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Fang R, He L, Wang Y, Wang L, Qian H, Yang S. The Investigation of the Subtle Structural Discrepancies between Oryza Sativa Recombinant and Plasma-Derived Human Serum Albumins to Design a Novel Nanoparticle as a Taxane Delivery System. Protein J 2024; 43:544-558. [PMID: 38581543 DOI: 10.1007/s10930-024-10194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 04/08/2024]
Abstract
To solve the large size faultiness of Oryza sativa recombinant human serum albumin nanoparticle (OsrHSA NP), the structural discrepancies between OsrHSA and plasma-derived human serum albumin (pdHSA) were analyzed deeply in this research. It demonstrated that there were some subtle structural discrepancies located in subdomain IA and IIA between OsrHSA and pdHSA, which included peptide backbone, disulphide bridge and some amino acids. Firstly, the structural discrepancies were investigated through literature comparison, it inferred that the structural discrepancies resulted from the fatty acid (FA) binding to OsrHSA at site 2 of subdomain IA and IIA. To form a cavity for accommodation of FA molecule in OsrHSA, the peptide backbone structure of subdomain IA and IIA would change, accompanied by the conformational transition of disulphide bridges and side chain structure change of some amino acids in subdomain IA and IIA. These alterations induced the exposure of tryptophan (Trp) and tyrosine (Tyr) residues in subdomain IA and IIA and the decrease of net negative charges of molecular surface. The former would promote more OsrHSA molecules aggregate, and the latter would weaken the electrostatic repulsion. As a result, the size of OsrHSA NP was more extensive than that of pdHSA NP (175.84 ± 15.63 nm vs. 31.67 ± 1.31 nm) when the concentration of Dimethyl Sulphoxide (DMSO) was 30% (v/v). In this study, the experimental scheme of OsrHSA NP preparation was improved. There were two changes in the enhanced preparation scheme: pH 8.2 PBS buffer and 63% DMSO. It indicated that the improved OsrHSA NP carrier was comparable to the pdHSA NP carrier. The size and drug loading of paclitaxel-loaded improved OsrHSA NP were 53.57 ± 3.63 nm and 7.25 ± 0.46% (w/w), and those of docetaxel-loaded improved OsrHSA NP were 44.75 ± 2.26 nm and 8.43 ± 0.74% (w/w). Moreover, both NPs exhibited good stability for 168 h at 7.4 pH values. It is established that the improved OsrHSA NP is comparable to the pdHSA NP as a taxane delivery system.
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Affiliation(s)
- Ru Fang
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Liang He
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Yanbin Wang
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Liling Wang
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Hua Qian
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Shaozong Yang
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China.
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Messina MS, Maynard HD. Modification of Proteins Using Olefin Metathesis. MATERIALS CHEMISTRY FRONTIERS 2020; 4:1040-1051. [PMID: 34457313 PMCID: PMC8388616 DOI: 10.1039/c9qm00494g] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Olefin metathesis has revolutionized synthetic approaches to carbon-carbon bond formation. With a rich history beginning in industrial settings through its advancement in academic laboratories leading to new and highly active metathesis catalysts, olefin metathesis has found use in the generation of complex natural products, the cyclization of bioactive materials, and in the polymerization of new and unique polymer architectures. Throughout this review, we will trace the deployment of olefin metathesis-based strategies for the modification of proteins, a process which has been facilitated by the extensive development of stable, isolable, and highly active transition-metal-based metathesis catalysts. We first begin by summarizing early works which detail peptide modification strategies that played a vital role in identifying stable metathesis catalysts. We then delve into protein modification using cross metathesis and finish with recent work on the generation of protein-polymer conjugates through ring-opening metathesis polymerization.
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Affiliation(s)
- Marco S Messina
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, USA
- California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, USA
| | - Heather D Maynard
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, USA
- California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, USA
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3
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Murphy RD, in het Panhuis M, Cryan SA, Heise A. Disulphide crosslinked star block copolypeptide hydrogels: influence of block sequence order on hydrogel properties. Polym Chem 2018. [DOI: 10.1039/c8py00741a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Strong redox responsive hydrogels with mechanical properties depending on the positioning of oligo(cysteine) within the star polypeptides were obtained.
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Affiliation(s)
- Robert D. Murphy
- Department of Chemistry
- Royal College of Surgeons in Ireland
- Dublin 2
- Ireland
| | - Marc in het Panhuis
- Soft Materials Group
- School of Chemistry
- and Australian Research Council Centre of Excellence for Electromaterials Science
- University of Wollongong
- Wollongong
| | - Sally-Ann Cryan
- Drug Delivery & Advanced Materials Team
- School of Pharmacy
- RCSI
- Dublin
- Ireland
| | - Andreas Heise
- Department of Chemistry
- Royal College of Surgeons in Ireland
- Dublin 2
- Ireland
- Centre for Research in Medical Devices (CURAM)
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Metrano AJ, Abascal NC, Mercado BQ, Paulson EK, Miller SJ. Structural studies of β-turn-containing peptide catalysts for atroposelective quinazolinone bromination. Chem Commun (Camb) 2016; 52:4816-9. [PMID: 26963788 DOI: 10.1039/c6cc01428c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe herein a crystallographic and NMR study of the secondary structural attributes of a β-turn-containing tetra-peptide, Boc-Dmaa-D-Pro-Acpc-Leu-NMe2, which was recently reported as a highly effective catalyst in the atroposelective bromination of 3-arylquinazolin-4(3H)-ones. Inquiries pertaining to the functional consequences of residue substitutions led to the discovery of a more selective catalyst, Boc-Dmaa-D-Pro-Acpc-Leu-OMe, the structure of which was also explored. This new lead catalyst was found to exhibit a type I'β-turn secondary structure both in the solid state and in solution, a structure that was shown to be an accessible conformation of the previously reported catalyst, as well.
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Affiliation(s)
- A J Metrano
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
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6
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Moretto A, Crisma M, Formaggio F, Toniolo C. Building a bridge between peptide chemistry and organic chemistry: intramolecular macrocyclization reactions and supramolecular chemistry with helical peptide substrates. Biopolymers 2011; 94:721-32. [PMID: 20564031 DOI: 10.1002/bip.21445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In our ongoing efforts to build a bridge between peptide chemistry and organic chemistry, we are currently investigating: (1) two types of intramolecular macrocyclization reactions in 3(10)-helical peptides, and (2) a peptido[2]rotaxane molecular machine as a supramolecular tool using a 3(10)-helical peptide as the axle. More specifically, we studied the following two reactions: (a) the intramolecular ring-closing olefin metathesis between two amino acid residues with side chains bearing an allyl group, and (b) the intramolecular Paternò-Yang photoreaction, using a benzophenone-based amino acid as a photoaffinity reagent for a Met residue. Both reactions involve formation of a new C--C bond. As for the supramolecular system examined, we were able to identify the two stations of a new peptido[2]rotaxane characterized by an -(Aib)(6)- axle and to reversibly switch the aromatic tetramide macrocyclic wheel from one station to the next. This article summarizes the information available in the literature from other groups and the published/unpublished data originated from our laboratory on these research areas.
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Affiliation(s)
- Alessandro Moretto
- Department of Chemistry, Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy
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7
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Jacobsen Ø, Klaveness J, Rongved P. Structural and pharmacological effects of ring-closing metathesis in peptides. Molecules 2010; 15:6638-77. [PMID: 20877250 PMCID: PMC6257744 DOI: 10.3390/molecules15096638] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 09/13/2010] [Accepted: 09/15/2010] [Indexed: 11/16/2022] Open
Abstract
Applications of ring-closing alkene metathesis (RCM) in acyclic α- and β-peptides and closely related systems are reviewed, with a special emphasis on the structural and pharmacological effects of cyclization by RCM.
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Pérez de Vega MJ, García-Aranda MI, González-Muñiz R. A role for ring-closing metathesis in medicinal chemistry: Mimicking secondary architectures in bioactive peptides. Med Res Rev 2010; 31:677-715. [DOI: 10.1002/med.20199] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Thakur SS, Balaram P. Characterization of alkali induced formation of lanthionine, trisulfides, and tetrasulfides from peptide disulfides using negative ion mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:783-791. [PMID: 19200754 DOI: 10.1016/j.jasms.2008.12.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2008] [Revised: 12/17/2008] [Accepted: 12/18/2008] [Indexed: 05/27/2023]
Abstract
Peptide disulfides are unstable under alkaline conditions, resulting in the formation of products containing lanthionine and polysulfide linkages. Electrospray ionization mass spectrometry has been used to characterize major species obtained when cyclic and acyclic peptide disulfides are exposed to alkaline media. Studies on a model cyclic peptide disulfide (Boc-Cys-Pro-Leu-Cys-NHMe) and an acyclic peptide, oxidized glutathione, bis ((gamma)Glu - Cys - Gly - COOH), are described. Disulfide cleavage reactions are initiated by the abstraction of C(alpha)H or C(beta)H protons of Cys residues, with subsequent elimination of H(2)S or H(2)S(2). The buildup of reactive thiol species which act on intermediates containing dehydroalanine residues, rationalizes the formation of lanthionine and polysulfide products. In the case of the cyclic peptide disulfide, the formation of cyclic products is facilitated by the intramolecular nature of the Michael addition reaction of thiols to the dehydroalanine residue. Mass spectral evidence for the intermediate species is presented by using alkylation of thiol groups as a trapping method. Mass spectral fragmentation in the negative ion mode of the peptides derived from trisulfides and tetrasulfides results in elimination of S(2).
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Affiliation(s)
- Suman S Thakur
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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10
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KISHORE R, RAGHOTHAMA S, BALARAM P. Cystine peptides. Spectroscopic studies on the conformations of a cyclic pentapeptide disulfide. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1987.tb02265.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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12
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Demizu Y, Shiigi H, Mori H, Matsumoto K, Onomura O. Convenient synthesis of an enantiomerically pure bicyclic proline and its N-oxyl derivatives. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Synthesis of small cyclic peptides constrained with 3-(3-aminomethylphenyl)propionic acid linkers using free radical-mediated macrocyclization. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.05.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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France S, Guerin DJ, Miller SJ, Lectka T. Nucleophilic chiral amines as catalysts in asymmetric synthesis. Chem Rev 2003; 103:2985-3012. [PMID: 12914489 DOI: 10.1021/cr020061a] [Citation(s) in RCA: 402] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan France
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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15
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Park HS, Kim C, Kang YK. Preferred conformations of cyclic Ac-Cys-Pro-Xaa-Cys-NHMe peptides: a model for chain reversal and active site of disulfide oxidoreductase. Biophys Chem 2003; 105:89-104. [PMID: 12932582 DOI: 10.1016/s0301-4622(03)00139-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The conformational study on cyclic Ac-Cys-Pro-Xaa-Cys-NHMe (Ac-CPXC-NHMe; X=Ala, Val, Leu, Aib, Gly, His, Phe, Tyr, Asn and Ser) peptides has been carried out using the Empirical Conformational Energy Program for Peptides, version 3 (ECEPP/3) force field and the hydration shell model in the unhydrated and hydrated states. This work has been undertaken to investigate structural implications of the CPXC sequence as the chain reversal for the initiation of protein folding and as the motif for active site of disulfide oxidoreductases. The backbone conformation DAAA is commonly the most feasible for cyclic CPXC peptides in the hydrated state, which has a type I beta-turn at the Pro-Xaa sequence. The proline residue and the hydrogen bond between backbones of two cystines as well as the formation of disulfide bond appear to play a role in stabilizing this preferred conformation of cyclic CPXC peptides. However, the distributions of backbone conformations and beta-turns may indicate that the cyclic CPXC peptide seems to exist as an ensemble of beta-turns and coiled conformations in aqueous solution. The intrinsic stability of the cyclic CPXC motif itself for the active conformation seems to play a role in determining electrochemical properties of disulfide oxidoreductases.
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Affiliation(s)
- Hae Sook Park
- Department of Radiotechnology, Cheju-halla College, Cheju 690-708, South Korea
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16
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17
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Sastry T, Banerji B, Kiran Kumar S, Kunwar A, Das J, Nandy JP, Iqbal J. A facile conversion of a 310 helical structure to a cyclic β-turn mimic in dehydrophenylalanine-derived small peptides through ring-closing metathesis. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)01601-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Ganesh S, Jayakumar R. Role of N-t-Boc group in helix initiation in a novel tetrapeptide. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2002; 59:249-56. [PMID: 12010515 DOI: 10.1034/j.1399-3011.2002.02989.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Protecting groups in N- and C-terminal positions play a decisive role in the conformational preference of smaller peptides. Conformational analysis of tetrapeptide derivatives containing Ala, Ile and Gly residues was performed. Peptide 1, Boc-Ala-Ile-Ile-Gly-OMe (Boc: tert-butyloxycarbonyl) has a predominantly helical turn conformation in all the alcoholic solvents studied, whereas in the solid state it has a beta-sheet conformation. In contrast, peptide 2, Ac-Ala-Ile-Ile-Gly-OMe (Ac: acetyl) has a random coil conformation in solution. The FTIR spectrum of peptide 1 shows a lower frequency of urethane carbonyl, indicating involvement of the carbonyl group in hydrogen bonding in the helical turn.
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Affiliation(s)
- S Ganesh
- Bioorganic Laboratory, Central Leather Research Institute, Adyar, Chennai, India.
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19
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Affiliation(s)
- J Venkatraman
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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20
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Jarvo ER, Copeland GT, Papaioannou N, Bonitatebus PJ, Miller SJ. A Biomimetic Approach to Asymmetric Acyl Transfer Catalysis. J Am Chem Soc 1999. [DOI: 10.1021/ja9931776] [Citation(s) in RCA: 182] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elizabeth R. Jarvo
- Contribution from the Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467-3860
| | - Gregory T. Copeland
- Contribution from the Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467-3860
| | - Nikolaos Papaioannou
- Contribution from the Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467-3860
| | - Peter J. Bonitatebus
- Contribution from the Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467-3860
| | - Scott J. Miller
- Contribution from the Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467-3860
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21
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Copeland GT, Jarvo ER, Miller SJ. Minimal Acylase-Like Peptides. Conformational Control of Absolute Stereospecificity. J Org Chem 1998; 63:6784-6785. [PMID: 11672295 DOI: 10.1021/jo981642w] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gregory T. Copeland
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167-3860
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22
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Ishikawa Y, Hirano Y, Yoshimoto J, Oka M, Hayashi T. Theoretical Conformational Analysis of Disulfide-Linked Tetrapeptides Ac-Cys-Pro-Xaa-Cys-NHMe Having Hydrophobic Xaa Amino-Acid Residues. Polym J 1998. [DOI: 10.1295/polymj.30.256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Miller SJ, Copeland GT, Papaioannou N, Horstmann TE, Ruel EM. Kinetic Resolution of Alcohols Catalyzed by Tripeptides Containing the N-Alkylimidazole Substructure. J Am Chem Soc 1998. [DOI: 10.1021/ja973892k] [Citation(s) in RCA: 196] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Scott J. Miller
- Department of Chemistry, Eugene F. Merkert Chemistry Center, Boston College Chestnut Hill, Massachusetts 02167-3860
| | - Gregory T. Copeland
- Department of Chemistry, Eugene F. Merkert Chemistry Center, Boston College Chestnut Hill, Massachusetts 02167-3860
| | - Nikolaos Papaioannou
- Department of Chemistry, Eugene F. Merkert Chemistry Center, Boston College Chestnut Hill, Massachusetts 02167-3860
| | - Thomas E. Horstmann
- Department of Chemistry, Eugene F. Merkert Chemistry Center, Boston College Chestnut Hill, Massachusetts 02167-3860
| | - Elizabeth M. Ruel
- Department of Chemistry, Eugene F. Merkert Chemistry Center, Boston College Chestnut Hill, Massachusetts 02167-3860
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24
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Theoretical conformational analysis of tetrapeptide Ac-Cys-Pro-D-Ala-Cys-NHMe with Disulfide Linkage. Polym Bull (Berl) 1997. [DOI: 10.1007/s002890050162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Theoretical conformational analysis of tetrapeptide Ac-Cys-Pro-Ala-Cys-NHMe with disulfide linkage. Polym Bull (Berl) 1997. [DOI: 10.1007/s002890050042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Yoshimoto J, Nishinaga A, Oka M, Hayashi T. Theoretical conformational analysis of tetrapeptide Ac-Cys-Pro-Gly-Cys-NHMe with disulfide linkage. Polym Bull (Berl) 1997. [DOI: 10.1007/s002890050026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Miller SJ, Blackwell HE, Grubbs RH. Application of Ring-Closing Metathesis to the Synthesis of Rigidified Amino Acids and Peptides. J Am Chem Soc 1996. [DOI: 10.1021/ja961626l] [Citation(s) in RCA: 361] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Roos HM, Van Rooyen PH, Wessels PL. Experimental studies and potential-energy calculations of the blocked tetrapeptide Ac-Lys-Gln-Gly-Ile-NMA from the third loop of a short-chain snake venom neurotoxin. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 43:337-43. [PMID: 8045679 DOI: 10.1111/j.1399-3011.1994.tb00528.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The conformational space of the tetrapeptide Ac-Lys-Gln-Gly-Ile-NMA from the beta-bend in the third loop of a short-chain snake venom neurotoxin was investigated with the aid of energy calculations. It was shown that this peptide has a preference for an alpha-helical conformation. This result was compared with the experimentally determined conformations, as observed using NMR and CD spectroscopy. With NMR spectroscopy a random-coil conformation of the peptide is indicated in H2O, DMSO and TFE. The results from the CD experiments suggest that the peptide exists as a random coil in water, but a small population of alpha-helical conformations is present in TFE. These results indicate that additional long-range interactions also play a role in the conformation of this tetrapeptide in the protein.
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Affiliation(s)
- H M Roos
- Department of Chemistry, University of Pretoria, South Africa
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29
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Goudreau N, Weng JH, Roques BP. Conformational analysis of CCK-B agonists using 1H-NMR and restrained molecular dynamics: comparison of biologically active Boc-Trp-(N-Me) Nle-Asp-Phe-NH2 and inactive Boc-Trp-(N-Me)Phe-Asp-Phe-NH2. Biopolymers 1994; 34:155-69. [PMID: 8142585 DOI: 10.1002/bip.360340202] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The tetrapeptide Boc-Trp-(N-Me)Nle-Asp-Phe-NH2 is a potent CCK-B agonist. Replacement in this analogue of the norleucine residue by a phenylalanine, to yield Boc-Trp-(N-Me) Phe-Asp-Phe-NH2, led to a 740-fold decrease in affinity whereas the same decrease in affinity was not observed in their nonmethylated counterparts. In order to ascertain the conformational preferences of these two N-methylated tetrapeptides, a study by two-dimensional (2D) nmr spectroscopy and molecular modeling was undertaken. The solution conformation of the two peptides was examined by 1H-nmr in a d6-DMSO/H2O (80:20) mixture. A cis-trans equilibrium, induced by N-methylation, was observed for both analogues, and the proton spectra of the two rotamers were fully characterized in each case. 1H-1H distance constraints, derived from 2D nuclear Overhauser effect spectroscopy and rotating frame nuclear Overhauser effect spectroscopy experiments, were used as inputs for subsequent restrained molecular dynamics simulations. Comparisons of the nmr and molecular modeling data point toward distinct conformational preferences for these two peptides with an opposite spatial orientation of the Trp residue, and could explain the large difference in their biological activities. Furthermore, the tridimensional structure of Boc-Trp-(N-Me)Nle-Asp-Phe-NH2 could serve as a model for the design of nonpeptide CCK-B agonists.
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Affiliation(s)
- N Goudreau
- Laboratoire de Pharmacochimie Moléculaire et Structurale, U.266 INSERM, URA D1500 CNRS, Faculté de Pharmacie, Paris
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30
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Roos HM, Van Rooyen PH, Wessels PL. Experimental studies and potential energy calculations of the blocked tetrapeptide Ac-Lys-Pro-Gly-Ile-NMA from the third loop of short-chain snake venom neurotoxins. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1993; 42:305-11. [PMID: 8244625 DOI: 10.1111/j.1399-3011.1993.tb00499.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The conformational space of the tetrapeptide Ac-Lys-Pro-Gly-Ile-NMA from the beta-bend present in the third loop of short-chain snake venom neurotoxins was investigated with the aid of energy calculations, resulting in the identification of an ensemble of beta-turn conformations. These results were compared with the experimentally determined conformations, as observed using NMR and CD spectroscopy. A random coil conformation of the peptide is indicated in polar hydrogen-bonding solvents. In less polar solvents the peptide backbone assumed a more rigid conformation, as reflected by the existence of at least a type II beta-turn conformation.
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Affiliation(s)
- H M Roos
- Department of Chemistry, University of Pretoria, South Africa
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31
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Siedler F, Rudolph-Böhner S, Doi M, Musiol HJ, Moroder L. Redox potentials of active-site bis(cysteinyl) fragments of thiol-protein oxidoreductases. Biochemistry 1993; 32:7488-95. [PMID: 8338847 DOI: 10.1021/bi00080a021] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The active sites of thiol-protein oxidoreductases consist of the characteristic Cys-X-X-Cys motif, and the redox potentials of these enzymes reflect the propensity of the bis(cysteinyl) sequence portion for disulfide loop formation. Thereby, as is known from comparing the three-dimensional (3D) structures of thioredoxin and glutaredoxin in the reduced and oxidized state, reduction of the disulfide bond is accompanied by minimal perturbation of the backbone folding of the active sites. In order to estimate the sequence-dependent intrinsic free energy of formation of the active-site disulfide loops in oxidoreductases, synthetic fragments corresponding to the sequences 31-38, 10-17, 134-141, and 34-41 of thioredoxin, glutaredoxin, thioredoxin reductase, and protein disulfide isomerase (PDI), respectively, were analyzed for their tendency to form 14-membered rings. For this purpose thiol/disulfide exchange experiments, with glutathione as reference redox pair, were performed on the bis(cysteinyl) octapeptides. As the free energy of ring closure of linear peptides consists mainly of the free energy of formation of the disulfide loop with a defined geometry from a statistical ensemble of conformations of the bis(cysteinyl) peptides, the observed differences in the equilibrium constants, although relatively small (within a factor 10), suggest that sequence-dependent information for loop formation is retained in the excised active-site fragments. These inherent redox potentials are, however, significantly affected and/or amplified in the native proteins by the conformational restraints imposed by the "structural domains" on the "functional domains".
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Affiliation(s)
- F Siedler
- Max Planck Institute of Biochemistry, Martinsried, Germany
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32
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Uma K, Kishore R, Balaram P. Stereochemical constraints in peptide design: analysis of the influence of a disulfide bridge and an alpha-aminoisobutyryl residue on the conformation of a hexapeptide. Biopolymers 1993; 33:865-71. [PMID: 8318661 DOI: 10.1002/bip.360330602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The competing effects of a disulfide bridge and an alpha-aminoisobutyryl residue (Aib) in determining the conformation of a hexapeptide have been investigated, by comparing the cyclic disulfide [sequence: see text] and the acylic peptide Boc-Cys (SBzl)-Val-Aib-Ala-Leu-Cys (SBzl)-NHMe (2). Previously published nmr and crystallographic studies [R. Kishore, S. Raghothama, and P. Balaram (1987) Biopolymers, Vol. 26, pp. 873-891; I. L. Karle, R. Kishore, S. Raghothama, & P. Balaram, (1988) Journal of the American Chemical Society Vol. 110, pp. 1958-1963] have established an antiparallel beta-hairpin structure for 1 with a central Aib-Ala beta-turn. A comparison of nmr data for 1 and 2 in chloroform and dimethylsulfoxide reveals that the acyclic peptide is conformationally labile. Evidence for a 3(10)-helical conformation in CDCl3 is obtained from sensitivity of NH chemical shifts to temperature and solvent perturbation and low JHNC alpha H values. Studies in solvent mixtures establish a conformational transition on going from CDCl3 to (CD3)2SO. The changes in NH nmr parameters, together with the observation of several interresidue C alpha i H-Ni+1H nuclear Overhauser effects support a conformation having a central beta-turn with extended arms in (CD3)2SO. A single Aib residue appears to stabilize a helix in apolar solvents, for the acyclic hexapeptide, while the disulfide bridge serves to lock the beta-hairpin conformation.
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Affiliation(s)
- K Uma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
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33
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Penkler LJ, Van Rooyen PH, Wessels PL. Conformational analysis of mu-selective [D-Ala2,MePhe4]enkephalins. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1993; 41:261-74. [PMID: 8385078 DOI: 10.1111/j.1399-3011.1993.tb00334.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The conformational space of the potent mu-selective opioids [D-Ala2,MePhe4,Gly-ol5]enkephalin (DAGO) and [D-Ala2,MePhe4,Met(O)-ol5]enkephalin (FK 33-824) has been analyzed by 1H-NMR spectroscopy and theoretical calculations involving systematic conformational searching and energy minimizations. A cis-trans equilibrium of the Gly3-MePhe4 amide bond is induced by the N-methyl group, and the more energetically favoured trans isomer is proposed as the biologically relevant form. A compact interaction between the side chains of Tyr1 and D-Ala2 was demonstrated by NOE and ROE effects in both peptides in D2O and DMSO-d6, further supported by shielding of the D-Ala2 methyl protons in both solvents. Analysis of coupling constants, NOE and ROE data indicated significant restriction of the conformational freedom of the MePhe4 side-chain for both peptides in the two solvents. The NMR results and theoretical calculations point towards folded low energy conformations characterized by a beta II-type turn around Gly3-MePhe4. For the trans isomer, a Tyr1-MePhe4 phenyl ring separation between 8.5 and 12.5 A was accompanied by proximity between the D-Ala2 side chain and the C-terminal in low energy conformations. The results are in good agreement with available data on related active enkephalins. The conformational effects induced by simultaneous incorporation of D-Ala2 and MePhe4 in enkephalins is discussed in the light of the enhanced mu-opioid receptor selectivity and activity of these peptides.
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Affiliation(s)
- L J Penkler
- Department of Chemistry, University of Pretoria, South Africa
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34
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Hölzemann G, Pachler KG, Eberhart B, Hölzel H, Kraft M, Barnickel G. Synthesis, conformational studies, and molecular dynamics calculations of two cyclic tetrapeptides with 17- and 18-membered rings. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1991; 37:283-92. [PMID: 1894444 DOI: 10.1111/j.1399-3011.1991.tb00741.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two cyclic tetrapeptides [Boc-cyclo(-Xxx-Pro-Asn-Lys-)OMe (Xxx = Asp or Glu)] were synthesized and investigated by NMR spectroscopy. They were designed in order to mimic the salt bridge found in physalaemin. Isomers of the urethane bond were observed in DMSO solution. The ROESY spectrum allowed the assignment of many signals of the minor isomer of both compounds. Conformational studies based on the temperature gradients of the NH chemical shifts, coupling constants, and ROEs revealed a similar conformation for the Asp analogue as proposed for physalaemin. A beta I turn with Pro and Asn in the corner positions was found for the major isomer. No hydrogen bonds were detected for the major isomer of the cyclic Glu analogue. Molecular dynamics calculations, using the NMR based initial structures, yielded sets of conformations in agreement with the experimental data. It is concluded that the salt bridge in physalaemin is best approximated by a lactam formed from the original amino acids.
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Affiliation(s)
- G Hölzemann
- Medicinal Chemistry Department, E. Merck, Darmstadt, Federal Republic of Germany
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35
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Hilbich C, Kisters-Woike B, Reed J, Masters CL, Beyreuther K. Aggregation and secondary structure of synthetic amyloid beta A4 peptides of Alzheimer's disease. J Mol Biol 1991; 218:149-63. [PMID: 2002499 DOI: 10.1016/0022-2836(91)90881-6] [Citation(s) in RCA: 461] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The deposition of amyloid beta A4 in the brain is a major pathological hallmark of Alzheimer's disease. Amyloid beta A4 is a peptide composed of 42 or 43 amino acid residues. In brain, it appears in the form of highly insoluble, filamentous aggregates. Using synthetic peptides corresponding to the natural beta A4 sequence as well as analog peptides, we demonstrate requirements for filament formation in vitro. We also determine aggregational properties and the secondary structure of beta A4. A comparison of amino-terminally truncated beta A4 peptides identifies a peptide spanning residues 10 to 43 as a prototype for amyloid beta A4. Infrared spectroscopy of beta A4 peptides in the solid state shows that their secondary structure consists of a beta-turn flanked by two strands of antiparallel beta-pleated sheet. Analog peptides containing a disulfide bridge were designed to stabilize different putative beta-turn positions. Limited proteolysis of these analogs allowed a localization of the central beta-turn at residues 26 to 29 of the entire sequence. Purified beta A4 peptides are soluble in water. Size-exclusion chromatography shows that they form dimers that, according to circular dichroism spectroscopy, adopt a beta-sheet conformation. Upon addition of salts, the bulk fraction of peptides precipitates and adopts a beta-sheet structure. Only a small fraction of peptides remains solubilized. They are monomeric and adopt a random coil conformation. This suggests that the formation of aggregates depends upon a hydrophobic effect that leads to intra- and intermolecular interactions between hydrophobic parts of the beta A4 sequence. This model is sustained by the properties of beta A4 analogs in which hydrophobic residues were substituted. These peptides show a markedly increased solubility in salt solutions and have lost the ability to form filaments. In contrast, the substitution of hydrophilic residues leads only to small deviations in the shape of filaments, indicating that hydrophilic residues contribute to the specificity of interactions between beta A4 peptides.
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Affiliation(s)
- C Hilbich
- Center for Molecular Biology, University of Heidelberg, F.R.G
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36
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Moroder L, Hübener G, Göhring-Romani S, Göhring W, Musiol HJ, Wünsch E. Fully synthetic immunogens. Part I. Kinetic studies on air oxidation of the human IgG1 bis-cysteinyl fragment 225-232. Tetrahedron 1990. [DOI: 10.1016/s0040-4020(01)85466-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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37
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Ishii H, Nadaoka O, Mimura Y, Inoue Y, Chûjô R. Synthesis and conformational analysis of Aib-containing peptide modelling for N-glycosylation site in N-glycoprotein. Int J Biol Macromol 1989; 11:329-34. [PMID: 2489100 DOI: 10.1016/0141-8130(89)90003-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A tetrapetide containing an Aib residue, Boc-Asn-Aib-Thr-Aib-OMe, was synthesized as a peptide model for the N-glycosylation site in N-glycoproteins. Backbone conformation of the peptide and possible intramolecular interaction between the Asn and Thr side chains were elucidated by means of n.m.r. spectroscopy. Temperature dependence of NH proton chemical shift and NOE experiments showed that Boc-Asn-Aib-Thr-Aib-OMe has a tendency to form a beta-turn structure with a hydrogen bond involving Thr and Aib4 NH groups. Incorporation of Aib residues in the peptide model promotes folding of the peptide backbone. With folded backbone conformation, carboxyamide protons of the Asn residue are not involved in hydrogen bond network, while the OH group of the Thr residue is a candidate for a hydrogen bond in DMSO-d6 solution.
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Affiliation(s)
- H Ishii
- Department of Industrial Chemistry, Tokyo National College of Technology
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38
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Convert O, Ploux O, Lavielle S, Cotrait M, Chassaing G. Analysis of tachykinin-binding site interactions using NMR and energy calculation data of potent cyclic analogues of substance P. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 954:287-302. [PMID: 2453217 DOI: 10.1016/0167-4838(88)90084-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The three-dimensional structures of [Cys3,6,Tyr8]-, [Gly2,Cys3,6,Tyr8]- and [DCys3,Cys6]substance P, designed as conformational analogues of substance P, have been studied by 1H-NMR (500 MHz) in different solvents and by energy calculations. As previously observed for substance P and physalaemin, two tachykinins acting via the NK-1 receptor, [Cys3,6,Tyr8]substance P presents an alpha-helical structure of the 4----8 sequence in methanol. This structure is stabilized by a beta-turn III via the formation of three hydrogen bonds involving the Cys-6, Phe-7 and Tyr-8 NH groups. In contrast to substance P, two of these hydrogen bonds are still present in dimethyl sulfoxide and in water the Cys-6 NH hydrogen bond is the only one remaining, such that a beta-turn structure inside the ring can be envisaged. In close agreement with the NMR data, the energy calculations lead to three types of folding for the core of [Cys3,6,Tyr8]substance P: a beta-turn III, a less stable beta-turn I (delta E = 3 kcal), and a beta-turn II (delta E = 4.6 kcal). The structure of Gly-Leu-Met-NH2 is strongly affected by changing the hydrophobicity of the medium. The most stable calculated conformation is the helix; however, numerous unrelated structures are destabilized by about 2-3 kcal/mol. These data are analyzed and discussed in connection with the high potency of [Cys3,6,Tyr8]substance P for both the NK-1 and NK-3 binding sites; that is the internal region of tachykinins (non-homologous amino acids) might present a similar three-dimensional structure when bound to the receptors (which may be at the origin of some lack of selectivity), whereas paradoxically the selectivity may be due to the common C-terminal sequence.
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Affiliation(s)
- O Convert
- Laboratoire de Chimie Organique Structurale, CNRS UA 455, Paris, France
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39
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Kishore R, Raghothama S, Balaram P. Cystine peptides: the intramolecular antiparallel beta-sheet conformation of a 20-membered cyclic peptide disulfide. Biopolymers 1987; 26:873-91. [PMID: 3607246 DOI: 10.1002/bip.360260608] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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40
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Sahal D, Balaram P. Peptide models of electrostatic interactions in proteins: NMR studies on two beta-turn tetrapeptides containing Asp-His and Asp-Lys salt bridges. Biochemistry 1986; 25:6004-13. [PMID: 3098281 DOI: 10.1021/bi00368a026] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Two model peptides Boc-Asp-Pro-Aib-X-NHMe [X = His (1) and X = Lys (2)] were synthesized to simulate intramolecular electrostatic interactions between ionizable side chains. Conformational analysis by 270-MHz 1H NMR in (CD3)2SO reveals that the backbone secondary structures of these two peptides are stabilized by two strong intramolecular hydrogen bonds, involving the consecutive carboxy-terminal NH groups. 1H NMR chemical shifts were measured in 1, 2, and a protected derivative, Boc-Asp(OBzl)-Pro-Aib-His-NHMe (3). These shifts were also measured for the model compounds Ac-Lys-NHMe, Boc-Asp-NHMe, and Boc-His-NHMe in their different states of ionization. An analysis of the chemical shifts of the ionization-sensitive reporter resonances suggests the formation of a strong intramolecular salt bridge in the lysyl peptide 2 and a bridge of moderate strength in the histidyl peptide 1. A comparison of the temperature dependence of chemical shifts in peptides 1-3 suggests that intramolecular salt bridge formation results in diminished backbone flexibility. The results establish that proximity effects confer far greater stability to intramolecular ion pair interactions vis-a-vis their intermolecular counterparts. The salt bridge interaction in peptide 1 displays a remarkable sensitivity to the dielectric constant of the solvent medium. The results suggest that these peptides are good simulators of the role of salt bridges in the structural dynamics of proteins.
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