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Biondi B, Formaggio F, Toniolo C, Peggion C, Crisma M. Isolated α-turns in peptides: a selected literature survey. J Pept Sci 2023:e3476. [PMID: 36603599 DOI: 10.1002/psc.3476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
The results of classifying into various types the 68 examples of isolated α-turns in the X-ray diffraction crystal structures of peptides documented in the literature are presented and discussed in this review article. α-Turns characterized by the trans disposition of all ω torsion angles are common for the backbone linear peptides investigated. In contrast, the cis arrangement of the N-terminal (ωi + 1 ) torsion angle, among those generated by the three residues internal to the α-turn, is a peculiar feature of 65% of the cyclic peptides. Among linear and cyclic peptides featuring the all-trans disposition of the ω torsion angles, only one third of the α-turns display φ,ψ values not too far from those characterizing regular α-helices. In general, our findings, taken together, suggest that a significant conformational diversity is compatible with the formation of an intramolecularly H-bonded C13 -member pseudocycle (α-turn) in linear and cyclic peptides.
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Affiliation(s)
- Barbara Biondi
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
| | - Fernando Formaggio
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Claudio Toniolo
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Cristina Peggion
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Marco Crisma
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
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2
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Damjanovic J, Miao J, Huang H, Lin YS. Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations. Chem Rev 2021; 121:2292-2324. [PMID: 33426882 DOI: 10.1021/acs.chemrev.0c01087] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions are vital to biological processes, but the shape and size of their interfaces make them hard to target using small molecules. Cyclic peptides have shown promise as protein-protein interaction modulators, as they can bind protein surfaces with high affinity and specificity. Dozens of cyclic peptides are already FDA approved, and many more are in various stages of development as immunosuppressants, antibiotics, antivirals, or anticancer drugs. However, most cyclic peptide drugs so far have been natural products or derivatives thereof, with de novo design having proven challenging. A key obstacle is structural characterization: cyclic peptides frequently adopt multiple conformations in solution, which are difficult to resolve using techniques like NMR spectroscopy. The lack of solution structural information prevents a thorough understanding of cyclic peptides' sequence-structure-function relationship. Here we review recent development and application of molecular dynamics simulations with enhanced sampling to studying the solution structures of cyclic peptides. We describe novel computational methods capable of sampling cyclic peptides' conformational space and provide examples of computational studies that relate peptides' sequence and structure to biological activity. We demonstrate that molecular dynamics simulations have grown from an explanatory technique to a full-fledged tool for systematic studies at the forefront of cyclic peptide therapeutic design.
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Affiliation(s)
- Jovan Damjanovic
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - He Huang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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3
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Slough DP, McHugh SM, Lin YS. Understanding and designing head-to-tail cyclic peptides. Biopolymers 2018; 109:e23113. [PMID: 29528114 PMCID: PMC6135719 DOI: 10.1002/bip.23113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/30/2023]
Abstract
Cyclic peptides (CPs) are an exciting class of molecules with a variety of applications. However, design strategies for CP therapeutics, for example, are generally limited by a poor understanding of their sequence-structure relationships. This knowledge gap often leads to a trial-and-error approach for designing CPs for a specific purpose, which is both costly and time-consuming. Herein, we describe the current experimental and computational efforts in understanding and designing head-to-tail CPs along with their respective challenges. In addition, we provide several future directions in the field of computational CP design to improve its accuracy, efficiency and applicability. These advances, combined with experimental techniques, shall ultimately provide a better understanding of these interesting molecules and a reliable working platform to rationally design CPs with desired characteristics.
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Affiliation(s)
| | | | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, United States
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4
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Toniolo C, Crisma M, Moretto A, Peggion C, Formaggio F, Alemán C, Cativiela C, Ramakrishnan C, Balaram P. Peptide δ-Turn: Literature Survey and Recent Progress. Chemistry 2015; 21:13866-77. [PMID: 26243713 DOI: 10.1002/chem.201501467] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Among the various types of α-peptide folding motifs, δ-turn, which requires a central cis-amide disposition, has been one of the least extensively investigated. In particular, this main-chain reversal topology has been studied in-depth neither in linear/cyclic peptides nor in proteins. This Minireview article assembles and critically analyzes relevant data from a literature survey on the δ-turn conformation in those compounds. Unpublished results from recent conformational energy calculations and a preliminary solution-state analysis on a small model peptide, currently ongoing in our laboratories, are also briefly outlined.
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Affiliation(s)
- Claudio Toniolo
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova (Italy).
| | - Marco Crisma
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova (Italy)
| | - Alessandro Moretto
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova (Italy)
| | - Cristina Peggion
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova (Italy)
| | - Fernando Formaggio
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova (Italy)
| | - Carlos Alemán
- Departament d'Enginyeria Quimica, ETSEIB, Universitat Politècnica de Catalunya, 08028 Barcelona (Spain)
| | - Carlos Cativiela
- Department of Organic Chemistry, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC - Universidad de Zaragoza, 50009 Zaragoza (Spain)
| | | | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science, 0091 Bangalore (India)
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5
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Crisma M, De Zotti M, Moretto A, Peggion C, Drouillat B, Wright K, Couty F, Toniolo C, Formaggio F. Single and multiple peptide γ-turns: literature survey and recent progress. NEW J CHEM 2015. [DOI: 10.1039/c4nj01564a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Published data on peptide isolated and repetitive γ-turns are reviewed. Advancements in our laboratories on these 3D-structures are also presented.
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Affiliation(s)
- Marco Crisma
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
| | - Marta De Zotti
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
| | | | | | - Bruno Drouillat
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - Karen Wright
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - François Couty
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - Claudio Toniolo
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
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6
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Culf AS, Čuperlović-Culf M, Léger DA, Decken A. Small head-to-tail macrocyclic α-peptoids. Org Lett 2014; 16:2780-3. [PMID: 24797336 DOI: 10.1021/ol501102b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A convenient and efficient methodology for the head-to-tail macrocyclization of small 3-mer, 4-mer, and 5-mer α-peptoid acids (9-, 12-, and 15-atom N-substituted glycine oligomers) is described. The cyclic trimer has a ccc amide sequence in the crystal structure, whereas the tetramer has ctct and the pentamer has ttccc stereochemistry. NMR analysis reveals rigid structures in solution. These synthetic macrocycles may prove useful in medicinal and materials applications.
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Affiliation(s)
- Adrian S Culf
- Atlantic Cancer Research Institute , 35 Providence Street, Moncton, NB E1C 8X3, Canada
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7
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Otero JM, Fernández F, Estévez JC, Nash R, Estévez RJ. A Nitro Sugar-Mediated Stereocontrolled Synthesis of β2-Amino Acids: Synthesis of a Polyhydroxylated trans-2-Aminocyclohexanecarboxylic Acid. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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9
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Nikiforovich GV, Kövér KE, Zhang WJ, Marshall GR. Cyclopentapeptides as Flexible Conformational Templates. J Am Chem Soc 2000. [DOI: 10.1021/ja991728m] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gregory V. Nikiforovich
- Contribution from the Center for Molecular Design and Department of Molecular Biology and Pharmacology, Washington University, St. Louis, Missouri 63130, and L. Kossuth University, H-4010 Debrecen, Hungary
| | - Katalin E. Kövér
- Contribution from the Center for Molecular Design and Department of Molecular Biology and Pharmacology, Washington University, St. Louis, Missouri 63130, and L. Kossuth University, H-4010 Debrecen, Hungary
| | - Wei-Jun Zhang
- Contribution from the Center for Molecular Design and Department of Molecular Biology and Pharmacology, Washington University, St. Louis, Missouri 63130, and L. Kossuth University, H-4010 Debrecen, Hungary
| | - Garland R. Marshall
- Contribution from the Center for Molecular Design and Department of Molecular Biology and Pharmacology, Washington University, St. Louis, Missouri 63130, and L. Kossuth University, H-4010 Debrecen, Hungary
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10
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Saviano M, Isernia C, Rossi F, Di Blasio B, Iacovino R, Mazzeo M, Pedone C, Benedetti E. Solid state structural analysis of the cyclooctapeptide cyclo- (Pro1-Pro-Phe-Phe-Ac6c-Ile-D-Ala-Val8). Biopolymers 2000; 53:189-99. [PMID: 10679623 DOI: 10.1002/(sici)1097-0282(200002)53:2<189::aid-bip9>3.0.co;2-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A solid state analysis of the cyclic octapeptide c(-Pro(1)-Pro-Phe-Phe-Ac(6)c-Ile-D-Ala-Val(8)-) (C8-CLA), containing the Pro-Pro-Phe-Phe sequence, followed by the bulky helicogenic C(alpha,alpha)-dialkylated 1-aminocyclohexane-1-carboxylic acid (Ac(6)c) residue and a D-Ala residue in position 7, has been carried out by x-ray diffraction. The crystals, grown from a DMSO solution, are monoclinic, space group P2(1) with a = 13.458(3) A, b = 19. 404(5) A, c = 21.508(4) A, and beta = 90.83(6) degrees, with two independent cyclic molecules in the asymmetric unit, two DMSO molecules, and three water molecules. The structure has been solved using the half and bake procedure by Sheldrick, and refined to final R1 and wR2 indices of 0.0613 and 0.1534 for 9867 reflections with I > 2sigma(I). This cyclic peptide, a deletion analogue of the naturally occurring cyclic nonapeptide cyclolinopeptide A [c(Pro-Pro-Phe-Phe-Leu-Ile-Ile-Leu-Val), CLA] has been designed to study the influence of the ring size reduction on the conformational behavior of CLA and more in general to obtain structural information on asymmetric cyclic octapeptides. The compound exhibits, in the solid state, a "banana-twisted" conformation with a cis peptide bond located between the two proline residues. Five intramolecular H bonds stabilize the structure: one type VIa beta-turn, two consecutive type III/I beta-turns, one gamma-turn, and one C(16) bend. The structure has also been compared with either the solution structure previously reported by us and obtained by nmr and computational analysis, and with solid state structural data reported in the literature on cyclic octapeptides.
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Affiliation(s)
- M Saviano
- Centro di Studio di Biocristallografia del CNR, Dipartimento di Chimica, Università di Napoli, via Mezzocannone 4,80134, Napoli, Italy
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11
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Zanotti G, Saviano M, Saviano G, Tancredi T, Rossi F, Pedone C, Benedetti E. Structure of cyclic peptides: the crystal and solution conformation of cyclo(Phe-Phe-Aib-Leu-Pro). THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1998; 51:460-6. [PMID: 9650721 DOI: 10.1111/j.1399-3011.1998.tb00645.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A solid-state and solution conformation analyses of the cyclopentapeptide cyclo(Phe-Phe-Aib-Leu-Pro) has been carried out by X-ray diffraction and nuclear magnetic resonance techniques. The structure of the hexagonal crystals, grown from a methanol solution [a = b = 16.530(4) A, c = 21.356(9) A, space group P6(5), Z = 6], shows the presence of one intramolecular N-H ..O=C hydrogen bond with the formation of a gamma-turn (C7). The Aib3 residue, at the center of the gamma-turn, presents unexpected values of the torsion angles [phi = 70.5 degrees and psi = -73.8 degrees], which have been observed only once before for this helicogenic residue. A cis peptide bond occurs between Leu4 and Pro5; all other peptide bonds are trans. The overall conformation for the cyclopentapeptide with one cis-peptide bond on one side and an intramolecular gamma-turn on the opposite side results in an equatorial topology of the side-chains of the Phe1, Phe2 and Leu4 residues. Indeed, the Calpha-Cbeta and Cbeta-Cgamma bonds of these residues lie approximately in the mean plane of the cyclic ring system. The structure is compared with data in the literature on cyclic pentapeptides. In addition the Pro-Phe-Phe moiety shows a conformation similar to that observed in other larger cyclic bioactive peptides, which indicates a reduced number of conformations for this sequence. The solution study was carried out in three different solvent systems: chloroform, acetonitrile and methanol in the temperature interval 220-300 K. In all three solvents the room temperature spectra show that the peptide is conformationally nonhomogeneous. In acetonitrile at low temperatures it is possible to reduce the conformational equilibrium to two predominant conformers which differ for the cis-trans isomerism of the Leu4-Pro5 peptide bond.
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Affiliation(s)
- G Zanotti
- Centro di Studio sulla Chimica del Farmaco del C.N.R, Università di Roma La Sapienza, Italy
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12
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Neumann WL, Franklin GW, Sample KR, Aston KW, Weiss RH, Riley DP. Synthesis of conformationally tailored pentaazacyclopentadecanes. Preorganizing peptide cyclizations. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(96)02446-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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13
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Schmidt U, Langner J. Cyclotetrapeptides and cyclopentapeptides: occurrence and synthesis. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1997; 49:67-73. [PMID: 9128102 DOI: 10.1111/j.1399-3011.1997.tb01122.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The structures reported for the three cancerostatic all-L-cyclotetrapeptides cyclo(Pro-Leu)2, cyclo(Pro-Val)2 and cyclo(Pro-Phe)2 isolated from a tunicate seem questionable. The synthetic compounds claimed to be identical to the naturally occurring cyclotetrapeptides are in fact not cyclotetrapeptides but rather cyclooctapeptides. We have not been able to prepare the tyrosinase inhibitor cyclo(Pro-Val-Pro-Tyr). Ring closure of H-Pro-Val-Pro-Tyr-OC6F5 gave rise to 31% of cyclo(Pro-Val-Pro-D-Tyr). The same product was obtained in 53% yield from H-Pro-Val-Pro-D-Tyr-OC6F5. For the ring closure to the all-L-cyclopentapeptide cyclo(Pro-Ala-Ala-Phe-Leu), all ring closure positions have been investigated. The reaction at the nitrogen atom of leucine leads to 21% of the all-L-cyclopentapeptide. Dimers or mixtures of monomers and dimers result from reaction at all other positions.
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Affiliation(s)
- U Schmidt
- Institute of Organic Chemistry, University of Stuttgart, Germany
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14
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Geometry optimization, energetics and solvation studies on four- and five-membered cyclic and disulfide-bridged peptides, using the programs quanta 3.3 and charmm 22. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/0166-1280(93)87147-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Ma S, Richardson JF, Spatola AF. Crystal structures of two cyclic pseudopentapeptides containing psi[CH2S] and psi[CH2SO] backbone surrogates. Biopolymers 1993; 33:1101-10. [PMID: 8343587 DOI: 10.1002/bip.360330712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The solid state conformations of cyclo [Gly-Pro psi[CH2S] Gly-D-Phe-Pro] and cyclo [Gly-Pro psi[CH2-(S)-SO]Gly-D-Phe-Pro] have been characterized by X-ray diffraction analysis. Crystals of the sulfide trihydrate are orthorhombic, P2(1)2(1)2(1), with a = 10.156(3) A, b = 11.704(3) A, c = 21.913(4) A, and Z = 4. Crystals of the sulfoxide are monoclinic, P2(1) with a = 10.662(1) A, b = 8.552(3) A, c = 12.947(2) A, beta = 94.28(2), and Z = 2. Unlike their all-amide parent, which adopts an all-trans backbone conformation and a type II beta-turn encompassing Gly-Pro-Gly-D-Phe, both of these peptides contain a cis Gly1-Pro2 bond and form a novel turn structure, i.e., a type II' beta-turn consisting of Gly-D-Phe-Pro-Gly. The turn structure in each of these peptides is stabilized by an intramolecular H bond between the carbonyl oxygen of Gly1 and the amide proton of D-Phe4. In the cyclic sulfoxide, the sulfinyl group is not involved in H bonding despite its strong potential as a hydrogen-bond acceptor. The crystal structure made it possible to establish the absolute configuration of the sulfinyl group in this peptide. The two crystal structures also helped identify a type II' beta-turn in the DMSO-d6 solution conformers of these peptides.
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Affiliation(s)
- S Ma
- Department of Chemistry, University of Louisville, Kentucky 40292
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16
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Liu ZP, Gierasch LM. Combined use of molecular dynamics simulations and NMR to explore peptide bond isomerization and multiple intramolecular hydrogen-bonding possibilities in a cyclic pentapeptide, cyclo(Gly-Pro-D-Phe-Gly-Val). Biopolymers 1992; 32:1727-39. [PMID: 1472655 DOI: 10.1002/bip.360321214] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The conformational behavior of a model cyclic pentapeptide--cyclo(Gly-L-Pro-D-Phe-Gly-L-Val)--has been explored through the combined use of in vacuo molecular dynamics simulations and a range of nmr experiments (preceding paper). The molecular dynamics analysis suggests that, despite the conformational constraints imposed by formation of the pentapeptide cycle, this pentapeptide undergoes conformational transitions between various hydrogen-bonded conformations, characterized by low energy barriers. An inverse gamma turn with Pro in position i + 1 and a gamma turn with D-Phe in position i + 1 are two alternatives occurring frequently. Like other DLDDL cyclic pentapeptides, cyclo(Gly-Pro-D-Phe-Gly-Val) is also stabilized by an inverse gamma-turn structure with the beta-branched Val residue in position i + 1, and this hydrogen bond is retained in the different conformational families. The gamma-turn around D-Phe3 and the inverse gamma turn around Val5 are consistent with the nmr observations. 3JNH-CH alpha coupling constants of the all-trans forms were calculated from one of the molecular dynamics trajectories and are comparable to nmr experimental data, suggesting that the conformational states visited during the simulation are representative of the conformational distribution in solution. In addition to the equilibrium among various hydrogen-bonded all-trans conformers, the observation in nmr spectra of two sets of resonances for all peptide protons indicated a slow conformational interconversion of the Gly-Pro peptide bond between trans and cis isomers. The activation energy between these two conformers was determined experimentally by magnetization transfer and was calculated by high temperature constrained molecular dynamics simulation. Both methods yield a free energy of activation of ca. 20 kcal/mol. Furthermore, the free energy of activation is dependent on the direction of rotation of the Gly-Pro peptide bond.
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Affiliation(s)
- Z P Liu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas 75235-9041
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17
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Bruch MD, Rizo J, Gierasch LM. Impact of a micellar environment on the conformations of two cyclic pentapeptides. Biopolymers 1992; 32:1741-54. [PMID: 1472656 DOI: 10.1002/bip.360321215] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In an effort to explore the influence of interfacial environments on reverse turns, we have performed a detailed analysis by nmr of the solution conformations of two cyclic pentapeptides in sodium dodecyl sulfate (SDS) micelles. The first peptide, cyclo (D-Phe1-Pro2-Gly3-D-Ala4-Pro5), adopts a single rigid conformation in solution (either chloroform or dimethylsulfoxide) and in crystals, whereas the second, cyclo (Gly1-Pro2-D-Phe3-Gly4-Val5), is much more flexible and adopts different conformations in the crystal and in solution. Both of these peptides are solubilized by SDS micelles, and nmr relaxation rates indicate that they are both partially immobilized by interaction with the micelles. Furthermore, some amide protons in both peptides participate in hydrogen bonds with water. In the presence of micelles, the former peptide retains a conformation essentially the same as that found in crystals and in solution, which consists of a beta turn and an inverse gamma turn. However, the micellar environment has a significant effect on the latter peptide. In particular, the population of a conformer containing a cis Gly-Pro peptide bond is increased significantly. The most likely conformation of the cis isomer, determined by a combination of nmr and restrained molecular dynamics, contains a Gly1-Pro2 delta turn and a gamma turn about D-Phe3. The nmr data on the trans isomer indicate that this isomer is averaging between two conformations that differ mainly in the orientation of the D-Phe3-Gly4 peptide bond.
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Affiliation(s)
- M D Bruch
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas 75235-9041
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18
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Stroup AN, Rockwell AL, Gierasch LM. Solution conformations of two flexible cyclic pentapeptides: cyclo(Gly-Pro-D-Phe-Gly-Ala) and cyclo(Gly-Pro-D-Phe-Gly-Val). Biopolymers 1992; 32:1713-25. [PMID: 1472654 DOI: 10.1002/bip.360321213] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In an effort to explore the residue preferences in three-residue reverse turns (so-called gamma-turns), two cyclic pentapeptides--cyclo(Gly1-Pro2-D-Phe3-Gly4-Ala5) (I) and cyclo(Gly1-Pro2-D-Phe3-Gly4-Val5) (II)--have been synthesized and analyzed by nmr. It was anticipated that the Gly-Pro-D-Phe-Gly portions of these molecules would favor a beta-turn conformation, leaving the remainder of the molecule to adopt a gamma turn, as seen in several previously studied model cyclic pentapeptides. The nmr data for both peptides in CDCl3 (5% DMSO-d6) and in neat DMSO-d6 indicate that the most populated conformation contains a distorted beta turn around Pro2-D-Phe3, which includes a gamma turn around D-Phe3. The distortion in the beta turn does not impede the formation of an inverse gamma turn around residue 5, and indeed, this conformation is observed in both peptides. Both the alanine and the bulkier valine residues are therefore found to be compatible with an inverse gamma turn. Molecular dynamics simulations on the title peptides are reported in the following paper. These simulations indicate that there is conformational flexibility around the D-Phe3-Gly4 peptide bond, which enables the formation of the gamma turn around D-Phe3. The third paper in this series explores the impact of a micellar environment on conformational equilibria in II.
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Affiliation(s)
- A N Stroup
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas 75235-9041
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19
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Nagarajaram HA, Paul PK, Ramanarayanan K, Soman KV, Ramakrishnan C. Conformational studies on beta-bend containing a cis peptide unit. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1992; 40:383-94. [PMID: 1483833 DOI: 10.1111/j.1399-3011.1992.tb00315.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Conformational studies have been carried out on the X-cis-Pro tripeptide system (a system of three linked peptide units, in the trans-cis-trans configuration) using energy minimization techniques. For X, residues Gly, L-Ala, D-Ala and L-Pro have been used. The energy minima have been classified into different groups based upon the conformational similarity. There are 15, 20, 18 and 6 minima that are possible for the four cases respectively and these fall into 11 different groups. A study of these minima shows that, (i) some minima contain hydrogen bonds--either 4-->1 or 1-->2 type, (ii) the low energy minima qualify themselves as bend conformations, (iii) cis' and trans' conformations are possible for the prolyl residue as also the C gamma-endo and C gamma-exo puckerings, and (iv) for Pro-cis-Pro, cis' at the first prolyl residue is ruled out, due to the high energy. The available crystal structure data on proteins and peptides, containing cis-Pro segment have been examined with a view to find the minima that occur in solid state. The data from protein show that they fall under two groups. The conformation at X in X-cis-Pro is near extended when it is a non-glycyl residue. In both peptides and proteins there exists a preference for trans' conformation at prolyl residue over cis' when X is a non-glycyl residue. The minima obtained can be useful in modelling studies.
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Affiliation(s)
- H A Nagarajaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
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Duriez MC, Pigot T, Picard C, Cazaux L, Tisnès P. Macrocyclic polyether tetralactams I : synthesis and cyclization studies. Tetrahedron 1992. [DOI: 10.1016/s0040-4020(01)80444-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Molecular conformation of achatin-I, an endogenous neuropeptide containing D-amino acid residue. X-ray crystal structure of its neutral form. FEBS Lett 1990; 276:95-7. [PMID: 1979949 DOI: 10.1016/0014-5793(90)80516-l] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The molecular conformation of achatin-I neutral form (H-Gly-D-Phe-Ala-Asp-OH), an endogenous neuropeptide, was elucidated by X-ray crystal analysis. The molecule has a type II' beta-turn structure with the D-Phe-Ala residues at the corner of the bend, which is further stabilized by two NH(Gly)...C gamma = O sigma(Asp) and NH(Asp)...C gamma = O sigma(Asp) intramolecular hydrogen bonds. This turn conformation may be an important feature of achatin-I related to its neuroexcitatory activity.
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22
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Stradley SJ, Rizo J, Bruch MD, Stroup AN, Gierasch LM. Cyclic pentapeptides as models for reverse turns: determination of the equilibrium distribution between type I and type II conformations of Pro-Asn and Pro-Ala beta-turns. Biopolymers 1990; 29:263-87. [PMID: 2328290 DOI: 10.1002/bip.360290130] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclic pentapeptides are excellent models for reverse turns and have been used extensively in our laboratory to explore the influence of different amino acid sequences on turn preference. This paper is divided into two parts: In the first, we review our previous studies of cyclic pentapeptides. We summarize work that demonstrates the range of conformations possible within the cyclic pentapeptide backbone, the importance of sequence chirality in determining the backbone fold, and the utility of these cyclic pentapeptides as models for various turns. In the second, we present new results on two cyclic pentapeptides that contain beta-turns with Pro-Ala or Pro-Asn sequences in the i + 1 and i + 2 positions. By stereochemical criteria, a type I beta-turn is expected to be preferred by such L-L sequences. On the other hand, in proteins Asn occurs frequently in the i + 2 position of type II turns. We asked whether the same propensity would be manifest in an isolated model peptide, and if so, what the interactions were that influenced the relative stability of the type I and type II turns. To address these questions we have compared the conformational behavior of two peptides: cyclo(Gly-Pro-Ala-D-Phe-Pro) and cyclo(D-Ala-Pro-Asn-Gly-Pro). From previous studies, we anticipated that both peptides would contain an inverse gamma-turn and a beta-turn which consisted of either Gly-Pro-Ala-D-Phe or D-Ala-Pro-Asn-Gly in positions i to i + 3, respectively. Nuclear magnetic resonance analysis confirms this overall backbone conformation. Furthermore, quantitative nuclear Overhauser effect measurements in combination with molecular dynamics simulations and torsionally-forced energy minimizations have enabled us to determine that both type I and type II beta-turns are present in equilibrium in these peptides. The introduction of Asn in position i + 2 shifts this equilibrium significantly towards type II. We have done preliminary assessment of the possible side-chain/backbone conformations that contribute to the shift in populations.
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Affiliation(s)
- S J Stradley
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas 75235-9041
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Brandmeier V, Feigel M, Bremer M. 2′-Aminomethylbiphenyl-2-carbonsäure als Bestandteil eines Cyclopeptids; Struktur im Kristall und Konformation in Lösung. Angew Chem Int Ed Engl 1989. [DOI: 10.1002/ange.19891010411] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Brandmeier V, Feigel M, Bremer M. 2?-Aminomethylbiphenyl-2-carboxylic Acid as Component of a Cyclopeptide; Crystal Structure and Conformation in Solution. ACTA ACUST UNITED AC 1989. [DOI: 10.1002/anie.198904861] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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