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Smith MH, Miles TF, Sheehan M, Alfieri KN, Kokona B, Fairman R. Polyglutamine fibrils are formed using a simple designed beta-hairpin model. Proteins 2010; 78:1971-9. [PMID: 20408173 DOI: 10.1002/prot.22713] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Polyglutamine repeats are found in proteins associated with many neurodegenerative diseases. These repeats are responsible for intracellular protein aggregation that resemble amyloid plaques and contain the hallmarks of cross-beta fibrillar structures. Recent work has suggested that the glutamines are involved in aggregation through two possible mechanisms: one involving only side-chain hydrogen bonding and a second involving interdigitation of the glutamines with tight van der Waal's packing (steric zipper model). We are interested in determining which interactions are particularly involved in early assembly processes and have developed a beta-hairpin model system to address this problem. Our model system is designed to stabilize a putative high-energy nucleating structure to provide a window to view early assembly processes. We have applied spectroscopy tools (circular dichroism, infrared, and dynamic light scattering) to probe the self-assembly of beta-sheet fibrils. These experiments established the conditions to study fibrillar morphology using atomic force microscopy. We show that fibrils are short with minimal lateral growth, suggesting that this may be a good model system for studying early assembly steps.
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Affiliation(s)
- Melanie H Smith
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041, USA
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52
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Abstract
Although much has been learned about the design of models of beta-sheets during the last decade, modest fold stabilities in water and terminal fraying remain a feature of most beta-hairpin peptides. In the case of hairpin capping, nature did not provide guidance for solving the problem. Some observations from prior turn capping designs, with further optimization, have provided a generally applicable, "unnatural" beta cap motif (alkanoyl-Trp at the N terminus and Trp-Thr-Gly at the C terminus) that provides a net contribution of 6 + kJ/mol to beta-hairpin stability, surpassing all other interactions that stabilize beta-hairpins including the covalent disulfide bond. The motif, made up entirely of natural residues, is specific to the termini of antiparallel beta-strands and reduces fraying at the ends of hairpins and other beta-sheet models. Utilizing this motif, 10- to 22-residue peptide scaffolds of defined stereochemistry that are greater than 98% folded in water have been prepared. The beta-cap can also be used to staple together short antiparallel beta-strands connected by a long flexible loop.
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53
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He Y, Chen C, Xiao Y. United-Residue (UNRES) Langevin Dynamics Simulations of trpzip2 Folding. J Comput Biol 2009; 16:1719-30. [DOI: 10.1089/cmb.2008.0070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yi He
- Biomolecular Physics and Molecular Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Changjun Chen
- Biomolecular Physics and Molecular Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Xiao
- Biomolecular Physics and Molecular Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
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54
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Wu L, McElheny D, Huang R, Keiderling TA. Role of Tryptophan−Tryptophan Interactions in Trpzip β-Hairpin Formation, Structure, and Stability. Biochemistry 2009; 48:10362-71. [PMID: 19788311 DOI: 10.1021/bi901249d] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ling Wu
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Rong Huang
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
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55
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Chiu HP, Kokona B, Fairman R, Cheng RP. Effect of Highly Fluorinated Amino Acids on Protein Stability at a Solvent-Exposed Position on an Internal Strand of Protein G B1 Domain. J Am Chem Soc 2009; 131:13192-3. [DOI: 10.1021/ja903631h] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hsien-Po Chiu
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, Department of Biology, Haverford College, Haverford, Pennsylvania 19041, and Department of Chemistry, National Taiwan University, Taipei, Taiwan 10617
| | - Bashkim Kokona
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, Department of Biology, Haverford College, Haverford, Pennsylvania 19041, and Department of Chemistry, National Taiwan University, Taipei, Taiwan 10617
| | - Robert Fairman
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, Department of Biology, Haverford College, Haverford, Pennsylvania 19041, and Department of Chemistry, National Taiwan University, Taipei, Taiwan 10617
| | - Richard P. Cheng
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, Department of Biology, Haverford College, Haverford, Pennsylvania 19041, and Department of Chemistry, National Taiwan University, Taipei, Taiwan 10617
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56
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Eidenschink L, Crabbe E, Andersen NH. Terminal sidechain packing of a designed beta-hairpin influences conformation and stability. Biopolymers 2009; 91:557-64. [PMID: 19263490 DOI: 10.1002/bip.21177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
While end capping in alpha-helices is well understood, the concept of capping a beta-hairpin is a relatively recent development; to date, favorable Coulombic interactions are the only example of sidechains at the termini influencing the overall stability of a beta-hairpin. While cross-strand hydrophobic residues generally provide hairpin stabilization, particular when flanking the turn region, those remote from this location appear to provide little stabilization. While probing for an optimal residue at a hydrogen bond position near the terminus of a designed beta-hairpin a conservative, hydrophobic, V --> I mutation was observed to not only result in a significant change in fold population but also effected major changes in the structuring shifts at numerous sites in the peptide. Mutational studies reveal that there is an interaction between the sidechain at this H-bonded site and the sidechain at the C-terminal non-H-bonded site of the hairpin. This interaction, which appears to be hydrophobic in character, requires a highly twisted hairpin structure. Modifications at the C-terminal site, for example an E --> A mutation (DeltaDeltaG(U) = 6 kJ/mol), have profound affects on fold structure and stability. The data suggests that this may be a case of hairpin end capping by the formation of a hydrophobic cluster.
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Affiliation(s)
- Lisa Eidenschink
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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57
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George Priya Doss C, Sethumadhavan R. Computational and structural analysis of deleterious functional SNPs in ARNT oncogene. Interdiscip Sci 2009; 1:220-8. [DOI: 10.1007/s12539-009-0042-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 05/08/2009] [Accepted: 05/08/2009] [Indexed: 11/30/2022]
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58
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Xiao Y, Chen C, He Y. Folding mechanism of β-hairpin trpzip2: heterogeneity, transition state and folding pathways. Int J Mol Sci 2009; 10:2838-2848. [PMID: 19582232 PMCID: PMC2705519 DOI: 10.3390/ijms10062838] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/18/2009] [Accepted: 06/19/2009] [Indexed: 01/30/2023] Open
Abstract
We review the studies on the folding mechanism of the β-hairpin tryptophan zipper 2 (trpzip2) and present some additional computational results to refine the picture of folding heterogeneity and pathways. We show that trpzip2 can have a two-state or a multi-state folding pattern, depending on whether it folds within the native basin or through local state basins on the high-dimensional free energy surface; Trpzip2 can fold along different pathways according to the packing order of tryptophan pairs. We also point out some important problems related to the folding mechanism of trpzip2 that still need clarification, e.g., a wide distribution of the computed conformations for the transition state ensemble.
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Affiliation(s)
- Yi Xiao
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +86-27-87556652
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59
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Eidenschink L, Kier BL, Huggins KNL, Andersen NH. Very short peptides with stable folds: building on the interrelationship of Trp/Trp, Trp/cation, and Trp/backbone-amide interaction geometries. Proteins 2009; 75:308-22. [PMID: 18831035 PMCID: PMC2656586 DOI: 10.1002/prot.22240] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
By combining a favorable turn sequence with a turn flanking Trp/Trp interaction and a C-terminal H-bonding interaction between a backbone amide and an i-2 Trp ring, a particularly stable (DeltaG(U) > 7 kJ/mol) truncated hairpin, Ac-WI-(D-Pro-D-Asn)-KWTG-NH(2), results. In this construct and others with a W-(4-residue turn)-W motif in severely truncated hairpins, the C-terminal Trp is the edge residue in a well-defined face-to-edge (FtE) aryl/aryl interaction. Longer hairpins and those with six-residue turns retain the reversed "edge-to-face" (EtF) Trp/Trp geometry first observed for the trpzip peptides. Mutational studies suggest that the W-(4-residue turn)-W interaction provides at least 3 kJ/mol of stabilization in excess of that due to the greater beta-propensity of Trp. The pi-cation, and Trp/Gly-H(N) interactions have been defined. The latter can give rise to >3 ppm upfield shifts for the Gly-H(N) in -WX(n)G- units both in turns (n = 2) and at the C-termini (n = 1) of hairpins. Terminal YTG units result in somewhat smaller shifts (extrapolated to 2 ppm for 100% folding). In peptides with both the EtF and FtE W/W interaction geometries, Trp to Tyr mutations indicate that Trp is the preferred "face" residue in aryl/aryl pairings, presumably because of its greater pi basicity.
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Affiliation(s)
- Lisa Eidenschink
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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60
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Doss CGP, Sethumadhavan R. Investigation on the role of nsSNPs in HNPCC genes--a bioinformatics approach. J Biomed Sci 2009; 16:42. [PMID: 19389263 PMCID: PMC2682794 DOI: 10.1186/1423-0127-16-42] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 04/24/2009] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND A central focus of cancer genetics is the study of mutations that are causally implicated in tumorigenesis. The identification of such causal mutations not only provides insight into cancer biology but also presents anticancer therapeutic targets and diagnostic markers. Missense mutations are nucleotide substitutions that change an amino acid in a protein, the deleterious effects of these mutations are commonly attributed to their impact on primary amino acid sequence and protein structure. METHODS The method to identify functional SNPs from a pool, containing both functional and neutral SNPs is challenging by experimental protocols. To explore possible relationships between genetic mutation and phenotypic variation, we employed different bioinformatics algorithms like Sorting Intolerant from Tolerant (SIFT), Polymorphism Phenotyping (PolyPhen), and PupaSuite to predict the impact of these amino acid substitutions on protein activity of mismatch repair (MMR) genes causing hereditary nonpolyposis colorectal cancer (HNPCC). RESULTS SIFT classified 22 of 125 variants (18%) as 'Intolerant." PolyPhen classified 40 of 125 amino acid substitutions (32%) as "Probably or possibly damaging". The PupaSuite predicted the phenotypic effect of SNPs on the structure and function of the affected protein. Based on the PolyPhen scores and availability of three-dimensional structures, structure analysis was carried out with the major mutations that occurred in the native protein coded by MSH2 and MSH6 genes. The amino acid residues in the native and mutant model protein were further analyzed for solvent accessibility and secondary structure to check the stability of the proteins. CONCLUSION Based on this approach, we have shown that four nsSNPs, which were predicted to have functional consequences (MSH2-Y43C, MSH6-Y538S, MSH6-S580L, and MSH6-K854M), were already found to be associated with cancer risk. Our study demonstrates the presence of other deleterious mutations and also endorses with in vivo experimental studies.
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Affiliation(s)
- C George Priya Doss
- Bioinformatics Division, School of Biotechnology, Chemical and Biomedical Engineering, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
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61
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Laufer B, Chatterjee J, Frank AO, Kessler H. Can N-methylated amino acids serve as substitutes for prolines in conformational design of cyclic pentapeptides? J Pept Sci 2009; 15:141-6. [PMID: 18985637 DOI: 10.1002/psc.1076] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The incorporation of proline into cyclic peptides seems to be the most promising way to induce beta-turn structures. Recently, however, it was shown that N-methylated amino acids might be even better suited than proline for introducing turn structures. Another property of proline, the ability to effect cis-peptide bonds, has also been reported for N-methylated amino acids. These findings raise the question if it might be possible to replace a proline by an N-methylated amino acid without altering the desired conformational features. The most important benefit of replacing proline by an N-methylated residue is that one recovers the side-chain functionalities, which could be used for enhancing binding selectivity, or to tune a cyclic peptide concerning its pharmacological properties.Here, we compare cyclic peptides containing one or two prolines or N-methylated alanines and a combination of both with respect to preferred conformations and cis-peptide bonds. In addition, the positions have been investigated where an N-alkylated amino acid has to be incorporated to mimic structural aspects usually introduced by proline residues.
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Affiliation(s)
- Burkhardt Laufer
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747 Germany
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62
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Takekiyo T, Wu L, Yoshimura Y, Shimizu A, Keiderling TA. Relationship between Hydrophobic Interactions and Secondary Structure Stability for Trpzip β-Hairpin Peptides. Biochemistry 2009; 48:1543-52. [DOI: 10.1021/bi8019838] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takahiro Takekiyo
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan, and Department of Environmental Engineering for Symbiosis Factory of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Ling Wu
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan, and Department of Environmental Engineering for Symbiosis Factory of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Yukihiro Yoshimura
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan, and Department of Environmental Engineering for Symbiosis Factory of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Akio Shimizu
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan, and Department of Environmental Engineering for Symbiosis Factory of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa 239-8686, Japan, and Department of Environmental Engineering for Symbiosis Factory of Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
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63
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Bour P, Kim J, Kapitan J, Hammer RP, Huang R, Wu L, Keiderling TA. Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide. Chirality 2008; 20:1104-19. [DOI: 10.1002/chir.20560] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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64
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Tam EM, Runyon ST, Santell L, Quan C, Yao X, Kirchhofer D, Skelton NJ, Lazarus RA. Noncompetitive inhibition of hepatocyte growth factor-dependent Met signaling by a phage-derived peptide. J Mol Biol 2008; 385:79-90. [PMID: 18973760 DOI: 10.1016/j.jmb.2008.09.091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 09/12/2008] [Accepted: 09/16/2008] [Indexed: 01/25/2023]
Abstract
Dysregulation of hepatocyte growth factor (HGF)-induced signaling via its receptor tyrosine kinase Met results in tumor progression and metastasis. To initiate signaling, pro-HGF must be proteolytically activated to reveal a secondary Met binding site within the serine protease-like beta-chain of HGF. Although HGF/Met is a large complex, we sought to discover relatively small antagonists that might interfere with this critical Met binding region. Pools of disulfide-constrained random peptide libraries displayed on phage were selected for binding to HGF, ultimately resulting in a disulfide-constrained 15-mer peptide (VNWVCFRDVGCDWVL) termed HB10, which bound to the recombinant human HGF beta-chain (HGF beta) and competitively inhibited binding to Met with an IC(50) of 450 nM. In MDA-MB435 cells, HB10 reduced HGF-dependent Met phosphorylation by 70%, and phosphorylation of downstream kinases AKT and ERK1/ERK2 by 74% and 69%, respectively. Addition of HB10 also inhibited HGF-dependent migration of these cells with an IC(50) of approximately 20 microM. The 2D (1)H-NMR structure of HB10 revealed a beta-hairpin loop stabilized by the disulfide bond and cross-strand pairing of Trp3 and Trp13. HGF beta mutants deficient in Met binding also have reduced HB10 binding, suggesting an overlapping binding site. Notably HB10 did not inhibit full length HGF binding to Met. Thus steric hindrance of the interaction between HGF beta domain binding to Met is sufficient for inhibiting full-length HGF-dependent Met signaling and cell migration that is consistent with a noncompetitive inhibitory mechanism of Met signal transduction.
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Affiliation(s)
- Eric M Tam
- Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080, USA
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65
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Abstract
Beta-sheets consist of extended polypeptide strands (beta-strands) connected by a network of hydrogen bonds and occur widely in proteins. Although the importance of beta-sheets in the folded structures of proteins has long been recognized, there is a growing recognition of the importance of intermolecular interactions among beta-sheets. Intermolecular interactions between the hydrogen-bonding edges of beta-sheets constitute a fundamental form of biomolecular recognition (like DNA base pairing) and are involved protein quaternary structure, protein-protein interactions, and peptide and protein aggregation. The importance of beta-sheet interactions in biological processes makes them potential targets for intervention in diseases such as AIDS, cancer, and Alzheimer's disease. This Account describes my research group's use of chemical model systems to study the structure and interactions of beta-sheets. Chemical model systems provide an excellent vehicle with which to explore beta-sheets, because they are smaller, simpler, and easier to manipulate than proteins. Synthetic chemical models also provide the opportunity to control or modulate natural systems or to develop other useful applications and may eventually lead to new drugs with which to treat diseases. In our "artificial beta-sheets", molecular template and turn units are combined with peptides to mimic the structures of parallel and antiparallel beta-sheets. The templates and turn units form folded, hydrogen-bonded structures with the peptide groups and help prevent the formation of complex, ill-defined aggregates. Templates that duplicate the hydrogen-bonding pattern of one edge of a peptide beta-strand while blocking the other edge have proven particularly valuable in preventing aggregate formation and in promoting the formation of simple monomeric and dimeric structures. Artificial beta-sheets that present exposed hydrogen-bonding edges can form well-defined hydrogen-bonded dimers. Dimerization occurs readily in chloroform solutions but requires additional hydrophobic interactions to occur in aqueous solution. Interactions among the side chains, as well as hydrogen bonding among the main chains, are important in dimer formation. NMR studies of artificial beta-sheets have elucidated the importance of hydrogen-bonding complementarity, size complementarity, and chiral complementarity in these interactions. These pairing preferences demonstrate sequence selectivity in the molecular recognition between beta-sheets. These studies help illustrate the importance of intermolecular edge-to-edge interactions between beta-sheets in peptides and proteins. Ultimately, these model systems may lead to new ways of controlling beta-sheet interactions and treating diseases in which they are involved.
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Affiliation(s)
- James S Nowick
- Department of Chemistry University of California, Irvine, Irvine, California 92617-4048, USA.
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66
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Noy K, Kalisman N, Keasar C. Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials. BMC STRUCTURAL BIOLOGY 2008; 8:27. [PMID: 18510728 PMCID: PMC2427033 DOI: 10.1186/1472-6807-8-27] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Accepted: 05/29/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND The structural stability of peptides in solution strongly affects their binding affinities and specificities. Thus, in peptide biotechnology, an increase in the structural stability is often desirable. The present work combines two orthogonal computational techniques, Molecular Dynamics and a knowledge-based potential, for the prediction of structural stability of short peptides (< 20 residues) in solution. RESULTS We tested the new approach on four families of short beta-hairpin peptides: TrpZip, MBH, bhpW and EPO, whose structural stabilities have been experimentally measured in previous studies. For all four families, both computational techniques show considerable correlation (r > 0.65) with the experimentally measured stabilities. The consensus of the two techniques shows higher correlation (r > 0.82). CONCLUSION Our results suggest a prediction scheme that can be used to estimate the relative structural stability within a peptide family. We discuss the applicability of this predictive approach for in-silico screening of combinatorial peptide libraries.
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Affiliation(s)
- Karin Noy
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel.
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67
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Webb TR, Venegas RE, Wang J, Deschenes A. Generation of New Synthetic Scaffolds Using Framework Libraries Selected and Refined via Medicinal Chemist Synthetic Expertise. J Chem Inf Model 2008; 48:882-8. [DOI: 10.1021/ci7001928] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas R. Webb
- ChemBridge Research Labs., Inc., ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, and Chemical Computing Group, Suite 910-1010 Sherbrooke St. W Montreal, Quebec, Canada H3A 2R7
| | - Ruben E. Venegas
- ChemBridge Research Labs., Inc., ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, and Chemical Computing Group, Suite 910-1010 Sherbrooke St. W Montreal, Quebec, Canada H3A 2R7
| | - Jian Wang
- ChemBridge Research Labs., Inc., ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, and Chemical Computing Group, Suite 910-1010 Sherbrooke St. W Montreal, Quebec, Canada H3A 2R7
| | - Alain Deschenes
- ChemBridge Research Labs., Inc., ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, and Chemical Computing Group, Suite 910-1010 Sherbrooke St. W Montreal, Quebec, Canada H3A 2R7
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O'Nuallain B, Allen A, Ataman D, Weiss DT, Solomon A, Wall JS. Phage display and peptide mapping of an immunoglobulin light chain fibril-related conformational epitope. Biochemistry 2007; 46:13049-58. [PMID: 17944486 DOI: 10.1021/bi701255m] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Amyloid fibrils and partially unfolded intermediates can be distinguished serologically from native amyloidogenic precursor proteins or peptides. In this regard, we previously had reported that mAb 11-1F4, generated by immunizing mice with a thermally denatured variable domain (VL) fragment of the human kappa4 Bence Jones protein Len, bound to a non-native conformational epitope located within the N-terminal 18 residues of fibrillar, as well as partially denatured, Ig light chains (O'Nuallain, B., et al. (2006) Biochemistry 46, 1240-1247). To define further the antibody binding site, we used random peptide phage display and epitope mapping of VL Len using wild-type and alanine-mutated Len peptides where it was shown that the antibody epitope was reliant on up to 10 of the first 15 residues of protein Len. Comparison of Vkappa and Vlambda N-terminal germline consensus sequences with protein Len and 11-1F4-binding phages indicated that this antibody's cross-reactivity with light chains was related to an invariant proline at position(s) 7 and/or 8, bulky hydrophobic residues at positions 11 and 13, and additionally, to the ability to accommodate amino acid diversity at positions 1-4. Sequence alignments of the phage peptides revealed a central proline, often flanked by aromatic residues. Taken together, these results have provided evidence for the structural basis of the specificity of 11-1F4 for both kappa and lambda light chain fibrils. We posit that the associated binding site involves a rare type VI beta-turn or touch-turn that is anchored by a cis-proline residue. The identification of an 11-1F4-related mimotope should facilitate development of pan-light chain fibril-reactive antibodies that could be used in the diagnosis and treatment of patients with AL amyloidosis.
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Affiliation(s)
- Brian O'Nuallain
- Human Immunology and Cancer/Alzheimer's Disease and Amyloid-Related Disorders Research Program, Department of Medicine, University of Tennessee Graduate School of Medicine, Knoxville, Tennessee 37920, USA
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69
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Levin S, Nowick JS. An artificial beta-sheet that dimerizes through parallel beta-sheet interactions. J Am Chem Soc 2007; 129:13043-8. [PMID: 17918935 DOI: 10.1021/ja073391r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This Article introduces a simple chemical model of a beta-sheet (artificial beta-sheet) that dimerizes by parallel beta-sheet formation in chloroform solution. The artificial beta-sheet consists of two N-terminally linked peptide strands that are linked with succinic or fumaric acid and blocked along one edge with a hydrogen-bonding template composed of 5-aminoanisic acid hydrazide. The template is connected to one of the peptide strands by a turn unit composed of (S)-2-aminoadipic acid (Aaa). 1H NMR spectroscopic studies show that these artificial beta-sheets fold in CDCl3 solution to form well-defined beta-sheet structures that dimerize through parallel beta-sheet interactions. Most notably, all of these compounds show a rich network of NOEs associated with folding and dimerization. The compounds also exhibit chemical shifts and coupling constants consistent with the formation of folded dimeric beta-sheet structures. The aminoadipic acid unit shows patterns of NOEs and coupling constants consistent with a well-defined turn conformation. The present system represents a significant step toward modeling the type of parallel beta-sheet interactions that occur in protein aggregation.
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Affiliation(s)
- Sergiy Levin
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, USA
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70
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Hughes RM, Benshoff ML, Waters ML. Effects of chain length and N-methylation on a cation-pi interaction in a beta-hairpin peptide. Chemistry 2007; 13:5753-64. [PMID: 17431866 DOI: 10.1002/chem.200601753] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The effects of N-methylation and chain length on a cation-pi interaction have been investigated within the context of a beta-hairpin peptide. Significant enhancement of the interaction and structural stabilization of the hairpin have been observed upon Lys methylation. Thermodynamic analysis indicates an increased entropic driving force for folding upon methylation of Lys residues. Comparison of lysine to analogues ornithine (Orn) and diaminobutyric acid (Dab) indicates that lysine provides the strongest cation-pi interaction and also provides the most stable beta-hairpin due to a combination of side chain-side chain interactions and beta-sheet propensities. These studies have significance for the recognition of methylated lysine in histone proteins.
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Affiliation(s)
- Robert M Hughes
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
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71
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Jäger M, Dendle M, Fuller AA, Kelly JW. A cross-strand Trp Trp pair stabilizes the hPin1 WW domain at the expense of function. Protein Sci 2007; 16:2306-13. [PMID: 17766376 PMCID: PMC2204138 DOI: 10.1110/ps.072904107] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Using the human Pin1 WW domain (hPin1 WW), we show that replacement of two nearest neighbor non-hydrogen-bonded residues on adjacent beta-strands with tryptophan (Trp) residues increases beta-sheet thermodynamic stability by 4.8 kJ mol(-1) at physiological temperature. One-dimensional NMR studies confirmed that introduction of the Trp-Trp pair does not globally perturb the structure of the triple-stranded beta-sheet, while circular dichroism studies suggest that the engineered cross-strand Trp-Trp pair adopts a side-chain conformation similar to that first reported for a designed "Trp-zipper" beta-hairpin peptide, wherein the indole side chains stack perpendicular to each other. Even though the mutated side chains in wild-type hPin1 WW are not conserved among WW domains and compose the beta-sheet surface opposite to that responsible for ligand binding, introduction of the cross-strand Trp-Trp pair effectively eliminates hPin1 WW function as assessed by the loss of binding affinity toward a natural peptide ligand. Maximizing both thermodynamic stability and the domain function of hPin1 WW by the above mentioned approach appears to be difficult, analogous to the situation with loop 1 optimization explored previously. That introduction of a non-hydrogen-bonded cross-strand Trp-Trp pair within the hPin1 WW domain eliminates function may provide a rationale for why this energetically favorable pairwise interaction has not yet been identified in WW domains or any other biologically evolved protein with known three-dimensional structure.
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Affiliation(s)
- Marcus Jäger
- Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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72
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Andersen NH, Olsen KA, Fesinmeyer RM, Tan X, Hudson FM, Eidenschink LA, Farazi SR. Minimization and optimization of designed beta-hairpin folds. J Am Chem Soc 2007; 128:6101-10. [PMID: 16669679 PMCID: PMC3164952 DOI: 10.1021/ja054971w] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Minimized beta hairpins have provided additional data on the geometric preferences of Trp interactions in TW-loop-WT motifs. This motif imparts significant fold stability to peptides as short as 8 residues. High-resolution NMR structures of a 16- (KKWTWNPATGKWTWQE, DeltaG(U)(298) >or= +7 kJ/mol) and 12-residue (KTWNPATGKWTE, DeltaG(U)(298) = +5.05 kJ/mol) hairpin reveal a common turn geometry and edge-to-face (EtF) packing motif and a cation-pi interaction between Lys(1) and the Trp residue nearest the C-terminus. The magnitude of a CD exciton couplet (due to the two Trp residues) and the chemical shifts of a Trp Hepsilon3 site (shifted upfield by 2.4 ppm due to the EtF stacking geometry) provided near-identical measures of folding. CD melts of representative peptides with the -TW-loop-WT- motif provided the thermodynamic parameters for folding, which reflect enthalpically driven folding at laboratory temperatures with a small DeltaC(p) for unfolding (+420 J K(-)(1)/mol). In the case of Asx-Pro-Xaa-Thr-Gly-Xaa loops, mutations established that the two most important residues in this class of direction-reversing loops are Asx and Gly: mutation to alanine is destabilizing by about 6 and 2 kJ/mol, respectively. All indicators of structuring are retained in a minimized 8-residue construct (Ac-WNPATGKW-NH(2)) with the fold stability reduced to DeltaG(U)(278) = -0.7 kJ/mol. NMR and CD comparisons indicate that -TWXNGKWT- (X = S, I) sequences also form the same hairpin-stabilizing W/W interaction.
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Affiliation(s)
- Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA.
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73
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Fisk JD, Schmitt MA, Gellman SH. Thermodynamic analysis of autonomous parallel beta-sheet formation in water. J Am Chem Soc 2007; 128:7148-9. [PMID: 16734453 PMCID: PMC2723805 DOI: 10.1021/ja060942p] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the first thermodynamic analysis of parallel beta-sheet formation in a model system that folds in aqueous solution. NMR chemical shifts were used to determine beta-sheet population, and van't Hoff anaysis provided thermodynamic parameters. Our approach relies upon the d-prolyl-1,1-dimethyl-1,2-diaminoethane unit to promote parallel beta-sheet formation between attached peptide strands. The development of a macrocyclic reference molecule to provide chemical shift data for the fully folded state was crucial to the quantitative anaylsis.
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74
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Cheng Z, Miskolzie M, Campbell RE. In vivo screening identifies a highly folded beta-hairpin peptide with a structured extension. Chembiochem 2007; 8:880-3. [PMID: 17457813 DOI: 10.1002/cbic.200600565] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zihao Cheng
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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75
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Ou DM, Chen CC, Chen CM. Contact-induced structure transformation in transmembrane prion propagation. Biophys J 2007; 92:2704-10. [PMID: 17259269 PMCID: PMC1831692 DOI: 10.1529/biophysj.106.098335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Based on recent experimental evidences of the transmission of prion diseases due to a particular transmembrane form (termed (Ctm)PrP), we propose a theoretical model for the molecular mechanism of such conformational diseases, in which a misfolded (Ctm)PrP induces a similar misfolding of another (Ctm)PrP. Computer simulations are performed to investigate the correlation between folding time and the concentration of misfolded PrP in various processes, including dimerization, trimerization, and cooperative dimerization. By comparing with the experimental correlation curve between incubation time and injected dose of scrapie prions, we conclude that cooperative dimerization may play an important role in the pathological mechanism of prion diseases.
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Affiliation(s)
- D-M Ou
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan
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76
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Nowick JS. What I have learned by using chemical model systems to study biomolecular structure and interactions. Org Biomol Chem 2006; 4:3869-85. [PMID: 17047863 DOI: 10.1039/b608953b] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical model systems provide valuable insights into biomolecular structure and interactions by allowing researchers to simplify, isolate, and manipulate aspects of the complex molecular machinery of living systems. This perspective describes my laboratory's design, synthesis, and study of chemical model systems that fold and self-assemble like proteins and elucidates the insights that have come from studying these systems. Many of these studies have focused on protein beta-sheets, which exhibit fascinating intra- and intermolecular interactions and play important roles in protein folding, aggregation, and molecular recognition.
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Affiliation(s)
- James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA.
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77
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Shi T, Spain SM, Rabenstein DL. A Striking Periodicity of thecis/trans Isomerization of Proline Imide Bonds in Cyclic Disulfide-Bridged Peptides. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503470] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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78
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Shi T, Spain SM, Rabenstein DL. A Striking Periodicity of thecis/trans Isomerization of Proline Imide Bonds in Cyclic Disulfide-Bridged Peptides. Angew Chem Int Ed Engl 2006; 45:1780-3. [PMID: 16470897 DOI: 10.1002/anie.200503470] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tiesheng Shi
- Department of Chemistry, University of California, Riverside, 92521, USA
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79
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Streicher WW, Makhatadze GI. Calorimetric evidence for a two-state unfolding of the beta-hairpin peptide trpzip4. J Am Chem Soc 2006; 128:30-1. [PMID: 16390106 DOI: 10.1021/ja056392x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
beta-Sheets are a common secondary structural element found in proteins. The difficulty in studying beta-sheet folding and stability is that their formation is often dependent on the tertiary structural environment within the protein. However, the discovery of water-soluble beta-hairpin peptides has allowed them to be used as model systems because they represent the smallest units of beta-sheet structure independent of tertiary structural context. Trpzip4 has been used as a model beta-hairpin peptide to study beta-hairpin folding and stability because it is highly soluble in aqueous solutions, maintains its monomeric state, and shows reversible cooperative thermal unfolding. The previously determined thermodynamic parameters for trpzip4 thermal unfolding vary depending on the spectroscopic probe used, which questions the assumption that trpzip4 unfolds in a two-state manner. Here we provide direct calorimetric evidence that the unfolding of trpzip4 follows a two-state unfolding mode. Furthermore, the thermal unfolding of trpzip4 monitored using near- and far-UV-CD yielded thermodynamic parameters similar to those determined calorimetrically, providing additional evidence for a two-state unfolding mode.
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Affiliation(s)
- Werner W Streicher
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
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80
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Bour P, Keiderling TA. Vibrational Spectral Simulation for Peptides of Mixed Secondary Structure: Method Comparisons with the Trpzip Model Hairpin. J Phys Chem B 2005; 109:23687-97. [PMID: 16375349 DOI: 10.1021/jp054107q] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared absorption and vibrational circular dichroism (IR and VCD) spectra of model fragments of TrpZip-style beta-hairpin structures are simulated using density functional theory (DFT) methods to estimate the influence of fragment size, end effects, conformational irregularities, peptide side chains, and solvent. Different fragmentation schemes, computing the strands and turn segments separately, were tested by varying the sizes of each and their respective overlaps. For suitably overlapping fragments, atomic property tensors were found to be reliably transferable, as tested by their ability to generate simulated spectra in good agreement with results from ab initio DFT computations for the entire peptide. This fragment approach significantly reduces computational times and opens up a wider range of systems that can be studied with a DFT-based approach as compared to previous methods based on uniform repeating sequences. However, vacuum calculations do not adequately represent the frequency dispersion of solvated molecules, and thus, some alternate strategies for solvation correction are explored for improving the simulation accuracy. Unlike for regular periodic secondary structure, the solvent significantly impacts the spectral shapes of hairpins, due to the different degrees of hydration of individual amide groups, which can be exposed to or shielded from water due to external vs internal hydrogen bonding. This is amplified by the shielding of selected amides from the solvent due to bulky side chains. The peptide plus solvent was structurally modeled with molecular dynamics methods, and then an electrostatic field-based parametrization correction was added to the force field and intensity tensors to compensate for the solvent dipolar field. The effect of the shielding and subsequent reordering of modes has a larger impact on VCD than IR band shapes.
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Affiliation(s)
- Petr Bour
- Institute for Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 16610 Praha 6, Czech Republic.
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81
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Phillips ST, Piersanti G, Bartlett PA. Quantifying amino acid conformational preferences and side-chain-side-chain interactions in beta-hairpins. Proc Natl Acad Sci U S A 2005; 102:13737-42. [PMID: 16162669 PMCID: PMC1202387 DOI: 10.1073/pnas.0506646102] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Indexed: 11/18/2022] Open
Abstract
The intrinsic conformational biases of individual amino acids and their interstrand side-chain-side-chain (SC-SC) interactions both contribute to the stability of beta-sheets. The relative magnitudes of these effects have been difficult to assess in the context of folded proteins, where tertiary contacts complicate the quantitative analysis of local effects. We now report the results of such an analysis in a much simpler system, a short, stabilized beta-hairpin structure where intrastrand (conformational) and interstrand (SC-SC) influences can be distinguished in the absence of competing protein tertiary interactions. A comprehensive comparison of all pairwise combinations of 11 N-terminal and 7 C-terminal amino acids within an 8-residue, @-tide-stabilized [in which @ denotes the 1,2-dihydro-3(6H)-pyridinyl unit] beta-hairpin reveals distinct differences between the various pairings and shows that the intrastrand and interstrand effects are of comparable magnitude in contributing to the stability of the folded forms over the unfolded forms.
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Affiliation(s)
- Scott T Phillips
- Center for New Directions in Organic Synthesis, Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
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82
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Pastor MT, Giménez-Giner A, Pérez-Payá E. The Role of an Aliphatic-Aromatic Interaction in the Stabilization of a Model β-Hairpin Peptide. Chembiochem 2005; 6:1753-6. [PMID: 16149104 DOI: 10.1002/cbic.200500178] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- M Teresa Pastor
- European Molecular Biology Laboratory, Structures and Biocomputing, 69012 Heidelberg, Germany
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83
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Larson RS, Brown DC, Ye C, Hjelle B. Peptide antagonists that inhibit Sin Nombre virus and hantaan virus entry through the beta3-integrin receptor. J Virol 2005; 79:7319-26. [PMID: 15919886 PMCID: PMC1143646 DOI: 10.1128/jvi.79.12.7319-7326.2005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Specific therapy is not available for the treatment of hantavirus cardiopulmonary syndrome caused by Sin Nombre virus (SNV). The entry of pathogenic hantaviruses into susceptible human cells is dependent upon expression of the alpha(v)beta(3) integrin, and transfection of human beta(3) integrin is sufficient to confer infectibility onto CHO (Chinese hamster ovary) cells. Furthermore, pretreatment of susceptible cells with anti-beta(3) antibodies such as c7E3 or its Fab fragment ReoPro prevents hantavirus entry. By using repeated selection of a cyclic nonamer peptide phage display library on purified alpha(v)beta(3), we identified 70 peptides that were competitively eluted with ReoPro. Each of these peptides was examined for its ability to reduce the number of foci of SNV strain SN77734 in a fluorescence-based focus reduction assay according to the method of Gavrilovskaya et al. (I. N. Gavrilovskaya, M. Shepley, R. Shaw, M. H. Ginsberg, and E. R. Mackow, Proc. Natl. Acad. Sci. USA 95:7074-7079, 1998). We found that 11 peptides reduced the number of foci to a greater extent than did 80 mug/ml ReoPro when preincubated with Vero E6 cells. In addition, 8 of the 70 peptides had sequence similarity to SNV glycoproteins. We compared all 18 peptide sequences (10 most potent, 7 peptides with sequence similarity to hantavirus glycoproteins, and 1 peptide that was in the group that displayed the greatest potency and had significant sequence similarity) for their abilities to inhibit SNV, Hantaan virus (HTNV), and Prospect Hill virus (PHV) infection. There was a marked trend for the peptides to inhibit SNV and HTNV to a greater extent than they inhibited PHV, a finding that supports the contention that SNV and HTNV use beta(3) integrins and PHV uses a different receptor, beta1 integrin. We then chemically synthesized the four peptides that showed the greatest ability to neutralize SNV. These peptides inhibited viral entry in vitro as free peptides outside of the context of a phage. Some combinations of peptides proved more inhibitory than did individual peptides. In all, we have identified novel peptides that inhibit entry by SNV and HTNV via beta(3) integrins and that can be used as lead compounds for further structural optimization and consequent enhancement of activity.
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Affiliation(s)
- Richard S Larson
- UNM School of Medicine, 2325 Camino de Salud, CRF 223, Albuquerque, NM 87131, USA.
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84
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Sim J, Kim SY, Lee J. Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method. Bioinformatics 2005; 21:2844-9. [PMID: 15814555 DOI: 10.1093/bioinformatics/bti423] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The solvent accessibility of amino acid residues plays an important role in tertiary structure prediction, especially in the absence of significant sequence similarity of a query protein to those with known structures. The prediction of solvent accessibility is less accurate than secondary structure prediction in spite of improvements in recent researches. The k-nearest neighbor method, a simple but powerful classification algorithm, has never been applied to the prediction of solvent accessibility, although it has been used frequently for the classification of biological and medical data. RESULTS We applied the fuzzy k-nearest neighbor method to the solvent accessibility prediction, using PSI-BLAST profiles as feature vectors, and achieved high prediction accuracies. With leave-one-out cross-validation on the ASTRAL SCOP reference dataset constructed by sequence clustering, our method achieved 64.1% accuracy for a 3-state (buried/intermediate/exposed) prediction (thresholds of 9% for buried/intermediate and 36% for intermediate/exposed) and 86.7, 82.0, 79.0 and 78.5% accuracies for 2-state (buried/exposed) predictions (thresholds of each 0, 5, 16 and 25% for buried/exposed), respectively. Our method also showed slightly better accuracies than other methods by about 2-5% on the RS126 dataset and a benchmarking dataset with 229 proteins. AVAILABILITY Program and datasets are available at http://biocom1.ssu.ac.kr/FKNNacc/ CONTACT jul@ssu.ac.kr.
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Affiliation(s)
- Jaehyun Sim
- Department of Bioinformatics and Life Science, Bioinformatics and Molecular Design Technology Innovation Center, Soongsil University, Seoul 156-743, South Korea
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85
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Abstract
In recent years, beta-hairpin peptides have been studied in great detail. Much of the focus has been on the thermodynamic stability of beta-hairpin structure. Structural measurements have been conducted with nuclear magnetic resonance, with additional information obtained from circular dichroism, Fourier transform infrared, and molecular dynamic simulation studies. Point mutations, both in the beta-strands and in the turn region, have systematically explored the role of turn sequence, side-chain-side-chain interactions, intramolecular hydrogen bonding, and beta-strand length on beta-hairpin peptide conformational stability. In addition to studying the elements of structural stability independently, the cooperative nature of the individual components to combine to form the overall structure has also been investigated. Because the beta-hairpin peptides often spontaneously form their conformation, they have begun to serve as models for studying peptide binding and therapeutic agents.
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Affiliation(s)
- Carol E Stotz
- The University of Kansas, 2095 Constant Avenue, Lawrence, Kansas 66047, USA
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86
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Searle MS, Ciani B. Design of β-sheet systems for understanding the thermodynamics and kinetics of protein folding. Curr Opin Struct Biol 2004; 14:458-64. [PMID: 15313241 DOI: 10.1016/j.sbi.2004.06.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Peptide beta-sheet systems have emerged as context-independent models for probing secondary structure propensities, the nature and magnitude of stabilizing weak interactions, and aspects of cooperativity both parallel and perpendicular to the strand direction. These systems have allowed fundamental advances in understanding non-covalent interactions relevant to both chemical and biological systems, and in describing the protein folding energy landscape.
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Affiliation(s)
- Mark S Searle
- School of Chemistry, Centre for Biomolecular Sciences, University Park, Nottingham NG7 2RD, UK.
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87
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Santiveri CM, Santoro J, Rico M, Jiménez MA. Factors involved in the stability of isolated beta-sheets: Turn sequence, beta-sheet twisting, and hydrophobic surface burial. Protein Sci 2004; 13:1134-47. [PMID: 15044739 PMCID: PMC2280049 DOI: 10.1110/ps.03520704] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 01/15/2004] [Accepted: 01/20/2004] [Indexed: 10/26/2022]
Abstract
We have recently reported on the design of a 20-residue peptide able to form a significant population of a three-stranded up-and-down antiparallel beta-sheet in aqueous solution. To improve our beta-sheet model in terms of the folded population, we have modified the sequences of the two 2-residue turns by introducing the segment DPro-Gly, a sequence shown to lead to more rigid type II' beta-turns. The analysis of several NMR parameters, NOE data, as well as Deltadelta(CalphaH), DeltadeltaC(beta), and Deltadelta(Cbeta) values, demonstrates that the new peptide forms a beta-sheet structure in aqueous solution more stable than the original one, whereas the substitution of the DPro residues by LPro leads to a random coil peptide. This agrees with previous results on beta-hairpin-forming peptides showing the essential role of the turn sequence for beta-hairpin folding. The well-defined beta-sheet motif calculated for the new designed peptide (pair-wise RMSD for backbone atoms is 0.5 +/- 0.1 A) displays a high degree of twist. This twist likely contributes to stability, as a more hydrophobic surface is buried in the twisted beta-sheet than in a flatter one. The twist observed in the up-and-down antiparallel beta-sheet motifs of most proteins is less pronounced than in our designed peptide, except for the WW domains. The additional hydrophobic surface burial provided by beta-sheet twisting relative to a "flat" beta-sheet is probably more important for structure stability in peptides and small proteins like the WW domains than in larger proteins for which there exists a significant contribution to stability arising from their extensive hydrophobic cores.
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Affiliation(s)
- Clara M Santiveri
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
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88
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89
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Abstract
beta-Hairpin peptides (two anti-parallel strands linked by a reverse beta-turn) have emerged as the simplest systems for probing weak interactions in beta-sheet folding. We describe a model 16-residue hairpin system (peptide beta1: KKYTVSINGKKITVSI) designed around the anti-parallel beta-sheet DNA binding motif of the Met repressor dimer in which two beta-strand sequences are linked through an Asn-Gly type I' beta-turn. The peptide is significantly folded in aqueous solution and has a well-defined conformation as evident from an abundance of NOE data. We review a number of analogues of beta1 designed to estimate the energetic contribution of electrostatic (ion pairing) interactions to hairpin stability, to examine effects of cooperativity and preorganization in determining the energetics of weak interactions, and examine the effects on stability and conformation of incorporation of a three-histidine motif on one face of the hairpin capable of zinc complexation.
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Affiliation(s)
- Mark S Searle
- School of Chemistry, Centre for Biomolecular Sciences University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.
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90
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Dhanasekaran M, Prakash O, Gong YX, Baures PW. Expected and unexpected results from combined β-hairpin design elements. Org Biomol Chem 2004; 2:2071-82. [PMID: 15254635 DOI: 10.1039/b315228f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A model beta-hairpin dodecapeptide [EFGWVpGKWTIK] was designed by including a favorable D-ProGly Type II' beta-turn sequence and a Trp-zip interaction, while also incorporating a beta-strand unfavorable glycine residue in the N-terminal strand. This peptide is highly folded and monomeric in aqueous solution as determined by combined analysis with circular dichroism and 1H NMR spectroscopy. A peptide representing the folded conformation of the model beta-hairpin [cyclic(EFGWVpGKWTIKpG)] and a linear peptide representing the unfolded conformation [EFGWVPGKWTIK] yield unexpected relative deviations between the CD and 1H NMR spectroscopic results that are attributed to variations in the packing interactions of the aromatic side chains. Mutational analysis of the model beta-hairpin indicates that the Trp-zip interaction favors folding and stability relative to an alternate hydrophobic cluster between Trp and Tyr residues [EFGYVpGKWTIK]. The significance of select diagonal interactions in the model beta-hairpin was tested by rearranging the cross-strand hydrophobic interactions to provide a folded peptide [EWFGIpGKTYWK] displaying evidence of an unusual backbone conformation at the hydrophobic cluster. This unusual conformation does not appear to be a result of the glycine residue in the beta-strand, as replacement with a serine results in a peptide [EWFSIpGKTYWK] with a similar and seemingly characteristic CD spectrum. However, an alternate arrangement of hydrophobic residues with a Trp-zip interaction in a similar position to the parent beta-hairpin [EGFWVpGKWITK] results in a folded beta-hairpin conformation. The differences between side chain packing of these peptides precludes meaningful thermodynamic analysis and illustrates the caution necessary when interpreting beta-hairpin folding thermodynamics that are driven, at least in part, by aromatic cross strand interactions.
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Cristian L, Lear JD, DeGrado WF. Determination of membrane protein stability via thermodynamic coupling of folding to thiol-disulfide interchange. Protein Sci 2003; 12:1732-40. [PMID: 12876322 PMCID: PMC2323959 DOI: 10.1110/ps.0378603] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Although progress has been made in understanding the thermodynamic stability of water-soluble proteins, our understanding of the folding of membrane proteins is at a relatively primitive level. A major obstacle to understanding the folding of membrane proteins is the discovery of systems in which the folding is in thermodynamic equilibrium, and the development of methods to quantitatively assess this equilibrium in micelles and bilayers. Here, we describe the application of disulfide cross-linking to quantitatively measure the thermodynamics of membrane protein association in detergent micelles. The method involves initiating disulfide cross-linking of a protein under reversible redox conditions in a thiol-disulfide buffer and quantitative assessment of the extent of cross-linking at equilibrium. The 19-46 alpha-helical transmembrane segment of the M2 protein from the influenza A virus was used as a model membrane protein system for this study. Previously it has been shown that transmembrane peptides from this protein specifically self-assemble into tetramers that retain the ability to bind to the drug amantadine. We used thiol-disulfide exchange to quantitatively measure the tetramerization equilibrium of this transmembrane protein in dodecylphosphocholine (DPC) detergent micelles. The association constants obtained agree remarkably well with those derived from analytical ultracentrifugation studies. The experimental method established herein should provide a broadly applicable tool for thermodynamic studies of folding, oligomerization and protein-protein interactions of membrane proteins.
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Affiliation(s)
- Lidia Cristian
- Department of Biochemistry & Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA
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Blandl T, Cochran AG, Skelton NJ. Turn stability in beta-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns. Protein Sci 2003; 12:237-47. [PMID: 12538887 PMCID: PMC2312432 DOI: 10.1110/ps.0228603] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The turn-forming ability of a series of three-residue sequences was investigated by substituting them into a well-characterized beta-hairpin peptide. The starting scaffold, bhpW, is a disulfide-cyclized 10-residue peptide that folds into a stable beta-hairpin with two antiparallel strands connected by a two-residue reverse turn. Substitution of the central two residues with the three-residue test sequences leads to less stable hairpins, as judged by thiol-disulfide equilibrium measurements. However, analysis of NMR parameters indicated that each molecule retains a significant folded population, and that the type of turn adopted by the three-residue sequence is the same in all cases. The solution structure of a selected peptide with a PDG turn contained an antiparallel beta-hairpin with a 3:5 type I + G1 bulge turn. Analysis of the energetic contributions of individual turn residues in the series of peptides indicates that substitution effects have significant context dependence, limiting the predictive power of individual amino acid propensities for turn formation. The most stable and least stable sequences were also substituted into a more stable disulfide-cyclized scaffold and a linear beta-hairpin scaffold. The relative stabilities remained the same, suggesting that experimental measurements in the bhpW context are a useful way to evaluate turn stability for use in protein design projects. Moreover, these scaffolds are capable of displaying a diverse set of turns, which can be exploited for the mimicry of protein loops or for generating libraries of reverse turns.
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Affiliation(s)
- Tamas Blandl
- Department of Protein Engineering, Genentech, South San Francisco, California 94080, USA
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