1
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Shekh S, Dhurjad P, Vijayasarathy M, Dolle A, Dhannura S, Sahoo DK, Sonti R, Gowd KH. Oxidative Folding Catalysts of Conotoxins Derived from the Venom Duct Transcriptome of C. frigidus and C. amadis. Biochemistry 2023; 62:3061-3075. [PMID: 37862039 DOI: 10.1021/acs.biochem.3c00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Two novel redox conopeptides with proline residues outside and within the active site disulfide loop were derived from the venom duct transcriptome of the marine cone snails Conus frigidus and Conus amadis. Mature peptides with possible post-translational modification of 4-trans-hydroxylation of proline, namely, Fr874, Fr890[P1O], Fr890[P2O], Fr906, Am1038, and Am1054, have been chemically synthesized and characterized using mass spectrometry. The estimated reduction potential of cysteine disulfides of synthetic peptides varied from -298 to -328 mV, similar to the active site cysteine disulfide motifs of the redox family of proteins. Fr906/Am1054 exhibited pronounced catalytic activity and assisted in improving the yields of natively folded globular form α-conotoxin ImI. Three-dimensional (3D) structures of the redox conopeptides were optimized using computational methods and verified by 2D-ROESY NMR spectroscopy: C. frigidus peptides adopt an N-terminal helical fold and C. amadis peptides adopt distinct structures based on the Phe4-Pro/Hyp5 peptide bond configuration. The shift in the cis-trans configuration of the Phe4-Pro/Hyp5 peptide bond of Am1038/Am1054 was observed between reduced free thiol and oxidized disulfide forms of the optimized peptides. The report confirms the position-specific effect of hydroxyproline on the oxidative folding of conotoxins and sequence diversity of redox conopeptides in the venom duct of cone snails.
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Affiliation(s)
- Shamasoddin Shekh
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Pooja Dhurjad
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, Telangana, India
| | - Marimuthu Vijayasarathy
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India
| | - Ashwini Dolle
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Shweta Dhannura
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Deepak Kumar Sahoo
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, Telangana, India
| | - Konkallu Hanumae Gowd
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
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2
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Lal J, Prajapati G, Meena R, Kant R, Sankar Ampapathi R, Reddy DN. Influence of Proline Chirality on Neighbouring Azaproline Residue Stereodynamic Nitrogen Preorganization. Chem Asian J 2023; 18:e202201023. [PMID: 36349404 DOI: 10.1002/asia.202201023] [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: 10/06/2022] [Revised: 11/04/2022] [Indexed: 11/10/2022]
Abstract
We report herein the first systematic crystal structural investigation of azaproline incorporated in homo- and heterochiral diprolyl peptides. The X-ray crystallography data of peptides 1-5 illustrates that stereodynamic nitrogen in azaproline adopted the stereochemistry of neighbouring proline residue without depending on its position in the peptide sequence. Natural bond orbital analysis of crystal structures indicates OazPro -C'Pro of peptides 4 and 5 participating in n→π* interaction with stabilization energy about 1.21-1.33 kcal/mol. Density functional theory calculations suggested that the endo-proline ring puckering favoured over exo-conformation by 6.72-7.64 kcal/mol. NBO and DFT data reveals that the n→π* interactions and proline ring puckering stabilize azaproline chirality with the neighbouring proline stereochemistry. The CD, solvent titration, variable-temperature and 2D NMR experimental results further supported the crystal structures conformation.
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Affiliation(s)
- Jhajan Lal
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow, 226031, India) .,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Gurudayal Prajapati
- Division of Sophisticated Analytical Instrument Facility and Research, CSIR-CDRI, Lucknow, 226031, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Rachana Meena
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow, 226031, India) .,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Ruchir Kant
- Biochemistry and Structural Biology Division, CSIR-CDRI, Lucknow, 226031, India
| | - Ravi Sankar Ampapathi
- Division of Sophisticated Analytical Instrument Facility and Research, CSIR-CDRI, Lucknow, 226031, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Damodara N Reddy
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow, 226031, India) .,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
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3
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Debnath S, Ghosh S, Kumar D, Vasudev PG, Satpati P, Chatterjee S. Effect of differential backbone di-substitution of gamma amino acid residues on the conformation and assembly of their Fmoc derivatives in solid and solution states. Chem Asian J 2022; 17:e202200356. [PMID: 35603989 DOI: 10.1002/asia.202200356] [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: 04/06/2022] [Revised: 05/23/2022] [Indexed: 11/11/2022]
Abstract
We studied the effect of variable backbone dimethyl-substitution of γ amino acid residues (γ 2,2 , γ 3,3 and γ 4,4 ) on the conformation and assembly, in crystals and solution of their Fmoc derivatives. Crystal structure of γ 2,2 and γ 4,4 derivatives showed distinct conformations (open/close for γ 2,2 /γ 4,4 ) that differed in torsion angles, hydrogen-bonding and most importantly the π-π Fmoc-stacking interactions (relatively favorable for γ 4,4 -close). Fmoc derivatives existed in an equilibrium between major-monomeric (low energy, non-hydrogen bonded) and minor-dimeric (high energy, hydrogen bonded) populations in solution. Rate of major/minor population exchange was dependent on the position of substitution, highest being for γ 4,4 derivative. In solution, assembly of Fmoc derivatives was solvent dependent, but it was independent of the position of geminal substitution. Crystallization was primarily governed by the stabilization of high-energy dimer by favorable π-π stacking involving Fmoc moieties. High free-energy of the dimers (γ 2,2 -close, γ 3,3 -open/close) offset favorable stacking interactions and hindered crystallization.
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Affiliation(s)
- Swapna Debnath
- Indian Institute of Technology Guwahati, Department of chemistry, INDIA
| | - Suvankar Ghosh
- Indian Institute of Technology Guwahati, Bioscience and Bioengineering, INDIA
| | - Dinesh Kumar
- CSIR-CIMAP: Central Institute of Medicinal and Aromatic Plants CSIR, Plant Biotechnology Division, INDIA
| | - Prema G Vasudev
- CSIR-CIMAP: Central Institute of Medicinal and Aromatic Plants CSIR, Plant Biotechnology Division, INDIA
| | - Priyadarshi Satpati
- Indian Institute of Technology Guwahati, Bioscience and BIoengineering, INDIA
| | - Sunanda Chatterjee
- Indian Institute of Technology Guwahati, CHEMISTRY, IIT GUWAHATI, 781039, GUWAHATI, INDIA
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4
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Misra R, Rudnick-Glick S, Adler-Abramovich L. From Folding to Assembly: Functional Supramolecular Architectures of Peptides Comprised of Non-Canonical Amino Acids. Macromol Biosci 2021; 21:e2100090. [PMID: 34142442 DOI: 10.1002/mabi.202100090] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/06/2021] [Indexed: 12/27/2022]
Abstract
The engineering of biological molecules is the fundamental concept behind the design of complex materials with desirable functions. Over the last few decades, peptides and proteins have emerged as useful building blocks for well-defined nanostructures with controlled size and dimensions. Short peptides in particular have received much attention due to their inherent biocompatibility, lower synthetic cost, and ease of tunability. In addition to the diverse self-assembling properties of short peptides comprising coded amino acids and their emerging applications in nanotechnology, there is now growing interest in the properties of peptides composed of non-canonical amino acids. Such non-natural oligomers have been shown in recent years to form well-defined secondary structures similar to natural proteins, with the ability to self-assemble to generate a wide variety of nanostructures with excellent biostability. This review describes recent events in the development of supramolecular assemblies of peptides composed completely of non-coded amino acids and their hybrid analogues. Special attention is paid to understanding the supramolecular assemblies at the atomic level and to considering their potential applications in nanotechnology.
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Affiliation(s)
- Rajkumar Misra
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Safra Rudnick-Glick
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
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5
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Lu S, Wu Y, Li J, Meng X, Hu C, Zhao Y, Wu C. Directed Disulfide Pairing and Folding of Peptides for the De Novo Development of Multicyclic Peptide Libraries. J Am Chem Soc 2020; 142:16285-16291. [PMID: 32914969 DOI: 10.1021/jacs.0c06044] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Disulfide-rich peptides (DRPs) have been an emerging frontier for drug discovery. There have been two DRPs approved as drugs (i.e., Ziconotide and Linaclotide), and many others are undergoing preclinical studies or in clinical trials. All of these DRPs are of nature origin or derived from natural peptides. It is still a challenge to design new DRPs without recourse to natural scaffolds due to the difficulty in handling the disulfide pairing. Here we developed a simple and robust strategy for directing the disulfide pairing and folding of peptides with up to six cysteine residues. Our strategy exploits the dimeric pairing of CPPC (cysteine-proline-proline-cysteine) motifs for directing disulfide formation, and DRPs with different multicyclic topologies were designed and synthesized by regulating the patterns of CPPC motifs and cysteine residues in peptides. As neither sequence manipulations nor unnatural amino acids are involved, the designed DRPs can be used as templates for the de novo development of biosynthetic multicyclic peptide libraries, enabling selection of DRPs with new functions directly from fully randomized sequences. We believe that this work represents as an important step toward the discovery and design of new multicyclic peptide ligands and therapeutics with structures not derived from natural scaffolds.
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Affiliation(s)
- Shuaimin Lu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, P.R. China
| | - Yapei Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, P.R. China
| | - Jinjing Li
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, P.R. China
| | - Xiaoting Meng
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, P.R. China
| | - Chenliang Hu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, P.R. China
| | - Yibing Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, P.R. China
| | - Chuanliu Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, P.R. China
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6
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Ilie A, Boucher A, Park J, Berghuis AM, McKinney RA, Orlowski J. Assorted dysfunctions of endosomal alkali cation/proton exchanger SLC9A6 variants linked to Christianson syndrome. J Biol Chem 2020; 295:7075-7095. [PMID: 32277048 PMCID: PMC7242699 DOI: 10.1074/jbc.ra120.012614] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic screening has identified numerous variants of the endosomal solute carrier family 9 member A6 (SLC9A6)/(Na+,K+)/H+ exchanger 6 (NHE6) gene that cause Christianson syndrome, a debilitating X-linked developmental disorder associated with a range of neurological, somatic, and behavioral symptoms. Many of these variants cause complete loss of NHE6 expression, but how subtler missense substitutions or nonsense mutations that partially truncate its C-terminal cytoplasmic regulatory domain impair NHE6 activity and endosomal function are poorly understood. Here, we describe the molecular and cellular consequences of six unique mutations located in the N-terminal cytoplasmic segment (A9S), the membrane ion translocation domain (L188P and G383D), and the C-terminal regulatory domain (E547*, R568Q, and W570*) of human NHE6 that purportedly cause disease. Using a heterologous NHE6-deficient cell expression system, we show that the biochemical, catalytic, and cellular properties of the A9S and R568Q variants were largely indistinguishable from those of the WT transporter, which obscured their disease significance. By contrast, the L188P, G383D, E547*, and W570* mutants exhibited variable deficiencies in biosynthetic post-translational maturation, membrane sorting, pH homeostasis in recycling endosomes, and cargo trafficking, and they also triggered apoptosis. These findings broaden our understanding of the molecular dysfunctions of distinct NHE6 variants associated with Christianson syndrome.
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Affiliation(s)
- Alina Ilie
- Department of Physiology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Annie Boucher
- Department of Physiology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Jaeok Park
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | | | - R Anne McKinney
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - John Orlowski
- Department of Physiology, McGill University, Montreal, Quebec H3G 0B1, Canada
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7
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Toward accurate prediction of amino acid derivatives structure and energetics from DFT: glycine conformers and their interconversions. J Mol Model 2020; 26:129. [DOI: 10.1007/s00894-020-4342-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/04/2020] [Indexed: 12/30/2022]
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8
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Yarava JR, Nishiyama Y, Raghothama S, Ramanathan KV. Conformational investigation of peptides using solid-state NMR spectroscopy-A study of polymorphism of β-turn peptides containing diprolines. Chem Biol Drug Des 2019; 95:394-407. [PMID: 31755652 DOI: 10.1111/cbdd.13649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/02/2019] [Accepted: 11/16/2019] [Indexed: 11/26/2022]
Abstract
The construction of complex protein folds relies on the precise conversion of a linear polypeptide chain into a compact 3-dimensional structure. In this context, study of isolated secondary structural modules containing short stretches of amino acids assumes significance. Additionally, peptides, both natural and synthetic, play a major role as potential drugs. With a view to understand the local conformations adopted by peptides in the solid state, we propose a multinuclear NMR approach utilizing spectra of nuclei in their natural isotopic abundance. Various solid-state NMR experiments have been utilized for assignment of the spectra. Additionally, the gauge-including projector augmented-wave (GIPAW) calculations were used to confirm the assignments. Particularly, the utility of the double-quantum-single-quantum correlation experiments is highlighted for the purpose of assignment and for inferring the conformation across the peptide bond. The methodology is illustrated for the case of designed peptides containing diproline residues occurring at the β-turns for identifying their cis-trans conformational polymorphism. The proposed method promises to be of use in the study of conformations of small- to medium-sized peptides such as antimicrobial peptides and in the study of polymorphism leading to applications in drug development protocols.
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Affiliation(s)
- Jayasubba Reddy Yarava
- NMR Research Centre, Indian Institute of Science, Bangalore, India.,Department of Physics, Indian Institute of Science, Bangalore, India
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., Musashino, Akishima, Japan.,RIKEN-JEOL Collaboration Center, Tsurumi, Yokohama, Japan
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9
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Costantini NV, Ganguly HK, Martin MI, Wenzell NA, Yap GPA, Zondlo NJ. The Distinct Conformational Landscapes of 4S-Substituted Prolines That Promote an endo Ring Pucker. Chemistry 2019; 25:11356-11364. [PMID: 31237705 DOI: 10.1002/chem.201902382] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Indexed: 12/28/2022]
Abstract
4-Substitution on proline directly impacts protein main chain conformational preferences. The structural effects of N-acyl substitution and of 4-substitution were examined by NMR spectroscopy and X-ray crystallography on minimal molecules with a proline 4S-nitrobenzoate. The effects of N-acyl substitution on conformation were attenuated in the 4S-nitrobenzoate context, due to the minimal role of the n→π* interaction in stabilizing extended conformations. By X-ray crystallography, an extended conformation was observed for most molecules. The formyl derivative adopted a δ conformation that is observed at the i+2 position of β-turns. Computational analysis indicated that the structures observed crystallographically represent the inherent conformational preferences of 4S-substituted prolines with electron-withdrawing 4-position substituents. The divergent conformational preferences of 4R- and 4S-substituted prolines suggest their wider structure-specific application in molecular design. In particular, the proline endo ring pucker favored by 4S-substituted prolines uniquely promotes the δ conformation [(ϕ, ψ) ≈(-80°, 0°)] found in β-turns. In contrast to other acyl capping groups, the pivaloyl group strongly promoted trans amide bond and polyproline II helix conformation, with a close n→π* interaction in the crystalline state, despite the endo ring pucker, suggesting its special capabilities in promoting compact conformations in ϕ due to its strongly electron-donating character.
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Affiliation(s)
- Nicholas V Costantini
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Himal K Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Maxwell I Martin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Nicole A Wenzell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
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10
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Rigling C, Kisunzu JK, Duschmalé J, Häussinger D, Wiesner M, Ebert MO, Wennemers H. Conformational Properties of a Peptidic Catalyst: Insights from NMR Spectroscopic Studies. J Am Chem Soc 2018; 140:10829-10838. [PMID: 30106584 DOI: 10.1021/jacs.8b05459] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Peptides have become valuable as catalysts for a variety of different reactions, but little is known about the conformational properties of peptidic catalysts. We investigated the conformation of the peptide H-dPro-Pro-Glu-NH2, a highly reactive and stereoselective catalyst for conjugate addition reactions, and the corresponding enamine intermediate in solution by NMR spectroscopy and computational methods. The combination of nuclear Overhauser effects (NOEs), residual dipolar couplings (RDCs), J-couplings, and temperature coefficients revealed that the tripeptide adopts a single predominant conformation in its ground state. The structure is a type I β-turn, which gains stabilization from three hydrogen bonds that are cooperatively formed between all functional groups (secondary amine, carboxylic acid, amides) within the tripeptide. In contrast, the conformation of the enamine intermediate is significantly more flexible. The conformational ensemble of the enamine is still dominated by the β-turn, but the backbone and the side chain of the glutamic acid residue are more dynamic. The key to the switch between rigidity and flexibility of the peptidic catalyst is the CO2H group in the side chain of the glutamic acid residue, which acts as a lid that can open and close. As a result, the peptidic catalyst is able to adapt to the structural requirements of the intermediates and transition states of the catalytic cycle. These insights might explain the robustness and high reactivity of the peptidic catalyst, which exceeds that of other secondary amine-based organocatalysts. The data suggest that a balance between rigidity and flexibility, which is reminiscent of the dynamic nature of enzymes, is beneficial for peptidic catalysts and other synthetic catalysts.
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Affiliation(s)
- Carla Rigling
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Jessica K Kisunzu
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Jörg Duschmalé
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland.,Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Markus Wiesner
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Marc-Olivier Ebert
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Helma Wennemers
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
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11
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Malo de Molina P, Alvarez F, Frick B, Wildes A, Arbe A, Colmenero J. Investigation of the dynamics of aqueous proline solutions using neutron scattering and molecular dynamics simulations. Phys Chem Chem Phys 2017; 19:27739-27754. [PMID: 28984889 DOI: 10.1039/c7cp05474b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We applied quasielastic neutron scattering (QENS) techniques to samples with two different contrasts (deuterated solute/hydrogenated solvent and the opposite label) to selectively study the component dynamics of proline/water solutions. Results on diluted and concentrated solutions (31 and 6 water molecules/proline molecule, respectively) were analyzed in terms of the susceptibility and considering a recently proposed model for water dynamics [Arbe et al., Phys. Rev. Lett., 2016, 117, 185501] which includes vibrations and the convolution of localized motions and diffusion. We found that proline molecules not only reduce the average diffusion coefficient of water but also extend the time/frequency range of the crossover region ('cage') between the vibrations and purely diffusive behavior. For the high proline concentration we also found experimental evidence of water heterogeneous dynamics and a distribution of diffusion coefficients. Complementary molecular dynamics simulations show that water molecules start to perform rotational diffusion when they escape the cage regime but before the purely diffusive behavior is established. The rotational diffusion regime is also retarded by the presence of proline molecules. On the other hand, a strong coupling between proline and water diffusive dynamics which persists with decreasing temperature is directly observed using QENS. Not only are the temperature dependences of the diffusion coefficients of both components the same, but their absolute values also approach each other with increasing proline concentration. We compared our results with those reported using other techniques, in particular using dielectric spectroscopy (DS). A simple approach based on molecular hydrodynamics and a molecular treatment of DS allows rationalizing the a priori puzzling inconsistency between QENS and dielectric results regarding the dynamic coupling of the two components. The interpretation proposed is based on general grounds and therefore should be applicable to other biomolecular solutions.
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Affiliation(s)
- Paula Malo de Molina
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU) - Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain.
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12
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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13
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Spectrophotometric study of kinetics and associated thermodynamics for the complexation of Pr(III) with l-proline in presence of Zn(II). ARAB J CHEM 2017. [DOI: 10.1016/j.arabjc.2013.07.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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Grünenfelder CE, Kisunzu JK, Trapp N, Kastl R, Wennemers H. Crystal structures of peptidic catalysts of the H-d
Pro-Pro-Xaa type. Biopolymers 2017; 108. [DOI: 10.1002/bip.22912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/27/2016] [Accepted: 07/04/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Claudio E. Grünenfelder
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Jessica K. Kisunzu
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Nils Trapp
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Robert Kastl
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
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15
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Yarava JR, Sonti R, Kantharaju K, Raghothama S, Ramanathan KV. Solid-state NMR at natural isotopic abundance for the determination of conformational polymorphism - the case of designed β-turn peptides containing di-prolines. Chem Commun (Camb) 2017; 53:1317-1320. [PMID: 28074945 DOI: 10.1039/c6cc08676d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The proton double quantum-carbon single quantum correlation experiment has been applied to designed peptides in the solid state in natural isotopic abundance. Analogous to nOe studies in solution, through-space double-quantum connectivities have been exploited to obtain the cis-trans conformational polymorphism of diproline residues occurring at β-turns in the peptides.
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Affiliation(s)
- Jayasubba Reddy Yarava
- Department of Physics, Indian Institute of Science, Bangalore-560012, India and NMR Research Center, Indian Institute of Science, Bangalore-560012, India. and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fedérale de Lausanne, Switzerland
| | - Rajesh Sonti
- NMR Research Center, Indian Institute of Science, Bangalore-560012, India. and Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India and Biozentrum, Structural Biology, Universität Basel, Basel, Switzerland
| | - K Kantharaju
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India and Department of Chemistry, Rani Channamma University, Belgavi, India
| | - S Raghothama
- NMR Research Center, Indian Institute of Science, Bangalore-560012, India.
| | - K V Ramanathan
- NMR Research Center, Indian Institute of Science, Bangalore-560012, India.
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16
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Raghavender US. Analysis of residue conformations in peptides in Cambridge structural database and protein-peptide structural complexes. Chem Biol Drug Des 2016; 89:428-442. [DOI: 10.1111/cbdd.12862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/27/2016] [Accepted: 08/25/2016] [Indexed: 01/29/2023]
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17
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Ingole TS, Vijayadas KN, Chaitanya KN, Kotmale AS, Gawade RL, Gonnade RG, Rajamohanan PR, Sanjayan GJ. Disruption of Native β-Turns: Consequence of Folding Competition between Native and Orthanilic Acid Proline-BasedPseudoβ-Turn. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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18
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Jedhe GS, Vijayadas KN, Kotmale AS, Sangtani E, Shinde DR, Gonnade RG, Rajamohanan PR, Sanjayan GJ. Residue dependent hydrogen-bonding preferences in orthanilic acid-based short peptide β-turn motifs. RSC Adv 2016. [DOI: 10.1039/c6ra05684a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This communication describes the competition between native β-turn (C10) and 2-aminobenzenesulfonic acid (SAnt)(orthanilic acid)-based pseudo β-turn (C11) in their hybrid peptides.
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Affiliation(s)
- Ganesh S. Jedhe
- Division of Organic Chemistry
- CSIR-National Chemical Laboratory
- Pune 411 008
- India
| | | | - Amol S. Kotmale
- Central NMR Facility
- CSIR-National Chemical Laboratory
- Pune 411 008
- India
| | - Ekta Sangtani
- Center for Materials Characterization
- CSIR-National Chemical Laboratory
- Pune 411 008
- India
| | - Dinesh R. Shinde
- Central NMR Facility
- CSIR-National Chemical Laboratory
- Pune 411 008
- India
| | - Rajesh G. Gonnade
- Center for Materials Characterization
- CSIR-National Chemical Laboratory
- Pune 411 008
- India
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19
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Goyal B, Kumar A, Srivastava KR, Durani S. Computational scrutiny of the effect of N-terminal proline and residue stereochemistry in the nucleation of α-helix fold. RSC Adv 2016. [DOI: 10.1039/c6ra10934a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
N-Terminal l- to d-residue mutation nucleate helical fold in Ac–DAla–LAla3–NHMe (Ib, m2), Ac–DPro–LAla3–NHMe (IIb, m1), and Ac–DPro–LPro–LAla2–NHMe (IIIb, m2) peptides.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | | | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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20
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Ingole TS, Kotmale AS, Gawade RL, Gonnade RG, Rajamohanan PR, Sanjayan GJ. 3-Aminothiophenecarboxylic acid (3-Atc)-induced folding in peptides. NEW J CHEM 2016. [DOI: 10.1039/c6nj01667g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This article demonstrates the consequences of incorporating a constrained β-amino acid into a peptide chain and its effect on conformation of oligomers.
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Affiliation(s)
- Tukaram S. Ingole
- Division of Organic Chemistry
- National Chemical Laboratory
- Pune 411 008
- India
| | - Amol S. Kotmale
- Central NMR Facility
- National Chemical Laboratory
- Pune 411 008
- India
| | - Rupesh L. Gawade
- Center for Materials Characterization
- National Chemical Laboratory
- Pune
- India
| | - Rajesh G. Gonnade
- Center for Materials Characterization
- National Chemical Laboratory
- Pune
- India
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21
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Goyal B, Srivastava KR, Kumar A, Patwari GN, Durani S. Probing the role of electrostatics of polypeptide main-chain in protein folding by perturbing N-terminal residue stereochemistry: DFT study with oligoalanine models. RSC Adv 2016. [DOI: 10.1039/c6ra22870d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Energetics of folding (ΔHE→F, in kcal mol−1) from the extended (E) structure to the folded (F) structure for Ia and Ib critically depend on the geometrical relationship between the backbone peptide units of the polypeptide structure.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | | | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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22
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Kesharwani MK, Karton A, Martin JML. Benchmark ab Initio Conformational Energies for the Proteinogenic Amino Acids through Explicitly Correlated Methods. Assessment of Density Functional Methods. J Chem Theory Comput 2015; 12:444-54. [DOI: 10.1021/acs.jctc.5b01066] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manoj K. Kesharwani
- Department
of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Amir Karton
- School
of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Jan M. L. Martin
- Department
of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
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23
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Pichumani K, George G, Hebbar S, Chatterjee B, Raghothama S. Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.03.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Chandrasekhar S, Kumar CP, Kumar TP, Haribabu K, Jagadeesh B, Lakshmi JK, Mainkar PS. Peptidomimetic organocatalysts: efficient Michael addition of ketones onto nitroolefins with very low catalyst loading. RSC Adv 2014. [DOI: 10.1039/c4ra04165h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The syntheses and applications of peptidomimetic triazole-based catalysts are described as efficient organocatalysts in Michael reaction with low loading.
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Affiliation(s)
- Srivari Chandrasekhar
- Division of Natural Products Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad, India
| | | | - Togapur Pavan Kumar
- Division of Natural Products Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad, India
| | - Kothapalli Haribabu
- Division of Natural Products Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad, India
| | - Bharatam Jagadeesh
- Centre for NMR and Structural Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad, India
| | - Jerripothula K. Lakshmi
- Centre for NMR and Structural Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad, India
| | - Prathama S. Mainkar
- Division of Natural Products Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad, India
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25
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Reddy DN, George G, Prabhakaran EN. Crystal-Structure Analysis of cis-X-Pro-Containing Peptidomimetics: Understanding the Steric Interactions at cisX-Pro Amide Bonds. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Reddy DN, George G, Prabhakaran EN. Crystal-structure analysis of cis-X-Pro-containing peptidomimetics: understanding the steric interactions at cis X-Pro amide bonds. Angew Chem Int Ed Engl 2013; 52:3935-9. [PMID: 23450815 DOI: 10.1002/anie.201209517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/18/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Damodara N Reddy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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27
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Kumarn S, Chimnoi N, Ruchirawat S. Synthesis of integerrimide A by an on-resin tandem Fmoc-deprotection–macrocyclisation approach. Org Biomol Chem 2013; 11:7760-7. [DOI: 10.1039/c3ob41447g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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28
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Scully CCG, Rai V, Poda G, Zaretsky S, Burns DC, Houliston RS, Lou T, Yudin AK. Bending Rigid Molecular Rods: Formation of Oligoproline Macrocycles. Chemistry 2012; 18:15612-7. [DOI: 10.1002/chem.201203266] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Indexed: 12/14/2022]
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29
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Mueller AH, Dockter C, Gough SP, Lundqvist U, von Wettstein D, Hansson M. Characterization of mutations in barley fch2 encoding chlorophyllide a oxygenase. PLANT & CELL PHYSIOLOGY 2012; 53:1232-46. [PMID: 22537757 DOI: 10.1093/pcp/pcs062] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The barley (Hordeum vulgare L.) mutants fch2 and clo-f2 comprise an allelic group of 14 Chl b-deficient lines. The genetic map position of fch2 corresponds to the physical map position of the gene encoding chlorophyllide a oxygenase. This enzyme converts chlorophyllide a to chlorophyllide b and it is essential for Chl b biosynthesis. The fch2 and clo-f2 barley lines were shown to be mutated in the gene for chlorophyllide a oxygenase. A five-base insertion was found in fch2 and base deletions in clo-f2.101, clo-f2.105, clo-f2.2800 and clo-f2.3613. In clo-f2.105 and clo-f2.108, nonsense base exchanges were discovered. All of these mutations led to a premature stop of translation and none of the mutants formed Chl b. The mutant clo-f2.2807 was transcript deficient and formed no Chl b. Missense mutations in clo-f2.102 (leading to the amino acid exchange D495N) and clo-f2.103 (G280D) resulted in a total lack of Chl b, whereas in the missense mutants clo-f2.107 (P419L), clo-f2.109 (A94T), clo-f2.122 (C320Y), clo-f2.123 (A94T), clo-f2.133 (A376V) and clo-f2.181 (L373F) intermediate contents of Chl b were determined. The missense mutations affect conserved residues, and their effect on chlorophyllide a oxygenase is discussed. The mutations in clo-f2.102, clo-f2.103, clo-f2.133 and clo-f2.181 may influence electron transfer as illustrated in the active site of a structural model protein. The changes in clo-f2.107, clo-f2.109, clo-f2.122 and clo-f2.123 may lead to Chlb deficiency by interfering with the regulation of chlorophyllide a oxygenase. The correlation of mutations and phenotypes strongly supports that the barley locus fch2 encodes chlorophyllide a oxygenase.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Catalytic Domain
- Chlorophyll/genetics
- Chlorophyll/metabolism
- Chromosome Mapping
- Chromosomes, Plant/genetics
- Chromosomes, Plant/metabolism
- Cloning, Molecular
- Codon, Nonsense/genetics
- Codon, Nonsense/metabolism
- Electron Transport
- Frameshift Mutation
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genes, Plant
- Hordeum/enzymology
- Hordeum/genetics
- Molecular Sequence Data
- Mutation, Missense
- Oxygenases/genetics
- Oxygenases/metabolism
- Phenotype
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Protein Structure, Tertiary
- Sequence Alignment
- Synteny
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30
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Ganguly HK, Majumder B, Chattopadhyay S, Chakrabarti P, Basu G. Direct Evidence for CH···π Interaction Mediated Stabilization of Pro-cisPro Bond in Peptides with Pro-Pro-Aromatic motifs. J Am Chem Soc 2012; 134:4661-9. [DOI: 10.1021/ja209334v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Himal K. Ganguly
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Barun Majumder
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Sarbani Chattopadhyay
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Pinak Chakrabarti
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Gautam Basu
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
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31
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Duschmalé J, Wennemers H. Adapting to substrate challenges: peptides as catalysts for conjugate addition reactions of aldehydes to α,β-disubstituted nitroolefins. Chemistry 2011; 18:1111-20. [PMID: 22189758 DOI: 10.1002/chem.201102484] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Indexed: 11/11/2022]
Abstract
Conjugate addition reactions of aldehydes to α,β-disubstituted nitroolefins are important because they provide synthetically useful γ-nitroaldehydes bearing three consecutive stereogenic centers. Such reactions are challenging due to the drastically lower reactivity of α,β-disubstituted nitroolefins compared to, for example, β-monosubstituted nitroolefins. The testing of a small collection of peptides of the type Pro-Pro-Xaa (Xaa=acidic amino acid) led to the identification of H-Pro-Pro-D-Gln-OH and H-Pro-Pro-Asn-OH as excellent stereoselective catalysts for this transformation. In the presence of 5 mol% of these peptides different combinations of aldehydes and α,β-disubstituted nitroolefins react readily with each other providing γ-nitroaldehydes in good yields and diastereoselectivities as well as excellent enantioselectivities. Chiral pyrrolidines as well as fully substituted γ-butyrolactams and γ-amino acids are easily accessible from the γ-nitroaldehydes. Mechanistic studies demonstrate that the configuration at all three stereogenic centers is induced by the peptidic catalysts. Only a minimal amount of products from homo-aldol reactions is observed demonstrating the high chemoselectivity of the peptidic catalysts.
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Affiliation(s)
- Jörg Duschmalé
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel, Switzerland
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32
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Profant V, Baumruk V, Li X, Šafařík M, Bouř P. Tracking of the Polyproline Folding by Density Functional Computations and Raman Optical Activity Spectra. J Phys Chem B 2011; 115:15079-89. [DOI: 10.1021/jp207706p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Václav Profant
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Vladimír Baumruk
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Xiaojun Li
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Martin Šafařík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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33
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Saha I, Shamala N. Investigating diproline segments in proteins: occurrences, conformation and classification. Biopolymers 2011; 97:54-64. [PMID: 21898361 DOI: 10.1002/bip.21703] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/18/2011] [Accepted: 07/18/2011] [Indexed: 11/06/2022]
Abstract
The covalent linkage between the side-chain and the backbone nitrogen atom of proline leads to the formation of the five-membered pyrrolidine ring and hence restriction of the backbone torsional angle ϕ to values of -60 °± 30° for the L-proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment (( L) Pro-( L) Pro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro-Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa-Pro-Yaa segments in proteins which gives us a better understanding on the restriction imposed on other residues by the diproline segment and the single proline residue. The study indicates that P(II) -P(II) and P(II) -α are the most favorable conformational states for the diproline segment. The analysis on Xaa-Pro-Yaa sequences reveals that the Xaa-Pro peptide bond exists preferably as the trans conformer rather than the cis conformer. The present study may lead to a better understanding of the behavior of proline occurring in diproline segments which can facilitate various designed diproline-based synthetic templates for biological and structural studies.
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Affiliation(s)
- Indranil Saha
- Department of Physics, Indian Institute of Science, Bangalore, India.
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34
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Gokhale A, Weldeghiorghis TK, Taneja V, Satyanarayanajois SD. Conformationally constrained peptides from CD2 to modulate protein-protein interactions between CD2 and CD58. J Med Chem 2011; 54:5307-19. [PMID: 21755948 DOI: 10.1021/jm200004e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cell adhesion molecule CD2 and its ligand CD58 provide good examples of protein-protein interactions in cells that participate in the immune response. To modulate the cell adhesion interaction, peptides were designed from the discontinuous epitopes of the β-strand region of CD2 protein. The two strands were linked by a peptide bond. β-Strands in the peptides were nucleated by inserting a β-sheet-inducing (D)-Pro-Pro sequence or a dibenzofuran (DBF) turn mimetic with key amino acid sequences from CD2 protein that binds to CD58. The solution structures of the peptides (5-10) were studied by NMR and molecular dynamics simulations. The ability of these peptides to inhibit cell adhesion interaction was studied by E-rosetting and lymphocyte epithelial assays. Peptides 6 and 7 inhibit the cell adhesion activity with an IC(50) of 7 and 11 nM, respectively, in lymphocyte epithelial adhesion assay. NMR and molecular modeling results indicated that peptides 6 and 7 exhibited β-hairpin structure in solution.
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Affiliation(s)
- Ameya Gokhale
- Department of Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana 71201, United States
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35
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Jacobsen Ø, Maekawa H, Ge NH, Görbitz CH, Rongved P, Ottersen OP, Amiry-Moghaddam M, Klaveness J. Stapling of a 310-Helix with Click Chemistry. J Org Chem 2011; 76:1228-38. [DOI: 10.1021/jo101670a] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Øyvind Jacobsen
- School of Pharmacy, University of Oslo, P.O. Box 1068 Blindern, 0316 Oslo, Norway
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, United States
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, United States
| | - Carl Henrik Görbitz
- Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway
| | - Pål Rongved
- School of Pharmacy, University of Oslo, P.O. Box 1068 Blindern, 0316 Oslo, Norway
| | - Ole Petter Ottersen
- Centre for Molecular Biology and Neuroscience, University of Oslo, P.O. Box 1105 Blindern, 0317 Oslo, Norway
| | - Mahmood Amiry-Moghaddam
- Centre for Molecular Biology and Neuroscience, University of Oslo, P.O. Box 1105 Blindern, 0317 Oslo, Norway
| | - Jo Klaveness
- School of Pharmacy, University of Oslo, P.O. Box 1068 Blindern, 0316 Oslo, Norway
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36
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Byun BJ, Song IK, Chung YJ, Ryu KH, Kang YK. Conformational Preferences of X-Pro Sequences: Ala-Pro and Aib-Pro Motifs. J Phys Chem B 2010; 114:14077-86. [DOI: 10.1021/jp107200f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Byung Jin Byun
- Department of Chemistry, Department of Biochemistry, and Database/Bioinformatics Laboratory, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Il Keun Song
- Department of Chemistry, Department of Biochemistry, and Database/Bioinformatics Laboratory, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Yong Je Chung
- Department of Chemistry, Department of Biochemistry, and Database/Bioinformatics Laboratory, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Keun Ho Ryu
- Department of Chemistry, Department of Biochemistry, and Database/Bioinformatics Laboratory, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Young Kee Kang
- Department of Chemistry, Department of Biochemistry, and Database/Bioinformatics Laboratory, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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37
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Satyanarayanajois SD, Büyüktimkin B, Gokhale A, Ronald S, Siahaan TJ, Latendresse JR. A peptide from the beta-strand region of CD2 protein that inhibits cell adhesion and suppresses arthritis in a mouse model. Chem Biol Drug Des 2010; 76:234-44. [PMID: 20572813 DOI: 10.1111/j.1747-0285.2010.01001.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cell adhesion molecules play a central role at every step of the immune response. The function of leukocytes can be regulated by modulating adhesion interactions between cell adhesion molecules to develop therapeutic agents against autoimmune diseases. Among the different cell adhesion molecules that participate in the immunologic response, CD2 and its ligand CD58 (LFA-3) are two of the best-characterized adhesion molecules mediating the immune response. To modulate the cell adhesion interaction, peptides were designed from the discontinuous epitopes of the beta-strand region of CD2 protein. The two strands were linked by a peptide bond. beta-Strands in the peptides were nucleated by inserting a beta-sheet-inducing Pro-Gly sequence with key amino acid sequences from CD2 protein that binds to CD58. Using a fluorescence assay, peptides that exhibited potential inhibitory activity in cell adhesion were evaluated for their ability to bind to CD58 protein. A model for peptide binding to CD58 protein was proposed based on docking studies. Administration of one of the peptides, P3 in collagen-induced arthritis in the mouse model, indicated that peptide P3 was able to suppress rheumatoid arthritis in mice.
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Affiliation(s)
- Seetharama D Satyanarayanajois
- Department of Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA 71201, USA.
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Kantharaju, Raghothama S, Aravinda S, Shamala N, Balaram P. Helical conformations of hexapeptides containing N-terminus diproline segments. Biopolymers 2010; 94:360-70. [DOI: 10.1002/bip.21395] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wiesner M, Neuburger M, Wennemers H. Tripeptides of the Type H-D-Pro-Pro-Xaa-NH2as Catalysts for Asymmetric 1,4-Addition Reactions: Structural Requirements for High Catalytic Efficiency. Chemistry 2009; 15:10103-9. [DOI: 10.1002/chem.200901021] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Jayanthi S, Chatterjee B, Raghothama S. Natural abundant solid state NMR studies in designed tripeptides for differentiation of multiple conformers. Biopolymers 2009; 91:851-60. [DOI: 10.1002/bip.21270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Dutta A, Drew MG, Pramanik A. Design of a turn-linker-turn foldamer by incorporating meta-amino benzoic acid in the middle of a helix forming hexapeptide sequence: A helix breaking approach. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.04.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Saha I, Chatterjee B, Shamala N, Balaram P. Crystal structures of peptide enantiomers and racemates: probing conformational diversity in heterochiral Pro-Pro sequences. Biopolymers 2009; 90:537-43. [PMID: 18335426 DOI: 10.1002/bip.20982] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Multiple conformational states in heterochiral diproline sequences have been characterized in the solid state by the determination of the crystal structures of seven tripeptides in enantiomeric and racemic forms. The sequences of the type Piv-DPro-LPro-DXxx-NHMe (D-L-D) [DXxx=DVal 1, DLeu 3, and DPhe 5] and their corresponding enatiomeric L-D-L sequences [LXxx=LVal 2, LLeu 4, and LPhe 6] have been investigated. Single crystals have been obtained for the pure enantiomers 1, 2, 3, 4 and for the racemates 1/2, 3/4, and 5/6. For Xxx=Leu, mirror image conformations (type II/II' beta-turns) at Pro-Leu segment are obtained. For Xxx=Val, a LPro-DPro type II beta-turn in 2 and an open/extended structure is obtained in the solvated form of the enantiomer 1. For Xxx=Phe, suitable crystals could not be obtained for enatiomeric peptides. The racemate 5/6 revealed a cis peptide bond between the diproline segment with the absence of any intramolecular hydrogen bonds. Crystal structures of enantiomers and racemates prove useful in characterizing the multiple conformational states that are accessible to Pro-Pro segments.
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Affiliation(s)
- Indranil Saha
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
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Kantharaju, Raghothama S, Raghavender US, Aravinda S, Shamala N, Balaram P. Conformations of heterochiral and homochiral proline-pseudoproline segments in peptides: Context dependentcis-transpeptide bond isomerization. Biopolymers 2009; 92:405-16. [DOI: 10.1002/bip.21207] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Jacobsen Ø, Klaveness J, Petter Ottersen O, Reza Amiry-Moghaddam M, Rongved P. Synthesis of cyclic peptide analogues of the 310 helical Pro138-Gly144 segment of human aquaporin-4 by olefin metathesis. Org Biomol Chem 2009; 7:1599-611. [DOI: 10.1039/b823559g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Chatterjee B, Saha I, Raghothama S, Aravinda S, Rai R, Shamala N, Balaram P. Designed peptides with homochiral and heterochiral diproline templates as conformational constraints. Chemistry 2008; 14:6192-204. [PMID: 18491347 DOI: 10.1002/chem.200702029] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L-Pro-L-Pro and D-Pro-L-Pro units. Four distinct classes of model peptides have been investigated: a) isolated D-Pro-L-Pro segments which form type II' beta-turn; b) D-Pro-L-Pro-L-Xxx sequences which form type II'-I (betaII'-I, consecutive beta-turns) turns; c) D-Pro-L-Pro-D-Xxx sequences; d) L-Pro-L-Pro-L-Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv-D-Pro-L-Pro-L-Xxx-NHMe are conformationally homogeneous, adopting consecutive beta-turn conformations. Peptides in the series Piv-D-Pro-L-Pro-D-Xxx-NHMe and Piv-L-Pro-L-Pro-L-Xxx-NHMe, display a heterogeneity of structures in crystals. A type VIa beta-turn conformation is characterized in Piv-L-Pro-L-Pro-L-Phe-OMe (18), while an example of a 5-->1 hydrogen bonded alpha-turn is observed in crystals of Piv-D-Pro-L-Pro-D-Ala-NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C-terminal Xxx residues on the structures of diproline segments. In L-Pro-L-Pro-L-Xxx sequences, the Xxx residues strongly determine the population of Pro-Pro cis conformers, with an overwhelming population of the trans form in L-Xxx=L-Ala (19).
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Affiliation(s)
- Bhaswati Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Joshi KB, Verma S. Sequence shuffle controls morphological consequences in a self-assembling tetrapeptide. J Pept Sci 2008; 14:118-26. [DOI: 10.1002/psc.955] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Dutt A, Drew MG, Pramanik A. Conformational and self-assembly studies of helix forming hexapeptides containing two α-amino isobutyric acids. Tetrahedron 2008. [DOI: 10.1016/j.tet.2007.11.016] [Citation(s) in RCA: 13] [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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Dasgupta B, Chakrabarti P, Basu G. Enhanced stability of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif. FEBS Lett 2007; 581:4529-32. [PMID: 17765893 DOI: 10.1016/j.febslet.2007.08.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 08/06/2007] [Accepted: 08/19/2007] [Indexed: 11/15/2022]
Abstract
Identification of sequence motifs that favor cis peptide bonds in proteins is important for understanding and designing proteins containing turns mediated by cis peptide conformations. From (1)H NMR solution studies on short peptides, we show that the Pro-Pro peptide bond in Pro-Pro-Phe almost equally populates the cis and trans isomers, with the cis isomer stabilized by a CHc...pi interaction involving the terminal Pro and Phe. We also show that Phe is over-represented at sequence positions immediately following cis Pro-Pro motifs in known protein structures. Our results demonstrate that the Pro-Pro cis conformer in Pro-Pro-Phe sequence motifs is as important as the trans conformer, both in short peptides as well as in natively folded proteins.
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Affiliation(s)
- Bhaskar Dasgupta
- Department of Biochemistry, Bose Institute, P-1/12 CIT, Scheme VIIM, Kolkata 700 054, India
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McLain SE, Soper AK, Terry AE, Watts A. Structure and Hydration of l-Proline in Aqueous Solutions. J Phys Chem B 2007; 111:4568-80. [PMID: 17419611 DOI: 10.1021/jp068340f] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The structure and hydration of L-proline in aqueous solution have been investigated using a combination of neutron diffraction with isotopic substitution, empirical potential structure refinement modeling, and small-angle neutron scattering at three concentrations, 1:10, 1:15, and 1:20 proline/water mole ratios. In each solution the carboxylate oxygen atoms from proline accept less than two hydrogen bonds from the surrounding water solvent and the amine hydrogen atoms donate less than one hydrogen bond to the surrounding water molecules. The solute-solute radial distribution functions indicate relatively weak interactions between proline molecules, and significant clustering or aggregation of proline is absent at all these concentrations. The spatial density distributions for the hydration of the COO- group in proline show a similar shape to that found previously in L-glutamic acid in aqueous solution but with a reduced coordination number.
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Affiliation(s)
- Sylvia E McLain
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom.
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