Beta Hairpin - Explore the Science & Experts | ideXlab

Scan Science and Technology

Contact Leading Edge Experts & Companies

Beta Hairpin

The Experts below are selected from a list of 1791 Experts worldwide ranked by ideXlab platform

P Balaram – 1st expert on this subject based on the ideXlab platform

  • directing peptide conformation with centrally positioned pre organized dipeptide segments studies of a 12 residue helix and β Hairpin
    Amino Acids, 2015
    Co-Authors: Siddappa Chandrappa, Srinivasarao Raghothama, M Madhusudana B Reddy, Rajesh Sonti, Krishnayan Basuroy, P Balaram

    Abstract:

    Secondary structure formation in oligopeptides can be induced by short nucleating segments with a high propensity to form hydrogen bonded turn conformations. Type I/III turns facilitate helical folding while type II’/I’ turns favour Hairpin formation. This principle is experimentally verified by studies of two designed dodecapeptides, Boc-Val-Phe-Leu-Phe-Val-Aib-Aib-Val-Phe-Leu-Phe-Val-OMe 1 and Boc-Val-Phe-Leu-Phe-Val- (D) Pro- (L) Pro-Val-Phe-Leu-Phe-Val-OMe 2. The N- and C-terminal flanking pentapeptide sequences in both cases are identical. Peptide 1 adopts a largely alpha-helical conformation in crystals, with a small 3(10) helical segment at the N-terminus. The overall helical fold is maintained in methanol solution as evidenced by NMR studies. Peptide 2 adopts an antiparallel BetaHairpin conformation stabilized by 6 interstrand hydrogen bonds. Key nuclear Overhauser effects (NOEs) provide evidence for the antiparallel BetaHairpin structure. Aromatic proton chemical shifts provide a clear distinction between the conformation of peptides 1 (helical) and 2 (BetaHairpin). The proximity of facing aromatic residues positioned at non-hydrogen bonding positions in the Hairpin results in extensively ring current shifted proton resonances in peptide 2.

  • expanding the peptide Beta turn in alpha gamma hybrid sequences 12 atom hydrogen bonded helical and Hairpin turns
    Journal of the American Chemical Society, 2009
    Co-Authors: Sunanda Chatterjee, Srinivasarao Raghothama, Narayanaswamy Shamala, Prema G Vasudev, Chandrasekharan Ramakrishnan, P Balaram

    Abstract:

    Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C-12 hydrogen bonded turns which may be considered as backbone expanded analogues of C-10 Beta-turns) found in alpha alpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alpha gamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C-gamma-C-Beta (theta(1)) and C-Beta-C-alpha (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms BetaHairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C-12 turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of BetaHairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C-12 hydrogen bonded structures which are energetically feasible in alpha gamma and gamma alpha sequences.

  • infinite pleated Beta sheet formed by the Beta Hairpin boc Beta phe Beta phe d pro gly Beta phe Beta phe ome
    Proceedings of the National Academy of Sciences of the United States of America, 2002
    Co-Authors: Isabella L Karle, Hosahudya N Gopi, P Balaram

    Abstract:

    A BetaHairpin conformation and extended Beta-pleated sheet assembly have been characterized by single crystal x-ray diffraction for the synthetic peptide t-butoxycarbonyl-Beta-Phe-Beta-Phe-D-Pro-Gly-b-Phe-b-Phe-methyl ester [b-Phe: (S)-b3 homophenylalanine]. The centrally located D-Pro-Gly segment nucleates a chain reversal in a type II’ Beta-turn conformation. Two intramolecular cross-strand hydrogen bonds stabilize the peptide fold. Intermolecular NH…O=C hydrogen bonds (two on each side of the Hairpin) connect the Hairpins into an infinitely extended Beta-sheet. The Beta-residues cause all CAOgroups to point in the same direction, resulting in a ‘‘polar’’ sheet by the unidirectional alignment of NH…O=C hydrogen bonds. In contrast, Beta-sheets formed by Beta-residues have alternating directions for the hydrogen bonds, thus resulting in an ‘‘apolar’’ sheet. The crystallographic parameters for C53H66N6O9.CH3OH are: space group P21, a = 9.854(2) A, b = 10.643(2) A, c = 25.296(4) A, Beta = 100.39(2)°, Z = 2, agreement factor R1 _ 0.065 for 3,706 data observed >4_(F) and a resolution of 0.90 A.

Srinivasarao Raghothama – 2nd expert on this subject based on the ideXlab platform

  • Conformations of heterochiral and homochiral proline-pseudoproline segments in peptides: context dependent cis-trans peptide bond isomerization.
    Biopolymers, 2020
    Co-Authors: Kantharaju, Srinivasarao Raghothama, Upadhyayula Surya Raghavender, Subrayashastry Aravinda, Narayanaswamy Shamala, Padmanabhan Balaram

    Abstract:

    The pseudoproline residue (Psi Pro, L-2,2-dimethyl-1,3-thiazolidine-4-carboxylic acid) has been introduced into heterochiral diproline segments that have been previously shown to facilitate the formation of BetaHairpins, containing central two and three residue turns. NMR studies of the octapeptide Boc-Leu-Phe-Val-(D)Pro-Psi Pro-Leu-Phe-Val-OMe (1), Boc-Leu-Val-Val-(D)Pro-Psi Pro-Leu-Val-Val-OMe (2), and the nonapeptide sequence Boc-Leu-Phe-Val-(D)Pro-Psi Pro-(D)Ala-Leu-Phe-Val-OMe (3) established well-registered BetaHairpin structures in chloroform solution, with the almost exclusive population of the trans conformation for the peptide bond preceding the Psi Pro residue. The BetaHairpin conformation of 1 is confirmed by single crystal X-ray diffraction. Truncation of the strand length in Boc-Val-(D)Pro-Psi Pro-Leu-OMe (4) results in air increase in the population of the cis conformer, with a cis/trans ratio of 3.65. Replacement of Psi Pro in 4 by (L)Pro in 5, results in almost exclusive population of the trans form, resulting in an incipient BetaHairpin conformation, stabilized by two intramolecular hydrogen bonds. Further truncation of the sequence gives an appreciable rise in the population of cis conformers in the tripeptide piv-(D)Pro-Psi Pro-Leu-OMe (6). In the homochiral segment Piv-Pro Psi Pro-Leu-OMe (7) only the cis form is observed with the NMR evidence strongly supporting a type VIa Beta-turn conformation, stabilized by a 4 -> 1 hydrogen bond between the Piv (CO) and Leu (3) NH groups. The crystal structure of the analog peptide 7a (Piv-Pro-Psi(H,CH3)Pro-Leu-NHMe) confirms the cis peptide bond geometry for the Pro-Psi(H,CH3)pro peptide bond, resulting in a type VIa Beta-turn conformation.

  • directing peptide conformation with centrally positioned pre organized dipeptide segments studies of a 12 residue helix and β Hairpin
    Amino Acids, 2015
    Co-Authors: Siddappa Chandrappa, Srinivasarao Raghothama, M Madhusudana B Reddy, Rajesh Sonti, Krishnayan Basuroy, P Balaram

    Abstract:

    Secondary structure formation in oligopeptides can be induced by short nucleating segments with a high propensity to form hydrogen bonded turn conformations. Type I/III turns facilitate helical folding while type II’/I’ turns favour Hairpin formation. This principle is experimentally verified by studies of two designed dodecapeptides, Boc-Val-Phe-Leu-Phe-Val-Aib-Aib-Val-Phe-Leu-Phe-Val-OMe 1 and Boc-Val-Phe-Leu-Phe-Val- (D) Pro- (L) Pro-Val-Phe-Leu-Phe-Val-OMe 2. The N- and C-terminal flanking pentapeptide sequences in both cases are identical. Peptide 1 adopts a largely alpha-helical conformation in crystals, with a small 3(10) helical segment at the N-terminus. The overall helical fold is maintained in methanol solution as evidenced by NMR studies. Peptide 2 adopts an antiparallel BetaHairpin conformation stabilized by 6 interstrand hydrogen bonds. Key nuclear Overhauser effects (NOEs) provide evidence for the antiparallel BetaHairpin structure. Aromatic proton chemical shifts provide a clear distinction between the conformation of peptides 1 (helical) and 2 (BetaHairpin). The proximity of facing aromatic residues positioned at non-hydrogen bonding positions in the Hairpin results in extensively ring current shifted proton resonances in peptide 2.

  • expanding the peptide Beta turn in alpha gamma hybrid sequences 12 atom hydrogen bonded helical and Hairpin turns
    Journal of the American Chemical Society, 2009
    Co-Authors: Sunanda Chatterjee, Srinivasarao Raghothama, Narayanaswamy Shamala, Prema G Vasudev, Chandrasekharan Ramakrishnan, P Balaram

    Abstract:

    Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C-12 hydrogen bonded turns which may be considered as backbone expanded analogues of C-10 Beta-turns) found in alpha alpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alpha gamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C-gamma-C-Beta (theta(1)) and C-Beta-C-alpha (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms BetaHairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C-12 turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of BetaHairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C-12 hydrogen bonded structures which are energetically feasible in alpha gamma and gamma alpha sequences.

Yukio Sugiura – 3rd expert on this subject based on the ideXlab platform

  • swapping of the Beta Hairpin region between sp1 and gli zinc fingers significant role of the Beta Hairpin region in dna binding properties of c2h2 type zinc finger peptides
    Biochemistry, 2005
    Co-Authors: Yasuhisa Shiraishi, Miki Imanishi, Tatsuya Morisaki, Yukio Sugiura

    Abstract:

    : The recent design strategy of zinc finger peptides has mainly focused on the alpha-helix region, which plays a direct role in DNA recognition. On the other hand, the study of non-DNA-contacting regions is extremely scarce. By swapping the BetaHairpin regions between the Sp1 and GLI zinc fingers, in this study, we investigated how the BetaHairpin region of the C(2)H(2)-type zinc finger peptides contributes to the DNA binding properties. Surprisingly, the Sp1 mutant with the GLI-type BetaHairpin had a higher DNA binding affinity than that of the wild-type Sp1. The result of the DNase I footprinting analyses also showed the change in the DNA binding pattern. In contrast, the GLI zinc finger completely lost DNA binding ability as a result of exchanging the BetaHairpin region. These results strongly indicate that the BetaHairpin region appears to function as a scaffold and has an important effect on the DNA binding properties of the C(2)H(2)-type zinc finger peptides.