike the many proteins that undergo binding-coupled folding upon interaction with their binding partners, the AP180 fragment is similarly unstructured in its bound and free states. Instead, we find that this fragment exhibits localized β-turn-like structures at the two clathrin binding sites both when free and when bound to clathrin. These observations are incorporated into a model in which weak binding by multiple, pre-structured clathrin binding elements regularly dispersed throughout a largely unstructured CBD allows efficient recruitment of clathrin to endocytic sites and dynamic assembly of the clathrin lattice.
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123
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Butterwick JA, MacKinnon R. Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP. J Mol Biol 2010; 403:591-606. [PMID: 20851706 DOI: 10.1016/j.jmb.2010.09.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 09/04/2010] [Accepted: 09/07/2010] [Indexed: 10/19/2022]
Abstract
Voltage-sensor domains (VSDs) are specialized transmembrane segments that confer voltage sensitivity to many proteins such as ion channels and enzymes. The activities of these domains are highly dependent on both the chemical properties and the physical properties of the surrounding membrane environment. To learn about VSD-lipid interactions, we used nuclear magnetic resonance spectroscopy to determine the structure and phospholipid interface of the VSD from the voltage-dependent K(+) channel KvAP (prokaryotic Kv from Aeropyrum pernix). The solution structure of the KvAP VSD solubilized within phospholipid micelles is similar to a previously determined crystal structure solubilized by a nonionic detergent and complexed with an antibody fragment. The differences observed include a previously unidentified short amphipathic α-helix that precedes the first transmembrane helix and a subtle rigid-body repositioning of the S3-S4 voltage-sensor paddle. Using (15)N relaxation experiments, we show that much of the VSD, including the pronounced kink in S3 and the S3-S4 paddle, is relatively rigid on the picosecond-to-nanosecond timescale. In contrast, the kink in S3 is mobile on the microsecond-to-millisecond timescale and may act as a hinge in the movement of the paddle during channel gating. We characterized the VSD-phospholipid micelle interactions using nuclear Overhauser effect spectroscopy and showed that the micelle uniformly coats the KvAP VSD and approximates the chemical environment of a phospholipid bilayer. Using paramagnetically labeled phospholipids, we show that bilayer-forming lipids interact with the S3 and S4 helices more strongly than with S1 and S2.
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Affiliation(s)
- Joel A Butterwick
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.
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124
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Korzhnev DM, Religa TL, Banachewicz W, Fersht AR, Kay LE. A Transient and Low-Populated Protein-Folding Intermediate at Atomic Resolution. Science 2010; 329:1312-6. [DOI: 10.1126/science.1191723] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Proteins can sample conformational states that are critical for function but are seldom detected directly because of their low occupancies and short lifetimes. In this work, we used chemical shifts and bond-vector orientation constraints obtained from nuclear magnetic resonance relaxation dispersion spectroscopy, in concert with a chemical shift–based method for structure elucidation, to determine an atomic-resolution structure of an “invisible” folding intermediate of a small protein module: the FF domain. The structure reveals non-native elements preventing formation of the native conformation in the carboxyl-terminal part of the protein. This is consistent with the kinetics of folding in which a well-structured intermediate forms rapidly and then rearranges slowly to the native state. The approach introduces a general strategy for structure determination of low-populated and transiently formed protein states.
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125
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Shen Y, Bax A. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. JOURNAL OF BIOMOLECULAR NMR 2010; 48:13-22. [PMID: 20628786 PMCID: PMC2935510 DOI: 10.1007/s10858-010-9433-9] [Citation(s) in RCA: 398] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 06/30/2010] [Indexed: 05/02/2023]
Abstract
NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and (13)C(beta) chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and (13)C(beta) atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for delta(15)N, delta(13)C', delta(13)C(alpha), delta(13)C(beta), delta(1)H(alpha) and delta(1)H(N), respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.
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Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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126
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Shenkarev ZO, Paramonov AS, Lyukmanova EN, Shingarova LN, Yakimov SA, Dubinnyi MA, Chupin VV, Kirpichnikov MP, Blommers MJJ, Arseniev AS. NMR structural and dynamical investigation of the isolated voltage-sensing domain of the potassium channel KvAP: implications for voltage gating. J Am Chem Soc 2010; 132:5630-7. [PMID: 20356312 DOI: 10.1021/ja909752r] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure and dynamics of the isolated voltage-sensing domain (VSD) of the archaeal potassium channel KvAP was studied by high-resolution NMR. The almost complete backbone resonance assignment and partial side-chain assignment of the (2)H,(13)C,(15)N-labeled VSD were obtained for the protein domain solubilized in DPC/LDAO (2:1) mixed micelles. Secondary and tertiary structures of the VSD were characterized using secondary chemical shifts and NOE contacts. These data indicate that the spatial structure of the VSD solubilized in micelles corresponds to the structure of the domain in an open state of the channel. NOE contacts and secondary chemical shifts of amide protons indicate the presence of tightly bound water molecule as well as hydrogen bond formation involving an interhelical salt bridge (Asp62-R133) that stabilizes the overall structure of the domain. The backbone dynamics of the VSD was studied using (15)N relaxation measurements. The loop regions S1-S2 and S2-S3 were found mobile, while the S3-S4 loop (voltage-sensor paddle) was found stable at the ps-ns time scale. The moieties of S1, S2, S3, and S4 helices sharing interhelical contacts (at the level of the Asp62-R133 salt bridge) were observed in conformational exchange on the micros-ms time scale. Similar exchange-induced broadening of characteristic resonances was observed for the VSD solubilized in the membrane of lipid-protein nanodiscs composed of DMPC, DMPG, and POPC/DOPG lipids. Apparently, the observed interhelical motions represent an inherent property of the VSD of the KvAP channel and can play an important role in the voltage gating.
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Affiliation(s)
- Zakhar O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia.
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127
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Saitô H, Ando I, Ramamoorthy A. Chemical shift tensor - the heart of NMR: Insights into biological aspects of proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:181-228. [PMID: 20633363 PMCID: PMC2905606 DOI: 10.1016/j.pnmrs.2010.04.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/26/2010] [Indexed: 05/19/2023]
Affiliation(s)
- Hazime Saitô
- Department of Life Science, Himeji Institute of Technology, University of Hyogo, Kamigori, Hyog, 678-1297, Japan
| | - Isao Ando
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, 152-0033, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
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128
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Kumar N, Kishore R. Determination of an unusual secondary structural element in the immunostimulating tetrapeptide rigin in aqueous environments: insights via MD simulations, 1
H NMR and CD spectroscopic studies. J Pept Sci 2010; 16:456-64. [DOI: 10.1002/psc.1260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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129
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Nunes AM, Zavitsanos K, Del Conte R, Malandrinos G, Hadjiliadis N. The Possible Role of 94−125 Peptide Fragment of Histone H2B in Nickel-Induced Carcinogenesis. Inorg Chem 2010; 49:5658-68. [DOI: 10.1021/ic1005665] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ana Mónica Nunes
- Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Kimon Zavitsanos
- Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Rebecca Del Conte
- Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 0019, Sesto Fiorentino, Italy
| | | | - Nick Hadjiliadis
- Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
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130
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Gortari ID, Portella G, Salvatella X, Bajaj VS, van der Wel PCA, Yates JR, Segall MD, Pickard CJ, Payne MC, Vendruscolo M. Time Averaging of NMR Chemical Shifts in the MLF Peptide in the Solid State. J Am Chem Soc 2010; 132:5993-6000. [DOI: 10.1021/ja9062629] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Itzam De Gortari
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Guillem Portella
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Xavier Salvatella
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Vikram S. Bajaj
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Patrick C. A. van der Wel
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Jonathan R. Yates
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Matthew D. Segall
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Chris J. Pickard
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Mike C. Payne
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
| | - Michele Vendruscolo
- TCM Group, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge CB3 0HE, United Kingdom, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Boston Massachusetts 02139
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131
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Markwick PRL, Cervantes CF, Abel BL, Komives EA, Blackledge M, McCammon JA. Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc 2010; 132:1220-1. [PMID: 20063881 PMCID: PMC2812018 DOI: 10.1021/ja9093692] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate 1HN, 15N, 13Cα, 13Cβ, and 13C′ chemical shifts of the ankyrin repeat protein IκBα (residues 67−206), the primary inhibitor of nuclear factor κ-B (NF-κB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the 15N, 13Cα, and 13Cβ nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range.
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Affiliation(s)
- Phineus R L Markwick
- Department of Chemistry and Biochemistry, University of California, San Diego, USA.
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132
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Galdiero S, Falanga A, Vitiello M, Raiola L, Russo L, Pedone C, Isernia C, Galdiero M. The presence of a single N-terminal histidine residue enhances the fusogenic properties of a Membranotropic peptide derived from herpes simplex virus type 1 glycoprotein H. J Biol Chem 2010; 285:17123-36. [PMID: 20348105 DOI: 10.1074/jbc.m110.114819] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Herpes simplex virus type 1 (HSV-1)-induced membrane fusion remains one of the most elusive mechanisms to be deciphered in viral entry. The structure resolution of glycoprotein gB has revealed the presence of fusogenic domains in this protein and pointed out the key role of gB in the entry mechanism of HSV-1. A second putative fusogenic glycoprotein is represented by the heterodimer comprising the membrane-anchored glycoprotein H (gH) and the small secreted glycoprotein L, which remains on the viral envelope in virtue of its non-covalent interaction with gH. Different domains scattered on the ectodomain of HSV-1 gH have been demonstrated to display membranotropic characteristics. The segment from amino acid 626 to 644 represents the most fusogenic region identified by studies with synthetic peptides and model membranes. Herein we have identified the minimal fusogenic sequence present on gH. An enlongation at the N terminus of a single histidine (His) has proved to profoundly increase the fusogenic activity of the original sequence. Nuclear magnetic resonance (NMR) studies have shown that the addition of the N-terminal His contributes to the formation and stabilization of an alpha-helical domain with high fusion propensity.
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Affiliation(s)
- Stefania Galdiero
- Department of Experimental Medicine, II University of Naples, Via De Crecchio 7, Napoli 80138, Italy.
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133
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Mori M, Kateb F, Bodenhausen G, Piccioli M, Abergel D. Toward Structural Dynamics: Protein Motions Viewed by Chemical Shift Modulations and Direct Detection of C′N Multiple-Quantum Relaxation. J Am Chem Soc 2010; 132:3594-600. [DOI: 10.1021/ja9103556] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mirko Mori
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 3, 50019 Sesto Fiorentino, Italy, Laboratoire des Biomolécules, associé au CNRS, Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, 1015 Lausanne, Switzerland
| | - Fatiha Kateb
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 3, 50019 Sesto Fiorentino, Italy, Laboratoire des Biomolécules, associé au CNRS, Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, 1015 Lausanne, Switzerland
| | - Geoffrey Bodenhausen
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 3, 50019 Sesto Fiorentino, Italy, Laboratoire des Biomolécules, associé au CNRS, Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, 1015 Lausanne, Switzerland
| | - Mario Piccioli
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 3, 50019 Sesto Fiorentino, Italy, Laboratoire des Biomolécules, associé au CNRS, Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, 1015 Lausanne, Switzerland
| | - Daniel Abergel
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 3, 50019 Sesto Fiorentino, Italy, Laboratoire des Biomolécules, associé au CNRS, Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, 1015 Lausanne, Switzerland
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134
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Castañeda CA, Fitch CA, Majumdar A, Khangulov V, Schlessman JL, García-Moreno BE. Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease. Proteins 2010; 77:570-88. [PMID: 19533744 DOI: 10.1002/prot.22470] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Prior computational studies of the acid-unfolding behavior of staphylococcal nuclease (SNase) suggest that the pK(a) values of its carboxylic groups are difficult to reproduce with electrostatics calculations with continuum methods. To examine the molecular determinants of the pK(a) values of carboxylic groups in SNase, the pK(a) values of all 20 Asp and Glu residues were measured with multidimensional and multinuclear NMR spectroscopy in an acid insensitive variant of SNase. The crystal structure of the protein was obtained to describe the microenvironments of the carboxylic groups. Fourteen Asp and Glu residues titrate with relatively normal pK(a) values that are depressed by less than 1.1 units relative to the normal pK(a) of Asp and Glu in water. Only six residues have pK(a) values shifted by more than 1.5 units. Asp-21 has an unusually high pK(a) of 6.5, which is probably the result of interactions with other carboxylic groups at the active site. The most perturbed pK(a) values appear to be governed by hydrogen bonding and not by Coulomb interactions. The pK(a) values calculated with standard continuum electrostatics methods applied to static structures are more depressed than the measured values because Coulomb effects are exaggerated in the calculations. The problems persist even when the protein is treated with the dielectric constant of water. This can be interpreted to imply that structural relaxation is an important determinant of the pK(a) values; however, no major pH-sensitive conformational reorganization of the backbone was detected using NMR spectroscopy.
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Affiliation(s)
- Carlos A Castañeda
- Department of Biophysics, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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135
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Cheung MS, Maguire ML, Stevens TJ, Broadhurst RW. DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 202:223-33. [PMID: 20015671 DOI: 10.1016/j.jmr.2009.11.008] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 11/04/2009] [Accepted: 11/13/2009] [Indexed: 05/05/2023]
Abstract
This paper introduces DANGLE, a new algorithm that employs Bayesian inference to estimate the likelihood of all possible values of the backbone dihedral angles phi and psi for each residue in a query protein, based on observed chemical shifts and the conformational preferences of each amino acid type. The method provides robust estimates of phi and psi within realistic boundary ranges, an indication of the degeneracy in the relationship between shift measurements and conformation at each site, and faithful secondary structure state assignments. When a simple degeneracy-based filtering procedure is applied, DANGLE offers an ideal compromise between accuracy and coverage when compared with other shift-based dihedral angle prediction methods. In addition, per residue analysis of shift/structure degeneracy has potential to be a useful new approach for studying the properties of unfolded proteins, with sufficient sensitivity to identify regions of residual structure in the acid denatured state of apomyoglobin.
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Affiliation(s)
- Ming-Sin Cheung
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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136
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Sharma AK, Ling Y, Greer AB, Hafler DA, Kent SC, Zhang Y, Rigby AC. Evaluating the intrinsic cysteine redox-dependent states of the A-chain of human insulin using NMR spectroscopy, quantum chemical calculations, and mass spectrometry. J Phys Chem B 2010; 114:585-91. [PMID: 19954153 DOI: 10.1021/jp908729h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous functional studies have proposed that solution-phase loading of human insulin A-chain peptides into cell surface Class II molecules may be limited by the redox state of intrinsic cysteine residues within the A-chain peptide. T cell functional studies of a human insulin A-chain analogue (KR A1-15) comprised of residues 1-15 of the A-chain peptide as well as an amino-terminal lysine-arginine extension have been carried out in a reducing environment. These data suggest that free thiol moieties within this peptide may participate in major histocompatibility complex (MHC) II/peptide interactions. Two-dimensional (1)H NMR spectroscopy data partnered with quantum chemical calculations identified that KR A1-15 exists in conformational flux sampling heterogeneous redox-dependent conformations including: one reduced and two oxidized states. These findings were further supported by mass spectrometry analysis of this peptide that confirmed the presence of a redox state dependent conformational equilibrium. Interestingly, the presence of a free thiol ((1)H(gamma)) resonance for cysteine 8 in the oxidized state supports the existence of the third redox-dependent conformation represented as a mixed disulfide conformation. We believe these data support the presence of a redox-dependent mechanism for regulating the activity of human insulin and provide a better understanding of redox chemistry that may be extended to other protein systems.
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Affiliation(s)
- Alok K Sharma
- Center for Vascular Biology Research, Division of Molecular and Vascular Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
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137
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Gely S, Lowry DF, Bernard C, Jensen MR, Blackledge M, Costanzo S, Bourhis JM, Darbon H, Daughdrill G, Longhi S. Solution structure of the C-terminal X domain of the measles virus phosphoprotein and interaction with the intrinsically disordered C-terminal domain of the nucleoprotein. J Mol Recognit 2010; 23:435-47. [DOI: 10.1002/jmr.1010] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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138
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Nunes AM, Zavitsanos K, Malandrinos G, Hadjiliadis N. Coordination of Cu2+and Ni2+ with the histone model peptide of H2B N-terminal tail (1-31 residues): A spectroscopic study. Dalton Trans 2010; 39:4369-81. [DOI: 10.1039/b927157k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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139
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Abstract
The main drawback of protein NMR spectroscopy today is still the extensive amount of time required for solving a single structure. The main bottleneck in this respect is the manual evaluation of the experimental spectra. A clear solution to this challenge is the development of automated methods for this purpose. At the current stage of development, this goal has been almost or in a few cases fully reached for favorable cases such as well-behaved, stably folding smaller proteins below the 25 kDa range. For larger and/or more difficult molecules, the input of a human expert is still required. However, even here, automated routines will substantially speed up the structure determination process. In this report, we will summarize recent developments in this field and especially emphasize practical aspects important for a successful automated protein structure determination in solution. An important aspect closely related to structure determination is structure validation. Therefore, we devote a section to automated approaches for this topic.
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Affiliation(s)
- Wolfram Gronwald
- Institute for Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
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140
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Lehtivarjo J, Hassinen T, Korhonen SP, Peräkylä M, Laatikainen R. 4D prediction of protein (1)H chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2009; 45:413-26. [PMID: 19876601 DOI: 10.1007/s10858-009-9384-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 10/09/2009] [Indexed: 05/11/2023]
Abstract
A 4D approach for protein (1)H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6-7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Halpha and HN shifts, respectively. However, for individual proteins the RMS errors were 0.17-0.34 and 0.34-0.65 ppm for the Halpha and HN shifts, respectively. X-ray structures gave better predictions than the corresponding NMR structures, indicating that chemical shifts contain invaluable information about local structures. The (1)H chemical shift prediction tool 4DSPOT is available from http://www.uku.fi/kemia/4dspot .
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Affiliation(s)
- Juuso Lehtivarjo
- Department of Biosciences, University of Kuopio, Kuopio, Finland.
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141
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Lundström P, Vallurupalli P, Hansen DF, Kay LE. Isotope labeling methods for studies of excited protein states by relaxation dispersion NMR spectroscopy. Nat Protoc 2009; 4:1641-8. [PMID: 19876024 DOI: 10.1038/nprot.2009.118] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The utility of nuclear magnetic resonance (NMR) spectroscopy as a tool for the study of biomolecular structure and dynamics has benefited from the development of facile labeling methods that incorporate NMR active probes at key positions in the molecule. Here we describe a protocol for the labeling of proteins that facilitates their study using a technique that is sensitive to millisecond conformational exchange processes. The samples necessary for an analysis of exchange dynamics are discussed, using the Abp1p SH3 domain from Saccharomyces cerevisiae as an example. For this system, the time frame for production of each sample, including in vitro refolding, is about 80 h. The samples so produced facilitate the measurement of accurate chemical shifts of low populated, invisible conformers that are part of the exchange pathway. The accuracy of the methodology has been established experimentally and the chemical shifts that are obtained provide important restraints in structure calculations of the excited state.
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Affiliation(s)
- Patrik Lundström
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
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142
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Kameda A, Morita EH, Sakurai K, Naiki H, Goto Y. NMR-based characterization of a refolding intermediate of beta2-microglobulin labeled using a wheat germ cell-free system. Protein Sci 2009; 18:1592-601. [PMID: 19606503 DOI: 10.1002/pro.179] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In patients with dialysis-related amyloidosis, beta2-microglobulin (beta2-m) is a major structural component of amyloid fibrils. It has been suggested that the partial unfolding of beta2-m is a prerequisite to the formation of amyloid fibrils, and that the folding intermediate trapped by the non-native trans-Pro32 isomer leads to the formation of amyloid fibrils. Although clarifying the structure of this refolding intermediate by high resolution NMR spectroscopy is important, this has been made difficult by the limited lifetime of the intermediate. Here, we studied the structure of the refolding intermediate using a combination of amino acid selective labeling with wheat germ cell-free protein synthesis and NMR techniques. The HSQC spectra of beta2-ms labeled selectively at either phenylalanine, leucine, or valine enabled us to monitor the structures of the refolding intermediate. The results suggested that the refolding intermediate has an overall fold and cores similar to the native structure, but contains disordered structures around Pro32. The fluctuation of the beta-sheet regions especially the last half of the betaB strand and the first half of the betaE strand, both suggested to be important for amyloidogenicity, may transform beta2-m into an amyloidogenic structure.
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Affiliation(s)
- Atsushi Kameda
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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143
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Kruschel D, Zagrovic B. Conformational averaging in structural biology: issues, challenges and computational solutions. MOLECULAR BIOSYSTEMS 2009; 5:1606-16. [PMID: 20023721 DOI: 10.1039/b917186j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Most experimental methods in structural biology provide time- and ensemble-averaged signals and, consequently, molecular structures based on such signals often exhibit only idealized, average features. Second, most experimental signals are only indirectly related to real, molecular geometries, and solving a structure typically involves a complicated procedure, which may not always result in a unique solution. To what extent do such conformationally-averaged, non-linear experimental signals and structural models derived from them accurately represent the underlying microscopic reality? Are there some structural motifs that are actually artificially more likely to be "seen" in an experiment simply due to the averaging artifact? Finally, what are the practical consequences of ignoring the averaging effects when it comes to functional and mechanistic implications that we try to glean from experimentally-based structural models? In this review, we critically address the work that has been aimed at studying such questions. We summarize the details of experimental methods typically used in structural biology (most notably nuclear magnetic resonance, X-ray crystallography and different types of spectroscopy), discuss their individual susceptibility to conformational (motional) averaging, and review several theoretical approaches, most importantly molecular dynamics simulations that are increasingly being used to aid experimentalists in interpreting structural biology experiments.
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Affiliation(s)
- Daniela Kruschel
- Laboratory of Computational Biophysics, Mediterranean Institute for Life Sciences, Mestrovicevo setaliste bb, Split, HR-21000, Croatia
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144
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González-Ruiz D, Gohlke H. Steering Protein−Ligand Docking with Quantitative NMR Chemical Shift Perturbations. J Chem Inf Model 2009; 49:2260-71. [DOI: 10.1021/ci900188r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Domingo González-Ruiz
- Fachbereich Biowissenschaften, Molekulare Bioinformatik, Goethe-Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany, and Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität, Universitätstrasse 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Fachbereich Biowissenschaften, Molekulare Bioinformatik, Goethe-Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany, and Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität, Universitätstrasse 1, 40225 Düsseldorf, Germany
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145
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Wittlich M, Thiagarajan P, Koenig BW, Hartmann R, Willbold D. NMR structure of the transmembrane and cytoplasmic domains of human CD4 in micelles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:122-7. [PMID: 19781520 DOI: 10.1016/j.bbamem.2009.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 08/31/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
Abstract
The human cluster determinant 4 (CD4) is a type I transmembrane glycoprotein involved in T-cell signalling. It is expressed primarily on the surface of T helper cells but also on subsets of memory and regulatory T lymphocytes (CD4(+) cells). It serves as a coreceptor in T-cell receptor recognition of MHC II antigen complexes. Besides its cellular functions, CD4 serves as the main receptor for human immunodeficiency virus type I (HIV-1). During T-cell infection, the CD4 extracellular domain is bound by HIV-1 gp120, the viral surface glycoprotein, which triggers a number of conformational changes ultimately resulting in virion entry of the cell. Subsequently, CD4 is downregulated in infected cells by multiple strategies that involve direct interactions of the HIV-1 proteins VpU and Nef with the cytoplasmic part of CD4. In the present work, we describe the NOE-based solution structure of the transmembrane and cytoplasmic domains of the cystein-free variant of CD4 (CD4mut) in dodecylphosphocholine (DPC) micelles. Furthermore, we have characterized micelle-inserted CD4mut by paramagentic relaxation enhancement (PRE) agents and (1)H-(15)N heteronuclear NOE data. CD4mut features a stable and well-defined transmembrane helix from M372 to V395 buried in the micellar core and a cytoplasmic helix ranging from A404 to L413. Experimental data suggest the amphipathic cytoplasmic helix to be in close contact with the micellar surface. The role of the amphipathic helix and its interaction with the micellar surface is discussed with respect to the biological function of the full-length CD4 protein.
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Affiliation(s)
- Marc Wittlich
- Forschungszentrum Jülich, Institut für Strukturbiochemie (ISB-3), 52425 Jülich, Germany
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146
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Kohlhoff KJ, Robustelli P, Cavalli A, Salvatella X, Vendruscolo M. Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances. J Am Chem Soc 2009; 131:13894-5. [DOI: 10.1021/ja903772t] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kai J. Kohlhoff
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Paul Robustelli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Andrea Cavalli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Xavier Salvatella
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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147
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Pup, a prokaryotic ubiquitin-like protein, is an intrinsically disordered protein. Biochem J 2009; 422:207-15. [DOI: 10.1042/bj20090738] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pup (prokaryotic ubiquitin-like protein) from Mycobacterium tuberculosis is the first ubiquitin-like protein identified in non-eukaryotic cells. Although different ubiquitin-like proteins from eukaryotes share low sequence similarity, their 3D (three-dimensional) structures exhibit highly conserved typical ubiquitin-like folds. Interestingly, our studies reveal that Pup not only shares low sequence similarity, but also presents a totally distinguished structure compared with other ubiquitin-like superfamily proteins. Diverse structure predictions combined with CD and NMR spectroscopic studies all demonstrate that Pup is an intrinsically disordered protein. Moreover, 1H-15N NOE (nuclear Overhauser effect) data and CSI (chemical shift index) analyses indicate that there is a residual secondary structure at the C-terminus of Pup. In M. tuberculosis, Mpa (mycobacterium proteasomal ATPase) is the regulatory cap ATPase of the proteasome that interacts with Pup and brings the substrates to the proteasome for degradation. In the present paper, SPR (surface plasmon resonance) and NMR perturbation studies imply that the C-terminus of Pup, ranging from residues 30 to 59, binds to Mpa probably through a hydrophobic interface. In addition, phylogenetic analysis clearly shows that the Pup family belongs to a unique and divergent evolutionary branch, suggesting that it is the most ancient and deeply branched family among ubiquitin-like proteins. This might explain the structural distinction between Pup and other ubiquitin-like superfamily proteins.
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148
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Hu KN, Havlin RH, Yau WM, Tycko R. Quantitative determination of site-specific conformational distributions in an unfolded protein by solid-state nuclear magnetic resonance. J Mol Biol 2009; 392:1055-73. [PMID: 19647001 DOI: 10.1016/j.jmb.2009.07.073] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 06/27/2009] [Accepted: 07/25/2009] [Indexed: 10/20/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) techniques are used to investigate the structure of the 35-residue villin headpiece subdomain (HP35) in folded, partially denatured, and fully denatured states. Experiments are carried out in frozen glycerol/water solutions, with chemical denaturation by guanidine hydrochloride (GdnHCl). Without GdnHCl, two-dimensional solid-state (13)C NMR spectra of samples prepared with uniform (13)C labeling of selected residues show relatively sharp cross-peaks at chemical shifts that are consistent with the known three-helix bundle structure of folded HP35. At high GdnHCl concentrations, most cross-peaks broaden and shift, qualitatively indicating disruption of the folded structure and development of static conformational disorder in the frozen denatured state. Conformational distributions at one residue in each helical segment are probed quantitatively with three solid-state NMR techniques that provide independent constraints on backbone varphi and psi torsion angles in samples with sequential pairs of carbonyl (13)C labels. Without GdnHCl, the combined data are well fit by alpha-helical conformations. At [GdnHCl]=4.5 M, corresponding to the approximate denaturation midpoint, the combined data are well fit by a combination of alpha-helical and partially extended conformations at each site, but with a site-dependent population ratio. At [GdnHCl]=7.0 M, corresponding to the fully denatured state, the combined data are well fit by a combination of partially extended and polyproline II conformations, again with a site-dependent population ratio. Two entirely different models for conformational distributions lead to nearly the same best-fit distributions, demonstrating the robustness of these conclusions. This work represents the first quantitative investigation of site-specific conformational distributions in partially folded and unfolded states of a protein by solid-state NMR.
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Affiliation(s)
- Kan-Nian Hu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 112, Bethesda, MD 20892-0520, USA
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149
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Auer R, Neudecker P, Muhandiram DR, Lundström P, Hansen DF, Konrat R, Kay LE. Measuring the Signs of 1Hα Chemical Shift Differences Between Ground and Excited Protein States by Off-Resonance Spin-Lock R1ρ NMR Spectroscopy. J Am Chem Soc 2009; 131:10832-3. [DOI: 10.1021/ja904315m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Renate Auer
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, A-1030 Vienna, Austria, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Molecular Biotechnology/IFM, Linköping University, SE-581 83 Linköping, Sweden
| | - Philipp Neudecker
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, A-1030 Vienna, Austria, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Molecular Biotechnology/IFM, Linköping University, SE-581 83 Linköping, Sweden
| | - D. Ranjith Muhandiram
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, A-1030 Vienna, Austria, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Molecular Biotechnology/IFM, Linköping University, SE-581 83 Linköping, Sweden
| | - Patrik Lundström
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, A-1030 Vienna, Austria, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Molecular Biotechnology/IFM, Linköping University, SE-581 83 Linköping, Sweden
| | - D. Flemming Hansen
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, A-1030 Vienna, Austria, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Molecular Biotechnology/IFM, Linköping University, SE-581 83 Linköping, Sweden
| | - Robert Konrat
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, A-1030 Vienna, Austria, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Molecular Biotechnology/IFM, Linköping University, SE-581 83 Linköping, Sweden
| | - Lewis E. Kay
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, A-1030 Vienna, Austria, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Molecular Biotechnology/IFM, Linköping University, SE-581 83 Linköping, Sweden
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150
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Abildgaard J, Hansen PE, Manalo MN, LiWang A. Deuterium isotope effects on 15N backbone chemical shifts in proteins. JOURNAL OF BIOMOLECULAR NMR 2009; 44:119-26. [PMID: 19455282 PMCID: PMC2697368 DOI: 10.1007/s10858-009-9316-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 04/06/2009] [Indexed: 05/09/2023]
Abstract
Quantum mechanical calculations are presented that predict that one-bond deuterium isotope effects on the (15)N chemical shift of backbone amides of proteins, (1)Delta(15)N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for (1)Delta(15)N(D) including the backbone dihedral angles, Phi and Psi, and the hydrogen bonding geometry is presented for glycine and amino acid residues with aliphatic side chains. The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N-H bond length. Another contributing factor is the effect of increased anharmonicity of the N-H stretching vibrational state upon hydrogen bonding, which results in an altered N-H/N-D equilibrium bond length ratio. The N-H stretching anharmonicity contribution falls off with the cosine of the N-H...O bond angle. For residues with uncharged side chains a very good prediction of isotope effects can be made. Thus, for proteins with known secondary structures, (1)Delta(15)N(D) can provide insights into hydrogen bonding geometries.
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Affiliation(s)
- Jens Abildgaard
- Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark
| | - Poul Erik Hansen
- Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark
| | - Marlon N. Manalo
- Department of Chemistry & Biochemistry, UC San Diego, La Jolla, CA USA
| | - Andy LiWang
- School of Natural Sciences, UC Merced, Merced, CA USA
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