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Rua AJ, Alexandrescu AT. Formerly degenerate seventh zinc finger domain from transcription factor ZNF711 rehabilitated by experimental NMR structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.588434. [PMID: 38645208 PMCID: PMC11030341 DOI: 10.1101/2024.04.06.588434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Domain Z7 of nuclear transcription factor ZNF711 has the consensus last metal-ligand H23 found in odd-numbered zinc-fingers of this protein replaced by a phenylalanine. Ever since the discovery of ZNF711 it has been thought that Z7 is probably non-functional because of the H23F substitution. The presence of H26 three positions downstream prompted us to examine if this histidine could substitute as the last metal ligand. The Z7 domain adopts a stable tertiary structure upon metal binding. The NMR structure of Zn2+-bound Z7 shows the classical ββα-fold of CCHH zinc fingers. Mutagenesis and pH titration experiments indicate that H26 is not involved in metal binding and that Z7 has a tridentate metal-binding site comprised of only residues C3, C6, and H19. By contrast, an F23H mutation that introduces a histidine in the consensus position forms a tetradentate ligand. The structure of the WT Z7 is stable causing restricted ring-flipping of phenyalanines 10 and 23. Dynamics are increased with either the H26A or F23H substitutions and aromatic ring rotation is no longer hindered in the two mutants. The mutations have only small effects on the Kd values for Zn2+ and Co2+ and retain the high thermal stability of the WT domain above 80 °C. Like two previously reported designed zinc fingers with the last ligand replaced by water, the WT Z7 domain is catalytically active, hydrolyzing 4-nitophenyl acetate. We discuss the implications of naturally occurring tridentate zinc fingers for cancer mutations and drug targeting of notoriously undruggable transcription factors. Our findings that Z7 can fold with only a subset of three metal ligands suggests the recent view that most everything about protein structure can be predicted through homology modeling might be premature for at least the resilient and versatile zinc-finger motif.
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Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut
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2
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Adams Z, Silvestri AP, Chiorean S, Flood DT, Balo BP, Shi Y, Holcomb M, Walsh SI, Maillie CA, Pierens GK, Forli S, Rosengren KJ, Dawson PE. Stretching Peptides to Generate Small Molecule β-Strand Mimics. ACS CENTRAL SCIENCE 2023; 9:648-656. [PMID: 37122474 PMCID: PMC10141592 DOI: 10.1021/acscentsci.2c01462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Indexed: 05/03/2023]
Abstract
Advances in the modulation of protein-protein interactions (PPIs) enable both characterization of PPI networks that govern diseases and design of therapeutics and probes. The shallow protein surfaces that dominate PPIs are challenging to target using standard methods, and approaches for accessing extended backbone structures are limited. Here, we incorporate a rigid, linear, diyne brace between side chains at the i to i+2 positions to generate a family of low-molecular-weight, extended-backbone peptide macrocycles. NMR and density functional theory studies show that these stretched peptides adopt stable, rigid conformations in solution and can be tuned to explore extended peptide conformational space. The diyne brace is formed in excellent conversions (>95%) and amenable to high-throughput synthesis. The minimalist structure-inducing tripeptide core (<300 Da) is amenable to further synthetic elaboration. Diyne-braced inhibitors of bacterial type 1 signal peptidase demonstrate the utility of the technique.
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Affiliation(s)
- Zoë
C. Adams
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Anthony P. Silvestri
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Unnatural
Products, Inc., 2161
Delaware Ave, Suite A., Santa Cruz, California 95060, United States
| | - Sorina Chiorean
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Brian P. Balo
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yifan Shi
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Matthew Holcomb
- Department
of Integrated Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shawn I. Walsh
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Colleen A. Maillie
- Department
of Integrated Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gregory K. Pierens
- Centre
for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stefano Forli
- Department
of Integrated Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - K. Johan Rosengren
- Institute
for Molecular Bioscience and School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Philip E. Dawson
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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3
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Kaplan AR, Kaus K, De S, Olson R, Alexandrescu AT. NMR structure of the Bacillus cereus hemolysin II C-terminal domain reveals a novel fold. Sci Rep 2017; 7:3277. [PMID: 28607368 PMCID: PMC5468326 DOI: 10.1038/s41598-017-02917-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/20/2017] [Indexed: 11/09/2022] Open
Abstract
In addition to multiple virulence factors, Bacillus cereus a pathogen that causes food poisoning and life-threatening wound infections, secretes the pore-forming toxin hemolysin II (HlyII). The HlyII toxin has a unique 94 amino acid C-terminal domain (HlyIIC). HlyIIC exhibits splitting of NMR resonances due to cis/trans isomerization of a single proline near the C-terminus. To overcome heterogeneity, we solved the structure of P405M-HlyIIC, a mutant that exclusively stabilizes the trans state. The NMR structure of HlyIIC reveals a novel fold, consisting of two subdomains αA-β1-β2 and β3-β4-αB-β5, that come together in a barrel-like structure. The barrel core is fastened by three layers of hydrophobic residues. The barrel end opposite the HlyIIC-core has a positively charged surface, that by binding negatively charged moieties on cellular membranes, may play a role in target-cell surface recognition or stabilization of the heptameric pore complex. In the WT domain, dynamic flexibility occurs at the N-terminus and the first α-helix that connects the HlyIIC domain to the HlyII-core structure. In the destabilizing P405M mutant, increased flexibility is evident throughout the first subdomain, suggesting that the HlyIIC structure may have arisen through gene fusion.
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Affiliation(s)
- Anne R Kaplan
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT, 06269-3125, USA
| | - Katherine Kaus
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 224 Hall-Atwater, 52 Lawn Ave., Middletown, CT, 06459-0175, USA
| | - Swastik De
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 224 Hall-Atwater, 52 Lawn Ave., Middletown, CT, 06459-0175, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06520-8114, USA
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, 224 Hall-Atwater, 52 Lawn Ave., Middletown, CT, 06459-0175, USA.
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT, 06269-3125, USA.
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Ng KS, Lam SL. NMR proton chemical shift prediction of C·C mismatches in B-DNA. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 252:87-93. [PMID: 25681800 DOI: 10.1016/j.jmr.2015.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 05/15/2023]
Abstract
Accurate prediction of DNA chemical shifts facilitates resonance assignment and allows recognition of different conformational features. Based on the nearest neighbor model and base pair replacement approach, we have determined a set of triplet chemical shift values and correction factors for predicting the proton chemical shifts of B-DNA containing an internal C·C mismatch. Our results provide a reliable chemical shift prediction with an accuracy of 0.07 ppm for non-labile protons and 0.09 ppm for labile protons. In addition, we have also shown that the correction factors for C·C mismatches can be used interchangeably with those for T·T mismatches. As a result, we have generalized a set of correction factors for predicting the flanking residue chemical shifts of pyrimidine·pyrimidine mismatches.
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Affiliation(s)
- Kui Sang Ng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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5
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Kaplan AR, Maciejewski MW, Olson R, Alexandrescu AT. NMR assignments for the cis and trans forms of the hemolysin II C-terminal domain. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:419-423. [PMID: 24234348 DOI: 10.1007/s12104-013-9530-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/29/2013] [Indexed: 06/02/2023]
Abstract
Pathogenic bacteria secrete pore-forming toxins (PFTs) to selectively defend against immune cells and to break through cellular barriers in the host. Understanding how PFTs attack cell membranes is not only essential for therapeutic intervention but for designing agents to deliver drugs to specific human cell subtypes, for example in anti-cancer or anti-viral therapies. Many toxins contain accessory domains that help recognize specific molecular epitopes on the membranes of target cells, including proteins, carbohydrates, and lipids. Here we report NMR assignments for the 94-residue 10 kDa C-terminal accessory domain of Bacillus cereus hemolysin II, HlyIIC, that has no known structural or functional homologues. The HlyIIC domain exists in a dynamic equilibrium due to cis/trans isomerization of its Gly86-Pro87 peptide bond. The cis and trans forms are about equally populated and are in slow exchange on the NMR timescale, giving rise to separate signals for approximately half of the residues in the domain. Assignments for the cis and trans forms were achieved with the aid of a P87M mutant that stabilizes the trans form, and separate sequential walks for the two forms in 3D NMR spectra of the wild-type HlyIIC. Based on backbone chemical shifts, the domain has a α1-α2-β1-β2-β3-β4-α3-β5 order of secondary structure elements. The last strand in the trans form and in the P87M mutant is shortened near Pro87 compared to the cis form. Both cis/trans isomerization and the P87M mutation cause large chemical shift changes throughout HlyIIC, suggesting that the proline is important in stabilizing the structure of the domain. The NMR assignments pave the way for solving the structures of the multiple conformational forms of HlyIIC and establishing their mechanism of interconversion.
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6
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Rizzo AA, Fraser LCR, Sheftic SR, Suhanovsky MM, Teschke CM, Alexandrescu AT. NMR assignments for the telokin-like domain of bacteriophage P22 coat protein. BIOMOLECULAR NMR ASSIGNMENTS 2013; 7:257-260. [PMID: 22987227 PMCID: PMC3537855 DOI: 10.1007/s12104-012-9422-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 09/05/2012] [Indexed: 06/01/2023]
Abstract
The bacteriophage P22 virion is assembled from identical coat protein monomers in a complex reaction that is generally conserved among tailed, double-stranded DNA bacteriophages and viruses. Many coat proteins of dsDNA viruses have structures based on the HK97 fold, but in some viruses and phages there are additional domains. In the P22 coat protein, a "telokin-like" domain was recently identified, whose structure has not yet been characterized at high-resolution. Two recently published low-resolution cryo-EM reconstructions suggest markedly different folds for the telokin-like domain that lead to alternative conclusions about its function in capsid assembly and stability. Here we report (1)H, (15)N, and (13)C NMR resonance assignments for the telokin-like domain. The secondary structure predicted from the chemical shift values obtained in this work shows significant discrepancies from both cryo-EM models but agrees better with one of the models. In particular, the functionally important "D-loop" in one model shows chemical shifts and solvent exchange protection more consistent with β-sheet structure. Our work will set the basis for a high-resolution NMR structure determination of the telokin-like domain that will help improve the cryo-EM models, and in turn lead to a better understanding of how coat protein monomers assemble into the icosahedral capsids required for virulence.
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Affiliation(s)
| | | | | | | | - Carolyn M. Teschke
- to whom correspondence should be addressed, Andrei T. Alexandrescu, Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd., Storrs, CT 06269-3125, USA. Tel:860-486-4414, fax: 860-486-4331, , Carolyn M. Teschke, Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd., Storrs, CT 06269-3125, USA. Tel:860-486-3992, fax: 860-486-4331,
| | - Andrei T. Alexandrescu
- to whom correspondence should be addressed, Andrei T. Alexandrescu, Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd., Storrs, CT 06269-3125, USA. Tel:860-486-4414, fax: 860-486-4331, , Carolyn M. Teschke, Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd., Storrs, CT 06269-3125, USA. Tel:860-486-3992, fax: 860-486-4331,
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7
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Wang B, He X, Merz KM. Quantum Mechanical Study of Vicinal J Spin-Spin Coupling Constants for the Protein Backbone. J Chem Theory Comput 2013; 9:4653-9. [PMID: 26589175 DOI: 10.1021/ct400631b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have performed densisty functional theory (DFT) calculations of vicinal J coupling constants involving the backbone torsional angle for the protein GB3 using our recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach (Xiao He et al. J. Phys. Chem. B 2009, 113, 10380-10388). Interestingly, the calculated values based on an NMR structure are more accurate than those based on a high-resolution X-ray strucure because the NMR structure was refined using a large number of residual dipolar couplings (RDCs) whereas the hydrogen atoms were added into the X-ray structure in idealized positions, confirming that the postioning of the hydrogen atoms relative to the backbone atoms is important to the accuracy of J coupling constant prediction. By comparing three Karplus equations, our results have demonstrated that hydrogen bonding, substituent and electrostatic effects could have significant impacts on vicinal J couplings even though they depend mostly on the intervening dihedral angles. The root-mean-square deviations (RMSDs) of the calculated (3)J(H(N),H(α)), (3)J(H(N),C(β)), (3)J(H(N),C') values based on the NMR structure are 0.52, 0.25, and 0.35 Hz, respectively, after taking the dynamic effect into consideration. The excellent accuracy demonstrates that our AF-QM/MM approach is a useful tool to study the relationship between J coupling constants and the structure and dynamics of proteins.
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Affiliation(s)
- Bing Wang
- Department of Chemistry and the Quantum Theory Project, University of Florida , Gainesville, Florida, 32611, United States
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China
| | - Kenneth M Merz
- Department of Chemistry and the Quantum Theory Project, University of Florida , Gainesville, Florida, 32611, United States
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8
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Kwok CK, Lam SL. NMR proton chemical shift prediction of T·T mismatches in B-DNA duplexes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 234:184-9. [PMID: 23892104 DOI: 10.1016/j.jmr.2013.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/24/2013] [Accepted: 06/28/2013] [Indexed: 05/15/2023]
Abstract
A proton chemical shift prediction scheme for B-DNA duplexes containing a T·T mismatch has been established. The scheme employs a set of T·T mismatch triplet chemical shift values, 5'- and 3'-correction factors extracted from reference sequences, and also the B-DNA chemical shift values predicted by Altona et al. The prediction scheme was tested by eight B-DNA duplexes containing T·T mismatches. Based on 560 sets of predicted and experimental proton chemical shift values, the overall prediction accuracy for non-labile protons was determined to be 0.07 ppm with an excellent correlation coefficient of 0.9996. In addition, the prediction accuracy for 96 sets of labile protons was found to be 0.22 ppm with a correlation coefficient of 0.9961. The prediction scheme developed herein can facilitate resonance assignments of B-DNA duplexes containing T·T mismatches and be generalized for the chemical shift prediction of other DNA mismatches. Our chemical shift data will also be useful for establishing structure-chemical shift information in B-DNA containing mismatches.
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Affiliation(s)
- Chun Kit Kwok
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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9
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Shu I, Scian M, Stewart JM, Kier BL, Andersen NH. 13C structuring shifts for the analysis of model β-hairpins and β-sheets in proteins: diagnostic shifts appear only at the cross-strand H-bonded residues. JOURNAL OF BIOMOLECULAR NMR 2013; 56:313-329. [PMID: 23851979 DOI: 10.1007/s10858-013-9749-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
The present studies have shown that (13)C=O, (13)C(α) and (13)C(β) of H-bonded strand residues in β-hairpins provide additional probes for quantitating the extent of folding in β-hairpins and other β-sheet models. Large differences in the structuring shifts (CSDs) of these (13)C sites in H-bonded versus non-H-bonded sites are observed: the differences between H-bonded and non-H-bonded sites are greater than 1.2 ppm for all three (13)C probes. This prompts us to suggest that efforts to determine the extent of hairpin folding from (13)C shifts should be based exclusively on the observation at the cross-strand H-bonded sites. Furthermore, the statistics suggest the (13)C' and (13)C(β) CSDs will provide the best differentiation with 100%-folded CSD values approaching -2.6 and +3 ppm, respectively, for the H-bonded sites. These conclusions can be extended to edge-strands of protein β-sheets. Our survey of reported (13)C shifts in β-proteins indicates that some of the currently employed random coil values need to be adjusted, particularly for ionization-induced effects.
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Affiliation(s)
- Irene Shu
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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10
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Ramírez-Gualito K, Richter M, Matzapetakis M, Singer D, Berger S. Structural characterization by NMR of a double phosphorylated chimeric peptide vaccine for treatment of Alzheimer's disease. Molecules 2013; 18:4929-41. [PMID: 23624647 PMCID: PMC6269680 DOI: 10.3390/molecules18054929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 11/16/2022] Open
Abstract
Rational design of peptide vaccines becomes important for the treatment of some diseases such as Alzheimer's disease (AD) and related disorders. In this study, as part of a larger effort to explore correlations of structure and activity, we attempt to characterize the doubly phosphorylated chimeric peptide vaccine targeting a hyperphosphorylated epitope of the Tau protein. The 28-mer linear chimeric peptide consists of the double phosphorylated B cell epitope Tau₂₂₉₋₂₃₇[pThr231/pSer235] and the immunomodulatory T cell epitope Ag85B₂₄₁₋₂₅₅ originating from the well-known antigen Ag85B of the Mycobacterium tuberculosis, linked by a four amino acid sequence -GPSL-. NMR chemical shift analysis of our construct demonstrated that the synthesized peptide is essentially unfolded with a tendency to form a β-turn due to the linker. In conclusion, the -GPSL- unit presumably connects the two parts of the vaccine without transferring any structural information from one part to the other. Therefore, the double phosphorylated epitope of the Tau peptide is flexible and accessible.
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Affiliation(s)
- Karla Ramírez-Gualito
- Institute of Analytical Chemistry, University Leipzig, Johannisallee 29, Leipzig 04103, Germany; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-341-973-6101; Fax: +49-341-971-1833
| | - Monique Richter
- Institute of Bioanalytical Chemistry, University Leipzig, Deutscher Platz 5, Leipzig 04103, Germany; E-Mails: (M.R.); (D.S.)
| | - Manolis Matzapetakis
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. Av. da República, Oeiras 2780-157, Portugal; E-Mail:
| | - David Singer
- Institute of Bioanalytical Chemistry, University Leipzig, Deutscher Platz 5, Leipzig 04103, Germany; E-Mails: (M.R.); (D.S.)
| | - Stefan Berger
- Institute of Analytical Chemistry, University Leipzig, Johannisallee 29, Leipzig 04103, Germany; E-Mail:
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Bertini I, Felli IC, Gonnelli L, Vasantha Kumar MV, Pierattelli R. High-resolution characterization of intrinsic disorder in proteins: expanding the suite of (13)C-detected NMR spectroscopy experiments to determine key observables. Chembiochem 2013; 12:2347-52. [PMID: 23106082 DOI: 10.1002/cbic.201100406] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Order in disorder: The characterization of intrinsically disordered proteins by NMR spectroscopy is a necessity on the one hand and a continuous challenge on the other. We propose two experiments that provide diagnostic parameters to monitor the degree of unfolding of a polypeptide. The test was performed on the yeast Cox17 protein, known to gain its function through maturation from an intrinsically disordered state (see figure).
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Affiliation(s)
- Ivano Bertini
- CERM University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.
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12
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Rawat A, Kumar D. NMR investigations of structural and dynamics features of natively unstructured drug peptide - salmon calcitonin: implication to rational design of potent sCT analogs. J Pept Sci 2012. [DOI: 10.1002/psc.2471] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Atul Rawat
- Centre of Biomedical Magnetic Resonance; Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Raibareli Road; Lucknow-; 226014; India
| | - Dinesh Kumar
- Centre of Biomedical Magnetic Resonance; Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Raibareli Road; Lucknow-; 226014; India
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13
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Sheftic SR, Garcia PP, White E, Robinson VL, Gage DJ, Alexandrescu AT. Nuclear magnetic resonance structure and dynamics of the response regulator Sma0114 from Sinorhizobium meliloti. Biochemistry 2012; 51:6932-41. [PMID: 22880754 DOI: 10.1021/bi300922z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Receiver domains control intracellular responses triggered by signal transduction in bacterial two-component systems. Here, we report the solution nuclear magnetic resonance structure and dynamics of Sma0114 from the bacterium Sinorhizobium meliloti, the first such characterization of a receiver domain from the HWE-kinase family of two-component systems. The structure of Sma0114 adopts a prototypical α(5)/β(5) Rossman fold but has features that set it apart from other receiver domains. The fourth β-strand of Sma0114 houses a PFxFATGY sequence motif, common to many HWE-kinase-associated receiver domains. This sequence motif in Sma0114 may substitute for the conserved Y-T coupling mechanism, which propagates conformational transitions in the 455 (α4-β5-α5) faces of receiver domains, to prime them for binding downstream effectors once they become activated by phosphorylation. In addition, the fourth α-helix of the consensus 455 face in Sma0114 is replaced with a segment that shows high flexibility on the pico- to nanosecond time scale by (15)N relaxation data. Secondary structure prediction analysis suggests that the absence of helix α4 may be a conserved property of the HWE-kinase-associated family of receiver domains to which Sma0114 belongs. In spite of these differences, Sma0114 has a conserved active site, binds divalent metal ions such as Mg(2+) and Ca(2+) that are required for phosphorylation, and exhibits micro- to millisecond active-site dynamics similar to those of other receiver domains. Taken together, our results suggest that Sma0114 has a conserved active site but differs from typical receiver domains in the structure of the 455 face that is used to effect signal transduction following activation.
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Affiliation(s)
- Sarah R Sheftic
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
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14
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Sheftic SR, Garcia PP, Robinson VL, Gage DJ, Alexandrescu AT. NMR assignments for the Sinorhizobium meliloti response regulator Sma0114. BIOMOLECULAR NMR ASSIGNMENTS 2011; 5:55-58. [PMID: 20936511 PMCID: PMC4343204 DOI: 10.1007/s12104-010-9266-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 09/22/2010] [Indexed: 05/30/2023]
Abstract
Response regulators are terminal ends of bacterial two-component systems that undergo extensive structural reorganization in response to phosphoryl transfer from their cognate histidine kinases. The response regulator encoded by the gene sma0114 of Sinorhizobium meliloti is a part of a unique class of two-component systems that employ HWE histidine kinases. The distinct features of Sma0114 include a PFxFATGY motif that houses the conserved threonine in the "Y-T coupling" conformational switch which mediates output response through downstream protein-protein interactions, and the replacement of the conserved phenylalanine/tyrosine in Y-T coupling by a leucine. Here we present (1)H, (15)N, and (13)C NMR assignments for Sma0114. We identify the secondary structure of the protein based on TALOS chemical shift analysis, (3)J(HNHα) coupling constants and hydrogen-deuterium exchange. The secondary structure determined by NMR is in good agreement with that predicted from the sequence. Both methods suggest that Sma0114 differs from standard CheY-like folds by missing the fourth α-helix. Our initial NMR characterization of Sma0114 paves the way to a full investigation of the structure and dynamics of this response regulator.
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Affiliation(s)
- Sarah R. Sheftic
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd., Storrs, CT 06269-3125, USA
| | - Preston P. Garcia
- Natural Sciences Department, Castleton State College, Castleton, VT 05735, USA
| | - Victoria L. Robinson
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd., Storrs, CT 06269-3125, USA
| | - Daniel J. Gage
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd., Storrs, CT 06269-3125, USA
| | - Andrei T. Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd., Storrs, CT 06269-3125, USA
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15
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Shu I, Stewart JM, Scian M, Kier BL, Andersen NH. β-Sheet 13C structuring shifts appear only at the H-bonded sites of hairpins. J Am Chem Soc 2011; 133:1196-9. [PMID: 21214243 DOI: 10.1021/ja1088953] [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
The (13)C chemical shifts measured for designed β-hairpins indicate that the structuring shifts (upfield for Cα and C', downfield for Cβ) previously reported as diagnostic for β-structuring in proteins appear only at the H-bonded strand residues. The resulting periodicity of structuring shift magnitudes is not, however, a consequence of H-bonding status; rather, it reflects a previously unrecognized alternation in the backbone torsion angles of β-strands. This feature of hairpins is also likely to be present in proteins. The study provides reference values for the expectation shifts for (13)C sites in β-structures that should prove useful in the characterization of the folding equilibria of β-sheet models.
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Affiliation(s)
- Irene Shu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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16
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Mielke SP, Krishnan V. Characterization of protein secondary structure from NMR chemical shifts. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 54:141-165. [PMID: 20160946 PMCID: PMC2766081 DOI: 10.1016/j.pnmrs.2008.06.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Steven P. Mielke
- UC Davis Genome Center, University of California, Davis, California
| | - V.V. Krishnan
- Department of Applied Science and Center for Comparative Medicine, University of California, Davis, California
- Department of Chemistry, California State University, Fresno, California
- Correspondence to or
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17
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Patil SM, Xu S, Sheftic SR, Alexandrescu AT. Dynamic alpha-helix structure of micelle-bound human amylin. J Biol Chem 2009; 284:11982-91. [PMID: 19244249 DOI: 10.1074/jbc.m809085200] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amylin is an endocrine hormone that regulates metabolism. In patients afflicted with type 2 diabetes, amylin is found in fibrillar deposits in the pancreas. Membranes are thought to facilitate the aggregation of amylin, and membrane-bound oligomers may be responsible for the islet beta-cell toxicity that develops during type 2 diabetes. To better understand the structural basis for the interactions between amylin and membranes, we determined the NMR structure of human amylin bound to SDS micelles. The first four residues in the structure are constrained to form a hairpin loop by the single disulfide bond in amylin. The last nine residues near the C terminus are unfolded. The core of the structure is an alpha-helix that runs from about residues 5-28. A distortion or kink near residues 18-22 introduces pliancy in the angle between the N- and C-terminal segments of the alpha-helix. Mobility, as determined by (15)N relaxation experiments, increases from the N to the C terminus and is strongly correlated with the accessibility of the polypeptide to spin probes in the solution phase. The spin probe data suggest that the segment between residues 5 and 17 is positioned within the hydrophobic lipid environment, whereas the amyloidogenic segment between residues 20 and 29 is at the interface between the lipid and solvent. This orientation may direct the aggregation of amylin on membranes, whereas coupling between the two segments may mediate the transition to a toxic structure.
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Affiliation(s)
- Sharadrao M Patil
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269-3125, USA
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18
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Csizmok V, Felli IC, Tompa P, Banci L, Bertini I. Structural and dynamic characterization of intrinsically disordered human securin by NMR spectroscopy. J Am Chem Soc 2009; 130:16873-9. [PMID: 19053469 DOI: 10.1021/ja805510b] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the molecular action of securin, the inhibitor of separase in mitosis, is of immense theoretical and biomedical importance. The residue-level structural description of an intrinsically disordered protein of this length (202 amino acids, containing 24 prolines), however, represents a particular challenge. Here we combined (1)H-detected and (13)C-detected protonless NMR experiments to achieve full assignment of securin's backbone amide resonances. Chemical shifts, (15)N relaxation rates (R(1), R(2), (1)H-(15)N NOEs), (1)H exchange rates with the solvent (CLEANEX-PM), and (1)H-(15)N residual dipolar couplings were determined along the entire length of the protein. This analysis showed that securin is not entirely disordered, but segregates into a largely disordered N-terminal half and a C-terminal half with transient segmental order, within which the segment D(150)-F(159) has a significant helical tendency and segments E(113)-S(127) and W(174)-L(178) also show a significant deviation from random-coil behavior. These results, in combination with bioinformatic and biochemical data on the securin/separase interaction, shed light on the inhibitory action of securin on separase.
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Affiliation(s)
- Veronika Csizmok
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Karolina ut 29, H-1113, Hungary
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19
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Schmidt HLF, Sperling LJ, Gao YG, Wylie BJ, Boettcher JM, Wilson SR, Rienstra CM. Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction. J Phys Chem B 2007; 111:14362-9. [PMID: 18052145 PMCID: PMC2774121 DOI: 10.1021/jp075531p] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of micro- or nanocrystalline proteins by magic-angle spinning (MAS) solid-state NMR (SSNMR) gives atomic-resolution insight into structure in cases when single crystals cannot be obtained for diffraction studies. Subtle differences in the local chemical environment around the protein, including the characteristics of the cosolvent and the buffer, determine whether a protein will form single crystals. The impact of these small changes in formulation is also evident in the SSNMR spectra; however, the changes lead only to correspondingly subtle changes in the spectra. Here, we demonstrate that several formulations of GB1 microcrystals yield very high quality SSNMR spectra, although only a subset of conditions enable growth of single crystals. We have characterized these polymorphs by X-ray powder diffraction and assigned the SSNMR spectra. Assignments of the 13C and 15N SSNMR chemical shifts confirm that the backbone structure is conserved, indicative of a common protein fold, but side chain chemical shifts are changed on the surface of the protein, in a manner dependent upon crystal packing and electrostatic interactions with salt in the mother liquor. Our results demonstrate the ability of SSNMR to reveal minor structural differences among crystal polymorphs. This ability has potential practical utility for studying the formulation chemistry of industrial and therapeutic proteins, as well as for deriving fundamental insights into the phenomenon of single-crystal growth.
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Affiliation(s)
- Heather L Frericks Schmidt
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61821, USA
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20
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Farès C, Amata I, Carlomagno T. 13C-detection in RNA bases: revealing structure-chemical shift relationships. J Am Chem Soc 2007; 129:15814-23. [PMID: 18052161 DOI: 10.1021/ja0727417] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemical shifts of the unprotonated carbons in the proton-deficient nucleobases of RNA are rarely reported, despite the valuable information that they contain about base-pairing and base-stacking. We have developed 13C-detected 2D-experiments to identify the unprotonated 13C in the RNA bases and have assigned all the base nuclei of uniformly 13C,15N-labeled HIV-2 TAR-RNA. The 13C chemical shift distributions revealed perturbations correlated with the base-pairing and base-stacking properties of all four base-types. From this work, we conclude that the information contained in the chemical shift perturbations within the base rings can provide valuable restraint information for solving RNA structures, especially in conformational averaged regions, where NOE-based information is not available.
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Affiliation(s)
- Christophe Farès
- Max-Planck-Institute for Biophysical Chemistry, Department of NMR-based Structural Biology, Am Fassberg 11, D-37077 Göttingen, Germany
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21
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Wei Y, Huyghues-Despointes BMP, Tsai J, Scholtz JM. NMR study and molecular dynamics simulations of optimized β-hairpin fragments of protein G. Proteins 2007; 69:285-96. [PMID: 17600831 DOI: 10.1002/prot.21494] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The stability and structure of several beta-hairpin peptide variants derived from the C-terminus of the B1 domain of protein G were investigated by a number of experimental and computational techniques. Our analysis shows that the structure and stability of this hairpin can be greatly affected by one or a few simple mutations. For example, removing an unfavorable charge near the N-terminus of the peptide (Glu42 to Gln or Thr) or optimization of the N-terminal charge-charge interactions (Gly41 to Lys) both stabilize the peptide, even in water. Furthermore, a simple replacement of a charged residue in the turn (Asp47 to Ala) changes the beta-turn conformation. Finally, we show that the effects of combining these single mutations are additive, suggesting that independent stabilizing interactions can be isolated and evaluated in a simple model system. Our results indicate that the structure and stability of this beta-hairpin peptide can be modulated in numerous ways and thus contributes toward a more complete understanding of this important model beta-hairpin as well as to the folding and stability of larger peptides and proteins.
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Affiliation(s)
- Yun Wei
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
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22
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Lam SL, Lai KF, Chi LM. Proton chemical shift prediction of A.A mismatches in B-DNA duplexes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 187:105-11. [PMID: 17475525 DOI: 10.1016/j.jmr.2007.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2007] [Revised: 03/29/2007] [Accepted: 04/04/2007] [Indexed: 05/15/2023]
Abstract
A proton chemical shift prediction method has been developed for double helical DNAs containing A.A mismatches. This method makes use of the chemical shift prediction scheme for normal B-DNA duplexes developed by Altona and co-workers and a set of A.A mismatch triplet chemical shift values and corrections factors extracted from reference sequences. The triplet values are used for predicting chemical shifts of A.A mismatches whereas the normal B-DNA chemical shifts and correction factors are used for the flanking residues of A.A mismatches. Both 5'- and 3'-correction factors have been determined from the chemical shift differences upon replacing the A.A mismatch in a duplex with an A.T base pair. Based on 560 sets of predicted and experimental chemical shifts, the overall prediction accuracy for various types of protons has been determined to be 0.07 ppm with an excellent correlation coefficient of 0.9996.
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Affiliation(s)
- Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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23
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Vila JA, Villegas ME, Baldoni HA, Scheraga HA. Predicting 13Calpha chemical shifts for validation of protein structures. JOURNAL OF BIOMOLECULAR NMR 2007; 38:221-35. [PMID: 17558470 DOI: 10.1007/s10858-007-9162-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 04/19/2007] [Accepted: 04/20/2007] [Indexed: 05/15/2023]
Abstract
The (13)C(alpha) chemical shifts for 16,299 residues from 213 conformations of four proteins (experimentally determined by X-ray crystallography and Nuclear Magnetic Resonance methods) were computed by using a combination of approaches that includes, but is not limited to, the use of density functional theory. Initially, a validation test of this methodology was carried out by a detailed examination of the correlation between computed and observed (13)C(alpha) chemical shifts of 10,564 (of the 16,299) residues from 139 conformations of the human protein ubiquitin. The results of this validation test on ubiquitin show agreement with conclusions derived from computation of the chemical shifts at the ab initio Hartree-Fock level. Further, application of this methodology to 5,735 residues from 74 conformations of the three remaining proteins that differ in their number of amino acid residues, sequence and three-dimensional structure, together with a new scoring function, namely the conformationally averaged root-mean-square-deviation, enables us to: (a) offer a criterion for an accurate assessment of the quality of NMR-derived protein conformations; (b) examine whether X-ray or NMR-solved structures are better representations of the observed (13)C(alpha) chemical shifts in solution; (c) provide evidence indicating that the proposed methodology is more accurate than automated predictors for validation of protein structures; (d) shed light as to whether the agreement between computed and observed (13)C(alpha) chemical shifts is influenced by the identity of an amino acid residue or its location in the sequence; and (e) provide evidence confirming the presence of dynamics for proteins in solution, and hence showing that an ensemble of conformations is a better representation of the structure in solution than any single conformation.
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Affiliation(s)
- Jorge A Vila
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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24
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Khakshoor O, Demeler B, Nowick JS. Macrocyclic beta-sheet peptides that mimic protein quaternary structure through intermolecular beta-sheet interactions. J Am Chem Soc 2007; 129:5558-69. [PMID: 17419629 PMCID: PMC2596933 DOI: 10.1021/ja068511u] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper reports the design, synthesis, and characterization of a family of cyclic peptides that mimic protein quaternary structure through beta-sheet interactions. These peptides are 54-membered-ring macrocycles comprising an extended heptapeptide beta-strand, two Hao beta-strand mimics [JACS 2000, 122, 7654] joined by one additional alpha-amino acid, and two delta-linked ornithine beta-turn mimics [JACS 2003, 125, 876]. Peptide 3a, as the representative of these cyclic peptides, contains a heptapeptide sequence (TSFTYTS) adapted from the dimerization interface of protein NuG2 [PDB ID: 1mio]. 1H NMR studies of aqueous solutions of peptide 3a show a partially folded monomer in slow exchange with a strongly folded oligomer. NOE studies clearly show that the peptide self-associates through edge-to-edge beta-sheet dimerization. Pulsed-field gradient (PFG) NMR diffusion coefficient measurements and analytical ultracentrifugation (AUC) studies establish that the oligomer is a tetramer. Collectively, these experiments suggest a model in which cyclic peptide 3a oligomerizes to form a dimer of beta-sheet dimers. In this tetrameric beta-sheet sandwich, the macrocyclic peptide 3a is folded to form a beta-sheet, the beta-sheet is dimerized through edge-to-edge interactions, and this dimer is further dimerized through hydrophobic face-to-face interactions involving the Phe and Tyr groups. Further studies of peptides 3b-3n, which are homologues of peptide 3a with 1-6 variations in the heptapeptide sequence, elucidate the importance of the heptapeptide sequence in the folding and oligomerization of this family of cyclic peptides. Studies of peptides 3b-3g show that aromatic residues across from Hao improve folding of the peptide, while studies of peptides 3h-3n indicate that hydrophobic residues at positions R3 and R5 of the heptapeptide sequence are important in oligomerization.
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Affiliation(s)
- Omid Khakshoor
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
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25
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Bezsonova I, Evanics F, Marsh JA, Forman-Kay JD, Prosser RS. Oxygen as a Paramagnetic Probe of Clustering and Solvent Exposure in Folded and Unfolded States of an SH3 Domain. J Am Chem Soc 2007; 129:1826-35. [PMID: 17253684 DOI: 10.1021/ja065173o] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The N-terminal SH3 domain of the Drosophila modular protein Drk undergoes slow exchange between a folded (Fexch) and highly populated unfolded (Uexch) state under nondenaturing buffer conditions, enabling both Fexch and Uexch states to be simultaneously monitored. The addition of dissolved oxygen, equilibrated to a partial pressure of either 30 atm or 60 atm, provides the means to study solvent exposure with atomic resolution via 13C NMR paramagnetic shifts in 1H,13C HSQC (heteronuclear single quantum coherence) spectra. Absolute differences in these paramagnetic shifts between the Fexch and Uexch states allow the discrimination of regions of the protein which undergo change in solvent exposure upon unfolding. Contact with dissolved oxygen for both the Fexch and Uexch states could also be assessed through 13C paramagnetic shifts which were normalized based on the corresponding paramagnetic shifts seen in the free amino acids. In the Fexch state, the 13C nuclei belonging to the hydrophobic core of the protein exhibited very weak normalized paramagnetic shifts while those with greater solvent accessible surface area exhibited significantly larger normalized shifts. The Uexch state displayed less varied 13C paramagnetic shifts although distinct regions of protection from solvent exposure could be identified by a lack of such shifts. These regions, which included Phe9, Thr12, Ala13, Lys21, Thr22, Ile24, Ile27, and Arg38, overlapped with those found to have residual nativelike and non-native structures in previous studies and in some cases provided novel information. Thus, the paramagnetic shifts from dissolved oxygen are highly useful in the study of a transient structure or clustering in disordered systems, where conventional NMR measurements (couplings, chemical shift deviations from random coil values, and NOEs) may give little information.
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Affiliation(s)
- Irina Bezsonova
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 1A8
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26
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Echenique P, Calvo I. Explicit factorization of external coordinates in constrained statistical mechanics models. J Comput Chem 2006; 27:1748-55. [PMID: 16917856 DOI: 10.1002/jcc.20499] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
If a macromolecule is described by curvilinear coordinates or rigid constraints are imposed, the equilibrium probability density that must be sampled in Monte Carlo simulations includes the determinants of different mass-metric tensors. In this work, the authors explicitly write the determinant of the mass-metric tensor G and of the reduced mass-metric tensor g, for any molecule, general internal coordinates and arbitrary constraints, as a product of two functions; one depending only on the external coordinates that describe the overall translation and rotation of the system, and the other only on the internal coordinates. This work extends previous results in the literature, proving with full generality that one may integrate out the external coordinates and perform Monte Carlo simulations in the internal conformational space of macromolecules.
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Affiliation(s)
- Pablo Echenique
- Departamento de Física Teórica, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
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27
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Li G, Li J, Wang W, Yang M, Zhang Y, Sun P, Yuan Z, He B, Yu Y. Adsorption Mechanism at the Molecular Level between Polymers and Uremic Octapeptide by the 2D1H NMR Technique. Biomacromolecules 2006; 7:1811-8. [PMID: 16768402 DOI: 10.1021/bm060126+] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To remove uremic octapeptide from the blood stream of uremic patients, various modified polyacylamide cross-linked absorbents were prepared. Adsorption experiments showed these absorbents have significant differences in adsorption capacity to the target peptide. In this paper, two-dimension proton nuclear magnetic resonance (2D 1H NMR) spectroscopy was used to investigate the interaction mechanism between the peptide and the adsorbents. Because of the insolubility of the absorbent, some soluble linear polymers with the same functional groups as the absorbents were employed as the model adsorbents in 2D 1H NMR. The preferred binding site for the peptide and polymers was identified to be at the C-terminal carboxyl group of the octapeptide via chemical shift perturbation effects. In this study, we found that hydrogen bonding, electrostatic, and hydrophobic interactions all play a role in the interaction force but had different contributions. Especially, the great chemical shift changes of the aromatic amino acid residues (Trp) during the interaction between butyl-modified polyacrylamide and octapeptide suggested the hydrophobic interaction, incorporated with the electrostatic force, played an important role in the binding reaction in aqueous solutions. This information not only rationally explained the results of the adsorption experiments, but also identified the effective binding site and mechanism, and shall provide a structural basis for designing better affinity-type adsorbents for the target peptide.
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Affiliation(s)
- Guohua Li
- The Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University, Tianjin 300071, People's Republic of China
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28
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Berjanskii MV, Wishart DS. A simple method to predict protein flexibility using secondary chemical shifts. J Am Chem Soc 2006; 127:14970-1. [PMID: 16248604 DOI: 10.1021/ja054842f] [Citation(s) in RCA: 346] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein motions play a critical role in many biological processes, such as enzyme catalysis, allosteric regulation, antigen-antibody interactions, and protein-DNA binding. NMR spectroscopy occupies a unique place among methods for investigating protein dynamics due to its ability to provide site-specific information about protein motions over a large range of time scales. However, most NMR methods require a detailed knowledge of the 3D structure and/or the collection of additional experimental data (NOEs, T1, T2, etc.) to accurately measure protein dynamics. Here we present a simple method based on chemical shift data that allows accurate, quantitative, site-specific mapping of protein backbone mobility without the need of a three-dimensional structure or the collection and analysis of NMR relaxation data. Further, we show that this chemical shift method is able to quantitatively predict per-residue RMSD values (from both MD simulations and NMR structural ensembles) as well as model-free backbone order parameters.
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Affiliation(s)
- Mark V Berjanskii
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8
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29
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Kennedy RJ, Walker SM, Kemp DS. Energetic characterization of short helical polyalanine peptides in water: analysis of 13C=O chemical shift data. J Am Chem Soc 2005; 127:16961-8. [PMID: 16316242 PMCID: PMC1560102 DOI: 10.1021/ja054645g] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Measured at 2 degrees C in water, NMR chemical shifts of (13)C=O labeled central alanine residues of peptides W-Lys(5)-(t)L(3)-Ala(n)-(t)L(3)-Lys(5)NH(2), n = 9, 11, 13, 15, 19 and W-Lys(5)-(t)L(3)-a-Ala(n)-A-Inp-(t)L(2)-Lys(5)NH(2) (a = D-Ala; (t)L = tert-leucine; Inp = 4-carboxypiperidine) are used to assign jt(L) and ct(L), the N- and C-terminal (t)L capping parameters and length-dependent values for w(Ala)(n), the alanine helical propensity for Ala(n) peptides. These parameters allow Lifson-Roig characterization of the stabilities of Ala(n)() helices in water. To facilitate chemical shift characterization, different (13)C/(12)C ratios are incorporated into specific Ala sites to code up to six residue sites per peptide. Large left/right chemical shift anisotropies are intrinsic to helical polyalanines, and a correcting L-R-based model is introduced. Capping parameters jt(L) = ct(L) lie in the range of 0.3 to 0.5; the (t)L residues are thus moderately helix-destabilizing. For helical conformations of lengths shorter than eight residues, assigned values for w(Ala) approach 1.0 but increase monotonically with length to a value of 1.59 for w(Ala)(19).
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Affiliation(s)
- Robert J Kennedy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, 02139, USA
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30
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Habeck M, Rieping W, Nilges M. Bayesian estimation of Karplus parameters and torsion angles from three-bond scalar couplings constants. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 177:160-5. [PMID: 16085438 DOI: 10.1016/j.jmr.2005.06.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Revised: 06/04/2005] [Accepted: 06/29/2005] [Indexed: 05/03/2023]
Abstract
We apply Bayesian inference to analyze three-bond scalar coupling constants in an objective and consistent way. The Karplus curve and a Gaussian error law are used to model scalar coupling measurements. By applying Bayes' theorem, we obtain a probability distribution for all unknowns, i.e., the torsion angles, the Karplus parameters, and the standard deviation of the Gaussian. We infer all these unknowns from scalar coupling data using Markov chain Monte Carlo sampling and analytically derive a probability distribution that only involves the torsion angles.
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Affiliation(s)
- Michael Habeck
- Unité de Bioinformatique Structurale, Institut Pasteur, CNRS URA 2185, Paris, France. habeck@pasteur@.fr
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31
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Andronesi OC, Becker S, Seidel K, Heise H, Young HS, Baldus M. Determination of Membrane Protein Structure and Dynamics by Magic-Angle-Spinning Solid-State NMR Spectroscopy†. J Am Chem Soc 2005; 127:12965-74. [PMID: 16159291 DOI: 10.1021/ja0530164] [Citation(s) in RCA: 245] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is shown that molecular structure and dynamics of a uniformly labeled membrane protein can be studied under magic-angle-spinning conditions. For this purpose, dipolar recoupling experiments are combined with novel through-bond correlation schemes that probe mobile protein segments. These NMR schemes are demonstrated on a uniformly [13C,15N] variant of the 52-residue polypeptide phospholamban. When reconstituted in lipid bilayers, the NMR data are consistent with an alpha-helical trans-membrane segment and a cytoplasmic domain that exhibits a high degree of structural disorder.
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Affiliation(s)
- Ovidiu C Andronesi
- Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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32
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Heitmann B, Job GE, Kennedy RJ, Walker SM, Kemp DS. Water-solubilized, cap-stabilized, helical polyalanines: calibration standards for NMR and CD analyses. J Am Chem Soc 2005; 127:1690-704. [PMID: 15701003 PMCID: PMC1941670 DOI: 10.1021/ja0457462] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR and CD studies are reported for two length series of solubilized, spaced, highly helical polyalanines that are N-capped by the optimal helix stabilizer (beta)Asp-Hel and C-capped by beta-aminoalanine beta and that are studied in water at 2 degrees C, pH 1-8. NMR analysis yields a structural characterization of the peptide Ac(beta)AspHelAla(8)betaNH(2) and selected members of one (beta)AspHelAla(n)beta series. At pH > 4.5 the (beta)AspHel cap provides a preorganized triad of carboxylate anion and two amide residues that is complementary to the helical polyalanine N-terminus. The C-terminal beta-aminoalanine assumes a helix-stabilizing conformation consistent with literature precedents. H(N)CO NMR experiments applied to capped, uniformly (13)C- and (15)N-labeled Ala(8) and Ala(12) peptides define Ala(n) hydrogen bonding signatures as alpha-helical without detectable 3(10) character. Relative NH-->ND exchange rates yield site protection factors PF(i) that define uniquely high fractional helicities FH for the peptide Ala(n) regions. These Ala(n) calibration series, studied in water and lacking helix-stabilizing tertiary structure, yield the first (13)C NMR chemical shifts, (3)J(HNH)(alpha) coupling constants, and CD ellipticities [theta(Molar)](lambda,n) characteristic of a fully helical alanine within an Ala(n) context. CD data are used to assign parameters X and [theta](lambda,infinity), required for rigorous calculation of FH values from CD ellipticities.
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Affiliation(s)
- Björn Heitmann
- Contribution from the Department of Chemistry, Room 18-296, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Gabriel E. Job
- Contribution from the Department of Chemistry, Room 18-296, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Robert J. Kennedy
- Contribution from the Department of Chemistry, Room 18-296, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Sharon M. Walker
- Contribution from the Department of Chemistry, Room 18-296, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Daniel S. Kemp
- Contribution from the Department of Chemistry, Room 18-296, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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33
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Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC. GROMACS: Fast, flexible, and free. J Comput Chem 2005; 26:1701-18. [PMID: 16211538 DOI: 10.1002/jcc.20291] [Citation(s) in RCA: 11034] [Impact Index Per Article: 580.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.
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Affiliation(s)
- David Van Der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S-75124 Uppsala, Sweden
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34
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Matousek WM, Alexandrescu AT. NMR structure of the C-terminal domain of SecA in the free state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1702:163-71. [PMID: 15488768 DOI: 10.1016/j.bbapap.2004.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2004] [Revised: 08/14/2004] [Accepted: 08/17/2004] [Indexed: 11/18/2022]
Abstract
SecA is an integral component of the prokaryotic Sec preprotein secretory translocase system. We report here the solution NMR structure of a fragment corresponding to the C-terminal domain of Escherichia coli SecA. In the presence of Zn2+, the fragment adopts a shortened version of the classic betabetaalpha zinc finger fold. The isolated C-terminal domain shows substantial differences from the X-ray structure of a homologous SecA domain bound to the chaperone-like cofactor SecB. The differences between the structures of the free and bound forms suggest that binding to SecB causes a perturbation of the C-terminal domain's intrinsically favored betabetaalpha fold.
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Affiliation(s)
- William M Matousek
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, U-3125, Storrs, CT 06269-3125, USA
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35
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Turano P. Insights into Partially Folded or Unfolded States of Metalloproteins from Nuclear Magnetic Resonance. Inorg Chem 2004; 43:7945-52. [PMID: 15578828 DOI: 10.1021/ic048962k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nuclear magnetic resonance (NMR) provides detailed insights into the conformational features of unfolded and partially folded proteins. In the case of metalloproteins, special attention should be devoted to the characterization of the properties of the metal binding sites, and specific approaches need to be developed depending on the nature of the metal ion and its coordination environment. At the same time, metal-based NMR parameters may help in getting a better picture of the average structural properties of the metalloprotein. A critical evaluation of the limits of applicability of paramagnetic effects for solution structure determination in partially folded or unfolded proteins is presented. The coupling between NMR characterization of structure and dynamic of the polypeptide chain and of the metal environment provides insights into the stabilizing role of metal ions in metalloproteins. The overall approach is illustrated for some case examples of increasing flexibility obtained far from native conditions for cytochrome c and superoxide dismutase, two metalloproteins that have been extensively studied in our lab and whose misfolded forms may be relevant for important biological processes.
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Affiliation(s)
- Paola Turano
- CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
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36
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Oxenoid K, Kim HJ, Jacob J, Sönnichsen FD, Sanders CR. NMR assignments for a helical 40 kDa membrane protein. J Am Chem Soc 2004; 126:5048-9. [PMID: 15099070 DOI: 10.1021/ja049916m] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Backbone nuclear magnetic resonance (NMR) assignments were achieved for diacylglycerol kinase (DAGK) in detergent micelles. DAGK is a homotrimeric integral membrane protein comprised of 121 residue subunits, each having three transmembrane segments. Assignments were made using TROSY-based pulse sequences. DAGK was found to be an almost exclusively helical protein. This work points to the feasibility of both solving the structure of DAGK using solution NMR methods and using NMR as a primary tool in structural studies of other helical integral membrane proteins of similar size and complexity.
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Affiliation(s)
- Kirill Oxenoid
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-8725, USA
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37
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Hronska M, van Beek JD, Williamson PTF, Vollrath F, Meier BH. NMR Characterization of Native Liquid Spider Dragline Silk from Nephila edulis. Biomacromolecules 2004; 5:834-9. [PMID: 15132669 DOI: 10.1021/bm0343904] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solid spider dragline silk is well-known for its mechanical properties. Nonetheless a detailed picture of the spinning process is lacking. Here we report NMR studies on the liquid silk within the wide sac of the major ampullate (m.a.) gland from the spider Nephila edulis. The resolution in the NMR spectra is shown to be significantly improved by the application of magic-angle spinning (MAS). From the narrow width of the resonance lines and the chemical shifts observed, it is concluded that the silk protein within the wide sac of the m.a. gland is dynamically disordered throughout the molecule in the sense that each amino acid of a given type senses an identical environment, on average. The NMR data obtained are consistent with an isotropic liquid phase.
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Affiliation(s)
- M Hronska
- ETH Zurich, Physical Chemistry, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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38
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Hansen DF, Led JJ. Mapping the Electronic Structure of the Blue Copper Site in Plastocyanin by NMR Relaxation. J Am Chem Soc 2004; 126:1247-52. [PMID: 14746497 DOI: 10.1021/ja0379464] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biological function of metalloproteins stems from the electronic and geometric structures of their active sites. Thus, in blue copper proteins such as plastocyanins, an unusual electronic structure of the metal site is believed to contribute to the rapid, long-range electron-transfer reactivity that characterizes these proteins. To clarify this structure-function relationship, numerous quantum chemical calculations of the electronic structure of the blue copper proteins have been made. However, the obtained structures depend strongly on the applied model. Experimental approaches based on ENDOR spectroscopy and X-ray absorption have also been used to elucidate the electronic structure of the blue copper site. Still, the determination of the electronic structure relies on a calibration with quantum chemical calculations, performed on small model complexes. Here we present an approach that allows a direct experimental mapping of the electron spin delocalization in paramagnetic metalloproteins using oxidized plastocyanin from Anabaena variabilis as an example. The approach utilizes the longitudinal paramagnetic relaxation of protons close to the metal site and relies on the dependence of these relaxations on the spatial distribution of the unpaired electron of the metal ion. Surprisingly it is found that the unpaired electron of the copper ion in plastocyanin is less delocalized than predicted by most of the quantum chemical calculations.
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Affiliation(s)
- D Flemming Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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39
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Nowick JS, Khakshoor O, Hashemzadeh M, Brower JO. DSA: a new internal standard for NMR studies in aqueous solution. Org Lett 2003; 5:3511-3. [PMID: 12967312 DOI: 10.1021/ol035347w] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text] The widely used internal standard for NMR studies in aqueous solution DSS (sodium 4,4-dimethyl-4-silapentane-1-sulfonate) can interact with cationic peptides, diminishing its value for such studies. This paper introduces DSA (4,4-dimethyl-4-silapentane-1-ammonium trifluoroacetate) as a new internal standard that does not suffer from this problem.
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Affiliation(s)
- James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, USA
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40
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Abstract
NMR characteristics of a model left-handed 3(1)-helical peptide are reported in this study. With temperature and sequence corrections on the predicted random coil (15)N chemical shifts, a significant (15)N chemical shift deviation is observed for the model 3(1) peptide. The (15)N chemical shift differences also correlate well with the molar ellipticities (at 220 nm) of the CD spectra at different temperatures, indicating that the (15)N chemical shift is a sensitive probe for 3(1)-helices. The average (3)J(HNalpha) and (1)J(CalphaHalpha) values of the model peptide are determined to be 6.5 and 142.6 Hz, respectively, which are consistent with the values calculated from the geometry of 3(1)-helices. With careful measurements of amide (15)N chemical shifts and incorporating temperature and sequence effect corrections, the (15)N chemical shifts can be used together with (3)J(HNalpha) and (1)J(CalphaHalpha) to differentiate 3(1)-helices from random coils with high confidence. Based on the observed NMR characteristics, a strategy is developed for probing left-handed 3(1)-helical structures from other secondary structures.
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Affiliation(s)
- Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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41
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Digilio G, Barbero L, Bracco C, Corpillo D, Esposito P, Piquet G, Traversa S, Aime S. NMR structure of two novel polyethylene glycol conjugates of the human growth hormone-releasing factor, hGRF(1-29)-NH2. J Am Chem Soc 2003; 125:3458-70. [PMID: 12643708 DOI: 10.1021/ja021264j] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two novel mono-PEGylated derivatives of hGRF(1-29)-NH(2) [human growth hormone-releasing factor, fragment 1-29] have been synthesized by regio-specific conjugation of Lys(12) or Lys(21) to a monomethoxy-PEG(5000) chain (compounds Lys(12)PEG-GRF and Lys(21)PEG-GRF). The PEG moiety has been covalently linked at the amino group of a norleucine residue via a carbamate bond. The Lys(12)PEG-GRF regioisomer was found to be slightly less active in vitro than both the unmodified peptide and Lys(21)PEG-GRF. To assess whether the differences in the biological activity of the PEGylated analogues could be related to conformational rearrangements induced by the PEG moiety, the structure of these PEGylated derivatives has been worked out (TFE solution) by means of NMR spectroscopy and molecular dynamics. Secondary structure shifts, hydrogen/deuterium exchange kinetics, temperature coefficients of amide protons, and NOE-based molecular models point out that hGRF(1-29)-NH(2), Lys(21)PEG-GRF and Lys(12)PEG-GRF share a remarkably similar pattern of secondary structure. All three compounds adopt an alpha-helix conformation which spans the whole length of the molecule, and which becomes increasingly rigid on going from the N-terminus to the C-terminus. Residues Lys(12) and Lys(21) are enclosed in all the compounds considered into well-defined alpha-helical domains, indicating that PEGylation either at Lys(12) or Lys(21) does not alter the tendency of the peptide to adopt a stable alpha-helix conformation, nor does it induce appreciable conformational mobility in the proximity of the PEGylation sites. No significant variation of the amphiphilic organization of the alpha-helix is observed among the three peptides. Therefore, the different biological activities observed for the PEGylated analogues are not due to conformational effects, but are rather due to sterical hindrance effects. The relationship between the biological activitiy of the mono-PEGylated derivatives and sterical hindrance is discussed in terms of the topology of interaction between hGRF(1-29)-NH(2) and its receptor.
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Affiliation(s)
- Giuseppe Digilio
- Bioindustry Park del Canavese, Via Ribes 5, I-10010 Colleretto Giacosa (TO), Italy.
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42
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Sibley AB, Cosman M, Krishnan VV. An empirical correlation between secondary structure content and averaged chemical shifts in proteins. Biophys J 2003; 84:1223-7. [PMID: 12547802 PMCID: PMC1302698 DOI: 10.1016/s0006-3495(03)74937-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
It is shown that the averaged chemical shift (ACS) of a particular nucleus in the protein backbone empirically correlates well to its secondary structure content (SSC). Chemical shift values of more than 200 proteins obtained from the Biological Magnetic Resonance Bank are used to calculate ACS values, and the SSC is estimated from the corresponding three-dimensional coordinates obtained from the Protein Data Bank. ACS values of (1)H(alpha) show the highest correlation to helical and sheet structure content (correlation coefficient of 0.80 and 0.75, respectively); (1)H(N) exhibits less reliability (0.65 for both sheet and helix), whereas such correlations are poor for the heteronuclei. SSC estimated using this correlation shows a good agreement with the conventional chemical shift index-based approach for a set of proteins that only have chemical shift information but no NMR or x-ray determined three-dimensional structure. These results suggest that even chemical shifts averaged over the entire protein retain significant information about the secondary structure. Thus, the correlation between ACS and SSC can be used to estimate secondary structure content and to monitor large-scale secondary structural changes in protein, as in folding studies.
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Affiliation(s)
- Anaika B Sibley
- Molecular Biophysics Group, L-448 Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
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43
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Meźó G, Majer Z, Vass E, Jimenez MA, Andreu D, Hudecz F. Conformational study of linear and cyclic peptides corresponding to the 276-284 epitope region of HSV gD-1. Biophys Chem 2003; 103:51-65. [PMID: 12504254 DOI: 10.1016/s0301-4622(02)00232-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The results of conformational analysis of linear and cyclic peptides from the 276SALLEDPVG(284) sequence of glycoprotein D of Herpes simplex virus are presented. The epitope peptides were synthesized by SPPS and on resin cyclization was applied for preparation of cyclic compounds. Circular dichroism spectroscopy, Fourier-transform infrared spectroscopy and nuclear magnetic resonance (NMR) were used to determine of the solution structure of both linear and cyclic peptides. The results indicated that the cyclopeptides containing the core of the epitope (DPVG) as a part of the cycle have more stable beta-turn structure than the linear peptides or the cyclic analogues, where the core motif is not a part of the cycle. NMR study of H-SALLc(EDPVGK)-NH(2) confirm presence of a type I beta-turn structure which includes the DPVG epitope core.
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Affiliation(s)
- G Meźó
- Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös University, Budapest, Hungary.
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44
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Jaroniec CP, Filip C, Griffin RG. 3D TEDOR NMR experiments for the simultaneous measurement of multiple carbon-nitrogen distances in uniformly (13)C,(15)N-labeled solids. J Am Chem Soc 2002; 124:10728-42. [PMID: 12207528 DOI: 10.1021/ja026385y] [Citation(s) in RCA: 235] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe three-dimensional magic-angle-spinning NMR experiments for the simultaneous measurement of multiple carbon-nitrogen distances in uniformly (13)C,(15)N-labeled solids. The approaches employ transferred echo double resonance (TEDOR) for (13)C-(15)N coherence transfer and (15)N and (13)C frequency labeling for site-specific resolution, and build on several previous 3D TEDOR techniques. The novel feature of the 3D TEDOR pulse sequences presented here is that they are specifically designed to circumvent the detrimental effects of homonuclear (13)C-(13)C J-couplings on the measurement of weak (13)C-(15)N dipolar couplings. In particular, homonuclear J-couplings lead to two undesirable effects: (i) they generate anti-phase and multiple-quantum (MQ) spin coherences, which lead to spurious cross-peaks and phase-twisted lines in the 2D (15)N-(13)C correlation spectra, and thus degrade the spectral resolution and prohibit the extraction of reliable cross-peak intensities, and (ii) they significantly reduce cross-peak intensities for strongly J-coupled (13)C sites (e.g., CO and C(alpha)). The first experiment employs z-filter periods to suppress the anti-phase and MQ coherences and generates 2D spectra with purely absorptive peaks for all TEDOR mixing times. The second approach uses band-selective (13)C pulses to refocus J-couplings between (13)C spins within the selective pulse bandwidth and (13)C spins outside the bandwidth. The internuclear distances are extracted by using a simple analytical model, which accounts explicitly for multiple spin-spin couplings contributing to cross-peak buildup. The experiments are demonstrated in two U-(13)C,(15)N-labeled peptides, N-acetyl-L-Val-L-Leu (N-ac-VL) and N-formyl-L-Met-L-Leu-L-Phe (N-f-MLF), where 20 and 26 (13)C-(15)N distances up to approximately 5-6 A were measured, respectively. Of the measured distances, 10 in N-ac-VL and 13 in N-f-MLF are greater than 3 A and provide valuable structural constraints.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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45
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Beger RD, Buzatu DA, Wilkes JG, Lay JO. Comparative structural connectivity spectra analysis (CoSCoSA) models of steroid binding to the corticosteroid binding globulin. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2002; 42:1123-31. [PMID: 12376999 DOI: 10.1021/ci025511e] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A three-dimensional quantitative spectrometric data-activity relationship (3D-QSDAR) model was developed that is built by combining NMR spectral information with structural information in a 3D-connectivity matrix. The 3D-connectivity matrix is built by displaying all possible carbon-to-carbon connections with their assigned carbon NMR chemical shifts and distances between the carbons. Selected 2D (13)C-(13)C COrrelation SpectroscopY (COSY) (through-bond nearest neighbors) and selected theoretical 2D (13)C-(13)C distance connectivity spectral slices from the 3D-connectivity matrix to produce a relationship among the spectral patterns for 30 steroids binding to corticosteroid binding globulin. We call this technique a comparative structural connectivity spectra analysis (CoSCoSA) modeling. A CoSCoSA principal component linear regression model based on the combination of (13)C-(13)C COSY and (13)C-(13)C distance spectra principal components (PCs) had an r(2) of 0.96 and a leave-one-out (LOO) cross-validation q(2) of 0.92. A CoSCoSA parallel distributed artificial neural network (PD-ANN) model based on the combination of (13)C-(13)C COSY and (13)C-(13)C distance spectra had an r(2) of 0.96, a leave-three-out q(3)(2) of 0.78, and a leave-ten-out q(10)(2) of 0.73. CoSCoSA modeling attempts to uniquely combine the quantum mechanics information from the NMR chemical shifts with internal molecular atom-to-atom distances into an accurate modeling technique. The CoSCoSA modeling technique has the flexibility and accuracy to outperform the cross-validated variance q(2) of previously published quantitative structure-activity relationship (QSAR), quantitative spectral data-activity relationship (QSDAR), self-organizing map (SOM), and electrotopological state (E-state) models.
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Affiliation(s)
- Richard D Beger
- Division of Chemistry, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079-9502, USA.
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46
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Coltart DM, Royyuru AK, Williams LJ, Glunz PW, Sames D, Kuduk SD, Schwarz JB, Chen XT, Danishefsky SJ, Live DH. Principles of mucin architecture: structural studies on synthetic glycopeptides bearing clustered mono-, di-, tri-, and hexasaccharide glycodomains. J Am Chem Soc 2002; 124:9833-44. [PMID: 12175243 DOI: 10.1021/ja020208f] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural characteristics of a mucin glycopeptide motif derived from the N-terminal fragment STTAV of the cell surface glycoprotein CD43 have been investigated by NMR. In this study, a series of molecules prepared by total synthesis were examined, consisting of the peptide itself, three glycopeptides having clustered sites of alpha-O-glycosylation on the serine and threonine side chains with the Tn, TF, and STF carbohydrate antigens, respectively, and one with the beta-O-linked TF antigen. Additionally, a glycopeptide having the sequence SSSAVAV, triglycosylated with the Le(y) epitope, was investigated. NMR data for the tri-STF-STTAV glycopeptide were used to solve the structure of this construct through restrained molecular dynamics calculations. The calculations revealed a defined conformation for the glycopeptide core rooted in the interaction of the peptide and the first N-acetylgalactosamine residue. The similarity of the NMR data for each of the alpha-O-linked glycopeptides demonstrates that this structure persists for each construct and that the mode of attachment of the first sugar and the peptide is paramount in establishing the organization of the core. The core provides a common framework on which a variety of glycans may be displayed. Remarkably, while there is a profound organizational effect on the peptide backbone with the alpha-linked glycans, attachment via a beta-linkage has little apparent consequence.
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Affiliation(s)
- Don M Coltart
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
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47
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Yao S, Smith-White MA, Potter EK, Norton RS. Stabilization of the helical structure of Y2-selective analogues of neuropeptide Y by lactam bridges. J Med Chem 2002; 45:2310-8. [PMID: 12014969 DOI: 10.1021/jm010543z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of helical structure in an analogue of NPY selective for the Y2 receptor, Ac[Leu28,31]NPY24-36, has been investigated by introducing a lactam bridge between positions 28 and 32. The resulting analogue, Ac-cyclo28/32[Ala24,Lys28,Leu31,Glu32]NPY24-36, is a potent Y2-selective agonist. Structural analysis by NMR shows that this analogue forms a helical structure in a 40% trifluoroethanol/water mixture, whereas in water only the region around the lactam bridge (Lys28-Glu32) adopts helical-like structure, with both N- and C-termini being poorly defined. The observation of well-defined helical structure in aqueous TFE contrasts with that reported for a similar analogue, Ac-cyclo28/32[Lys28,Glu32]NPY25-36 (Rist et al. FEBS Lett. 1996, 394, 169-173), which consisted of a hairpin-like structure that brought the N- and C-termini into proximity. We have therefore determined the structures of this analogue, as well as those of Ac-cyclo28/32[Ala24,Lys28,Leu31,Glu32]NPY24-36 and Ac-cyclo28/32[Ala24,Lys28,Glu32]NPY24-36, under identical solution conditions (30% TFE/H2O mixture at 308 K) and find essentially the same helical structure in all three peptides. These findings support the proposal that these Y2-selective analogues adopt a helical structure when bound to the Y2 receptor.
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Affiliation(s)
- Shenggen Yao
- Biomolecular Research Institute, 343 Royal Parade, Parkville, Victoria 3052, Australia
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48
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Abstract
Molecular modelling is a powerful methodology for analysing the three dimensional structure of biological macromolecules. There are many ways in which molecular modelling methods have been used to address problems in structural biology. It is not widely appreciated that modelling methods are often an integral component of structure determination by NMR spectroscopy and X-ray crystallography. In this review we consider some of the numerous ways in which modelling can be used to interpret and rationalise experimental data and in constructing hypotheses that can be tested by experiment. Genome sequencing projects are producing a vast wealth of data describing the protein coding regions of the genome under study. However, only a minority of the protein sequences thus identified will have a clear sequence homology to a known protein. In such cases valuable three-dimensional models of the protein coding sequence can be constructed by homology modelling methods. Threading methods, which used specialised schemes to relate protein sequences to a library of known structures, have been shown to be able to identify the likely protein fold even in cases where there is no clear sequence homology. The number of protein sequences that cannot be assigned to a structural class by homology or threading methods, simply because they belong to a previously unidentified protein folding class, will decrease in the future as collaborative efforts in systematic structure determination begin to develop. For this reason, modelling methods are likely to become increasingly useful in the near future. The role of the blind prediction contests, such as the Critical Assessment of techniques for protein Structure Prediction (CASP), will be briefly discussed. Methods for modelling protein-ligand and protein-protein complexes are also described and examples of their applications given.
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Affiliation(s)
- Mark J Forster
- Informatics Laboratory, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire, UK.
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49
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White JL, Wang X. Structural Investigations of Solid Proteins at Natural Abundance Using 2D Multiple-Pulse NMR. Macromolecules 2002. [DOI: 10.1021/ma012067s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeffery L. White
- Department of Chemistry, North Carolina State University, Campus Box 8204, Raleigh, North Carolina 27695-8204
| | - Xingwu Wang
- Department of Chemistry, North Carolina State University, Campus Box 8204, Raleigh, North Carolina 27695-8204
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Almeida MS, Cabral KMS, Kurtenbach E, Almeida FCL, Valente AP. Solution structure of Pisum sativum defensin 1 by high resolution NMR: plant defensins, identical backbone with different mechanisms of action. J Mol Biol 2002; 315:749-57. [PMID: 11812144 DOI: 10.1006/jmbi.2001.5252] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pisum sativum defensin 1 (Psd1) is a 46 amino acid residue plant defensin isolated from seeds of pea. The three-dimensional structure in solution of Psd1 was determined by two-dimensional NMR data recorded at 600 MHz. Experimental restraints were used for structure calculation using CNS and torsion-angle molecular dynamics. The 20 lowest energy structures were selected and further subjected to minimization, giving a root-mean-square deviation of 0.78(+/- 0.22) A in the backbone and 1.91(+/-0.60) A for over all atoms of the molecule. The protein has a globular fold with a triple-stranded antiparalell beta-sheet and an alpha-helix (from residue Asn17 to Leu27). Psd1 presents the so called "cysteine stabilized alpha/beta motif" and presents identical three-dimensional topology in the backbone with other defensins and neurotoxins. Comparison of the electrostatic surface potential among proteins with high three-dimensional (selected using the softwares TOP and DALI) topology gave insights into the mode of action of Psd1. The surface topologies between proteins that present antifungal activity or sodium channel inhibiting activity are different. On the other hand the surface topology presents several common features with potassium channel inhibitors, suggesting that Psd1 presents this activity. Other common features with potassium channel inhibitors were found including the presence of a lysine residue essential for inhibitory activity. The identity of Psd1 in primary sequence is not enough to infer a mechanism of action, in contrast with the strategy proposed here.
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Affiliation(s)
- Marcius S Almeida
- Departamento de Bioquímica Médica, ICB/CCS/UFRJ. CEP., Rio de Janeiro, 21941-590, Brazil
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