1
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Linden A, Magirius JEF, Heimgartner H. Solid-state conformations of linear depsipeptide amides with an alternating sequence of α,α-disubstituted α-amino acid and α-hydroxy acid. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2020; 76:1-9. [PMID: 31919301 DOI: 10.1107/s2053229619016073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 11/28/2019] [Indexed: 11/10/2022]
Abstract
Depsipeptides and cyclodepsipeptides are analogues of the corresponding peptides in which one or more amide groups are replaced by ester functions. Reports of crystal structures of linear depsipeptides are rare. The crystal structures and conformational analyses of four depsipeptides with an alternating sequence of an α,α-disubstituted α-amino acid and an α-hydroxy acid are reported. The molecules in the linear hexadepsipeptide amide in (S)-Pms-Acp-(S)-Pms-Acp-(S)-Pms-Acp-NMe2 acetonitrile solvate, C47H58N4O9·C2H3N, (3b), as well as in the related linear tetradepsipeptide amide (S)-Pms-Aib-(S)-Pms-Aib-NMe2, C28H37N3O6, (5a), the diastereoisomeric mixture (S,R)-Pms-Acp-(R,S)-Pms-Acp-NMe2/(R,S)-Pms-Acp-(R,S)-Pms-Acp-NMe2 (1:1), C32H41N3O6, (5b), and (R,S)-Mns-Acp-(S,R)-Mns-Acp-NMe2, C30H37N3O6, (5c) (Pms is phenyllactic acid, Acp is 1-aminocyclopentanecarboxylic acid and Mns is mandelic acid), generally adopt a β-turn conformation in the solid state, which is stabilized by intramolecular N-H...O hydrogen bonds. Whereas β-turns of type I (or I') are formed in the cases of (3b), (5a) and (5b), which contain phenyllactic acid, the torsion angles for (5c), which incorporates mandelic acid, indicate a β-turn in between type I and type III. Intermolecular N-H...O and O-H...O hydrogen bonds link the molecules of (3a) and (5b) into extended chains, and those of (5a) and (5c) into two-dimensional networks.
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Affiliation(s)
- Anthony Linden
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - J E Florian Magirius
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Heinz Heimgartner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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2
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Lee J, Jang G, Kang P, Choi MG, Choi SH. Helical α/β-depsipeptides with alternating residue types: conformational change from the 11-helix to the 14/15-helix. Org Biomol Chem 2016; 14:8438-42. [DOI: 10.1039/c6ob01602b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Short α/β-depsipeptides of which the third residue from the N-terminus is an (S)-lactic acid residue predominantly adopt 14/15-helical conformations analogous to the α-helix.
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Affiliation(s)
- Jaeyeon Lee
- Department of Chemistry
- Yonsei University
- Seoul
- Republic of Korea
| | - Geunhyeok Jang
- Department of Chemistry
- Yonsei University
- Seoul
- Republic of Korea
| | - Philjae Kang
- Department of Chemistry
- Yonsei University
- Seoul
- Republic of Korea
| | - Moon-Gun Choi
- Department of Chemistry
- Yonsei University
- Seoul
- Republic of Korea
| | - Soo Hyuk Choi
- Department of Chemistry
- Yonsei University
- Seoul
- Republic of Korea
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3
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Nguyen MM, Eckes KM, Suggs LJ. Charge and sequence effects on the self-assembly and subsequent hydrogelation of Fmoc-depsipeptides. SOFT MATTER 2014; 10:2693-702. [PMID: 24647784 PMCID: PMC4018732 DOI: 10.1039/c4sm00009a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Herein we report on the self-assembly of a family of Fmoc-depsipeptides into nanofibers and hydrogels. We show that fiber formation occurs in depsipeptide structures in which the fluorenyl group is closely associated and that side-chain charge and sequence affect the extent of self-assembly and subsequent gelation. Using fluorescence emission spectroscopy and circular dichroism, we show that self-assembly can be monitored and is observed in these slow-gelling systems prior to hydrogel formation. We also demonstrate that the ionic strength of salt-containing solutions affects the time at which self-assembly results in gelation of the bulk solution. From transmission electron microscopy, we report that morphological changes progress over time and are observed as micelles transitioning to fibers prior to the onset of gelation. Gelled depsipeptides degraded at a slower rate than non-gelled samples in the presence of salt, while hydrolysis in water of both gels and solution samples was minimal even after 14 days. Our work shows that while incorporating ester functionality within a peptide backbone reduces the number of hydrogen bonding sites available for forming and stabilizing supramolecular assemblies, the substitution does not prohibit self-assembly and subsequent gelation.
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Affiliation(s)
- Mary M. Nguyen
- The University of Texas at Austin, Department of Biomedical Engineering, 107 W Dean Keeton Street, Austin, TX, 78712, USA. Fax: 512 471 0616; Tel: 512 232 8593
| | - Kevin M. Eckes
- The University of Texas at Austin, Department of Biomedical Engineering, 107 W Dean Keeton Street, Austin, TX, 78712, USA. Fax: 512 471 0616; Tel: 512 232 8593
| | - Laura J. Suggs
- The University of Texas at Austin, Department of Biomedical Engineering, 107 W Dean Keeton Street, Austin, TX, 78712, USA. Fax: 512 471 0616; Tel: 512 232 8593
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4
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Abstract
Peptide-bond isosteres can enable a deep interrogation of the structure and function of a peptide or protein by amplifying or attenuating particular chemical properties. In this Minireview, the electronic, structural, and conformational attributes of four such isosteres-thioamides, esters, alkenes, and fluoroalkenes-are examined in detail. In particular, the ability of these isosteres to partake in noncovalent interactions is compared with that of the peptide bond. The consequential perturbations provide a useful tool for chemical biologists to reveal new structure-function relationships, and to endow peptides and proteins with desirable attributes.
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Affiliation(s)
- Amit Choudhary
- Graduate Program in Biophysics, University of Wisconsin–Madison, 1525 Linden Drive, Madison, WI 53706-1534 (USA)
| | - Ronald T. Raines
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 (USA), Fax: (+1) 608-890-2583
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706-1322 (USA)
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5
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Kang YK, Byun BJ. Conformational Preferences and Cis−Trans Isomerization of l-Lactic Acid Residue. J Phys Chem B 2008; 112:9126-34. [DOI: 10.1021/jp801200m] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Byung Jin Byun
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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6
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Oku H, Yamada K, Katakai R. Conformational change from antiparallel beta-sheet to alpha-helix in a series of depsipeptide, -(Leu-Leu-Lac)(n)-: syntheses, spectroscopic studies, and crystal structures of Boc-Leu-Lac-OEt and Boc-(Leu-Leu-Lac)(n)-OEt (n = 1, 2). Biopolymers 2008; 89:270-83. [PMID: 18067154 DOI: 10.1002/bip.20904] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The depsipeptides Boc-Leu-Lac-OEt (1) and Boc-(Leu-Leu-Lac)(n)-OEt (n = 1, 2) (2 and 3, respectively) (Boc = tert-butyloxycarbonyl, Lac = L-lactic acid residue) has been synthesized and studied by crystallographic, CD spectroscopic, and ESI-MS analyses. In the packing cells, those three compounds adopt beta-strand conformations. Each molecule is linked into a dimer (1) or an infinite assembly (2 and 3) by tight hydrogen bonds of the type NH...O==C. Interestingly, the hexamer, 3 shows the first example of antiparallel pleated beta-sheet crystal structure for a depsipeptide molecule. In the packing cells, especially for 3, the ester groups O--C==O are perpendicularly oriented to the amide groups NH--C==O and beta-sheet planes to avoid the interaction between --O--(ester) and O==C. Therefore, when the chain length become longer, the O...O==C repulsion interaction works as a beta-sheet breaker and hence promotes an alpha-helical structure as observed for Boc-(Leu-Leu-Lac)(3)-Leu-Leu-OEt (4) (Oku et al. Biopolymers 2004, 75, 242-254) and Boc-(Leu-Leu-Lac)(n)-OEt (n = 4-6) (5-7) (Katakai et al., Biopolymers 1996, 38, 285-290), in which the O...O==C repulsion does not cause significant structural changes in alpha-helical main chains. Therefore from the structural and spectroscopic analyses, we have found governing factors for the specificity in the beta-sheet and alpha-helix decision in this series of depsipeptides, -(Leu-Leu-Lac)(n)-.
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Affiliation(s)
- Hiroyuki Oku
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu, Gunma, Japan.
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7
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Scheike JA, Baldauf C, Spengler J, Albericio F, Pisabarro MT, Koksch B. Amide-to-Ester Substitution in Coiled Coils: The Effect of Removing Hydrogen Bonds on Protein Structure. Angew Chem Int Ed Engl 2007; 46:7766-9. [PMID: 17876795 DOI: 10.1002/anie.200702218] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jessica A Scheike
- Department of Chemistry and Biochemistry, Free University of Berlin, Takustrasse 3, 14195 Berlin, Germany
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8
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Scheike J, Baldauf C, Spengler J, Albericio F, Pisabarro M, Koksch B. Estersubstitutionen in α-helicalen Coiled-Coil-Peptiden: Effekt der Eliminierung von Wasserstoffbrücken auf die Struktur von Proteinen. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702218] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Oku H, Kimura Y, Ohama M, Ueyama N, Yamada K, Katakai R. Synthesis, crystal structure, and coordination properties of a helical peptide having β-(3-pyridyl)-l-alanine and l-glutamic acid residues. J Organomet Chem 2007. [DOI: 10.1016/j.jorganchem.2006.03.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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Deechongkit S, Dawson PE, Kelly JW. Toward Assessing the Position-Dependent Contributions of Backbone Hydrogen Bonding to β-Sheet Folding Thermodynamics Employing Amide-to-Ester Perturbations. J Am Chem Soc 2004; 126:16762-71. [PMID: 15612714 DOI: 10.1021/ja045934s] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding alpha-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester O (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. Beta-sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.
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Affiliation(s)
- Songpon Deechongkit
- Department of Chemistry, The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC 506, La Jolla, CA 92037, USA
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11
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Deechongkit S, You SL, Kelly JW. Synthesis of all nineteen appropriately protected chiral alpha-hydroxy acid equivalents of the alpha-amino acids for Boc solid-phase depsi-peptide synthesis. Org Lett 2004; 6:497-500. [PMID: 14961607 DOI: 10.1021/ol036102m] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] The preparation of depsi-peptides, amide-to-ester-substituted peptides used to probe the role of hydrogen bonding in protein folding energetics, is accomplished by replacing specific l-alpha-amino acid residues by their alpha-hydroxy acid counterparts in a solid-phase synthesis employing a t-Boc strategy. Herein we describe the efficient stereoselective synthesis of all 19 appropriately protected alpha-hydroxy acid equivalents of the l-alpha-amino acids, employing commercially available materials, expanding the number of available alpha-hydroxy acids from 9 to 19.
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Affiliation(s)
- Songpon Deechongkit
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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12
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Oku H, Ohyama T, Hiroki A, Yamada K, Fukuyama K, Kawaguchi H, Katakai R. Addition of a peptide fragment on an ?-helical depsipeptide induces ?/310-conjugated helix: Synthesis, crystal structure, and CD spectra of Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt. Biopolymers 2004; 75:242-54. [PMID: 15316916 DOI: 10.1002/bip.20117] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The depsipeptide Boc(1)-Leu(2)-Leu(3)-Ala(4)-Leu(5)-Leu(6)-Lac(7)-Leu(8)-Leu(9)-Lac(10)-Leu(11)-Leu(12)-Lac(13)-Leu(14)-Leu(15)-OEt(16) (1) (Boc = tert-butyloxycarbonyl, Lac = L-lactic acid residue) has been synthesized from the peptide Boc-Leu-Leu-Ala-OEt (2) and a depsipeptide, Boc-(Leu-Leu-Lac)(3)-Leu-Leu-OEt (3). Single crystals of 1 were successfully obtained and the structure has been solved by direct methods (such as Sir2002 and Shake-and-Bake). Interestingly, 1 adopts an alpha/3(10)-conjugated helix containing a kink at the junction of peptide and depsipeptide segments, Leu3-Lac7. This is significantly different from the conformation of 3, which has a straight alpha-helical structure with standard phi and psi angles. Microcrystalline CD spectra were also studied to compare structural properties of 1 and 3. The differences between alpha/3(10)- and alpha-helices appear in these CD spectra.
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Affiliation(s)
- Hiroyuki Oku
- Department of Chemistry, Gunma University, Kiryu, Gunma 376-8515, Japan
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13
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Katakai R, Kobayashi K, Yamada K, Oku H, Emori N. Synthesis of sequential polydepsipeptides utilizing a new approach for the synthesis of depsipeptides. Biopolymers 2004; 73:641-4. [PMID: 15048767 DOI: 10.1002/bip.20013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Sequential polydepsipeptides were synthesized by the depsipeptide active ester method using a new approach for the direct synthesis of N-protected depsipeptide free acids from hydroxy acids. The method uses synthesis of Boc-didepsipeptides by reaction of free hydroxy acids with Boc-amino acid N-hydroxysuccinimide esters catalyzed by 4-dimethylaminopyridine and chain elongation of the free depsipeptides by the reaction with Boc-amino acid N-hydroxysuccinimide esters in an organic solvent system of acetonitrile-tetrahydrofuran. The Boc-depsipeptide free acids were activated as their N-hydroxysuccinimide esters, which were polymerized after removal of the Boc-protecting group.
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Affiliation(s)
- Ryoichi Katakai
- Department of Chemistry, Gunma University, Tenjin-cho, Kiryu 376-8515, Japan.
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14
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Yamada K, Sato J, Oku H, Katakai R. Conformation of the transmembrane domains in peripheral myelin protein 22. Part 1. Solution-phase synthesis and circular dichroism study of protected 17-residue partial peptides in the first putative transmembrane domain. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2003; 62:78-87. [PMID: 12823620 DOI: 10.1034/j.1399-3011.2003.00073.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Charcot-Marie-Tooth disease (CMT) is the most commonly inherited peripheral neuropathy. DNA duplication and point mutation of the gene encoding peripheral myelin protein 22 (PMP22) have been found in CMT type 1A dominants. To investigate the influence of the point mutation of PMP22 on the secondary structure, protected partial peptides in the putative first transmembrane domain, wild type Boc-IVLH(Bom)VAVLVLLFVSTIV-OMe (1) and its Pro16 mutant Boc-IVLH(Bom)VAVPVLLFVSTIV-OMe (2) were synthesized. Circular dichorism (CD)-spectral analysis suggested that peptide 1 adopts a stable alpha-helical conformation in membrane-mimetic solvent,1-BuOH/1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) system. On the contrary, the mutant 2 favors beta-sheet conformation in the same solvent system. Interestingly, alpha-helix to beta-sheet transition of 2 was observed at higher contents of 1-BuOH than 70%.
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Affiliation(s)
- K Yamada
- Department of Chemistry, Gunma University, Gunma 376-8515, Japan
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15
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Crisma M, Formaggio F, Ruzza P, Calderan A, Elardo S, Borin G, Toniolo C. N-benzhydryl-glycolamide: the first protecting group in peptide synthesis with a strong conformational bias. Biopolymers 2003; 71:17-27. [PMID: 12712498 DOI: 10.1002/bip.10373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have synthesized and examined the preferred conformation of a set of N-benzhydryl-glycolamide esters from N(alpha)-protected (or N(alpha)-blocked) alpha-amino acids. Experiments were performed in CDCl(3) solution by Fourier transform infrared absorption and (1)H-NMR techniques, and in the crystalline state by x-ray diffraction. The results of our analysis strongly support the view that this type of N(alpha)-acylated alpha-aminoacyl esters has a marked tendency to fold into a beta-turn conformation, the nature of which is dictated by the structural propensity of the amino acid constituent at the i+1 position.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Organic Chemistry, University of Padova, Italy.
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16
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Aravinda S, Shamala N, Das C, Balaram P. Structural analysis of peptide helices containing centrally positioned lactic acid residues. Biopolymers 2002; 64:255-67. [PMID: 12115133 DOI: 10.1002/bip.10192] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The effect of insertion of lactic acid (Lac) residues into peptide helices has been probed using specifically designed sequences. The crystal structures of 11-residue and 14-residue depsipeptides Boc-Val-Val-Ala-Leu-Val-Lac-Leu-Aib-Val-Ala-Leu-OMe (1) and Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Val-Lac-Leu-Aib-Val-Ala-Leu-OMe (3), containing centrally positioned Lac residues, have been determined. The structure of an 11-residue peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe (2), analog of a which is an amide previously determined Lac-containing depsipeptide, Boc-Val-Ala-Leu-Aib-Val-Lac-Leu-Aib-Val-Ala-Leu-OMe I. L. Karle, C. Das, and P. Balaram, Biopolymers, Vol. 59, (2001) pp. 276-289], is also reported. Peptide 1 adopts a helical fold, which is stabilized by mixture of 4-->1 and 5-->1 hydrogen bonds. Peptide 2 adopts a completely alpha-helical conformation stabilized by eight successive 5-->1 hydrogen bonds. Peptide 3 appears to be predominately alpha-helical, with seven 5-->1 hydrogen bonds and three 4-->1 interaction interspersed in the sequence. In the structure of peptide 3 in addition to water molecules in the head-to-tail region, hydration at an internal segment of the helix is also observed. A comparison of five related peptide helices, containing a single Lac residue, reveals that the hydroxy acid can be comfortably accommodated at interior positions in the helix, with the closest C=O...O distances lying between 2.8 and 3.3 A.
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Affiliation(s)
- S Aravinda
- Department of Physics, Indian Institute of Science, Bangalore- 560 012, India
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