Peptide hairpin nucleation with the obligatory Type I' beta-turn Aib-DPro segment.
ABSTRACT The alpha-aminoisobutyric acid-D-proline (Aib-(D)Pro) dipeptide is an obligatory Type I' beta-turn forming segment that nucleates hairpin formation.
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ABSTRACT: The effect of incorporation of a centrally positioned Ac(6)c-Xxx segment where Xxx = (L)Val/(D)Val into a host oligopeptide composed of l-amino acid residues has been investigated. Studies of four designed octapeptides Boc-Leu-Phe-Val-Ac(6)c-Xxx-Leu-Phe-Val-OMe (Xxx = (D)Val 1, (L)Val 2) Boc-Leu-Val-Val-Ac(6)c-Xxx-Leu-Val-Val-OMe (Xxx = (D)Val 3, (L)Val 4) are reported. Diagnostic nuclear Overhouse effects characteristic of hairpin conformations are observed for Xxx = (D)Val peptides (1 and 3) while continuous helical conformation characterized by sequential N(i)H ↔ N(i+1)H NOEs are favored for Xxx = (L)Val peptides (2 and 4) in methanol solutions. Temperature co-efficient of NH chemical shifts are in agreement with distinctly different conformational preferences upon changing the configuration of the residue at position 5. Crystal structures of peptides 2 and 4 (Xxx = (L)Val) establish helical conformations in the solid state, in agreement with the structures deduced from NMR data. The results support the design principle that centrally positioned type I β-turns may be used to nucleate helices in short peptides, while type I'β-turns can facilitate folding into β-hairpins.Organic & Biomolecular Chemistry 02/2012; 10(14):2815-23. · 3.49 Impact Factor
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ABSTRACT: The crystal structures of several designed peptide hairpins have been determined in order to establish features of molecular conformations and modes of aggregation in the crystals. Hairpin formation has been induced using a centrally positioned (D)Pro-Xxx segment (Xxx = (L)Pro, Aib, Ac6c, Ala; Aib = α-aminoisobutyric acid; Ac6c = 1-aminocyclohexane-1-carboxylic acid). Structures of the peptides Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (), Boc-Leu-Tyr-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (, polymorphic forms labeled as and ), Boc-Leu-Val-Val-(D)Pro-(L)Pro-Leu-Val-Val-OMe (), Boc-Leu-Phe-Val-(D)Pro-Aib-Leu-Phe-Val-OMe (, polymorphic forms labeled as and ), Boc-Leu-Phe-Val-(D)Pro-Ac6c-Leu-Phe-Val-OMe () and Boc-Leu-Phe-Val-(D)Pro-Ala-Leu-Phe-Val-OMe () are described. All the octapeptides adopt type II' β-turn nucleated hairpins, stabilized by three or four cross-strand intramolecular hydrogen bonds. The angle of twist between the two antiparallel strands lies in the range of -9.8° to -26.7°. A detailed analysis of packing motifs in peptide hairpin crystals is presented, revealing three broad modes of association: parallel packing, antiparallel packing and orthogonal packing. An attempt to correlate aggregation modes in solution with observed packing motifs in crystals has been made by indexing of crystal faces in the case of three of the peptide hairpins. The observed modes of hairpin aggregation may be of relevance in modeling multiple modes of association, which may provide insights into the structure of insoluble polypeptide aggregates.Organic & Biomolecular Chemistry 05/2013; · 3.49 Impact Factor
Conference Paper: Novel atomization method based on SAW streaming[Show abstract] [Hide abstract]
ABSTRACT: It is possible to atomize the liquid using surface acoustic wave (SAW) device. In this paper, we describe a novel atomization method based on SAW streaming. Stable generation and direction control of the mist are experimentally examined. We realize to continuously generate the mist by placing a filter paper, which retain a liquid on the SAW propagation surface. Also we demonstrate a mist direction control with an electrostatic field. Furthermore, practical atomization system is designed and performed.Ultrasonics, 2003 IEEE Symposium on; 11/2003
COMMUNICATIONwww.rsc.org/obc | Organic & Biomolecular Chemistry
Peptide hairpin nucleation with the obligatory Type I’ b-turn Aib-DPro
Upadhyayula Surya Raghavender,aSubrayashastry Aravinda,aRajkishor Rai,bNarayanaswamy Shamala*aand
Received 22nd March 2010, Accepted 28th May 2010
First published as an Advance Article on the web 8th June 2010
an obligatory Type I’ b-turn forming segment that nucleates
Synthetic peptide hairpins have been successfully constructed
using the strategy of placing strong turn forming segments in the
structures.2Design strategies have therefore employedDPro-Xxx
segments as the preferred choice for the hairpin nucleating
peptide hairpins containing centralDPro-Xxx segments are now
available.4The overwhelming majority of these structures have a
central Type II’ b-turn unit which results in the formation of a
flattened hairpin structure. In contrast, the Type I’ b-turn formed
in a central Aib-DAla segment results in a considerable twisting
of the antiparallel strands with a twist angle of -55.8◦.5The only
bone homologated b-amino acids in the strands.6An attempt to
Phe-Val-Aib-DVal-Leu-Phe-Val-Val-OMe, led to the observation
segment was accommodated in the center of the helix withDVal
compares the two examples of Aib-DXxx (DXxx =DVal andDAla)
sequences adopting two distinct local folds.
nucleating segment, we turned to the Aib-DPro dipeptide. Fig. 2a
illustrates the localised region of conformational space accessible
to Aib residues as shown by overlap of the allowed region for
residues cluster closely in the regions which correspond to right-
handed (aR), f negative, and left-handed (aL), f positive, of
the helical conformations.8While D-amino acids largely populate
conformations with positive (f, y) values, several examples of
D-amino acids adopting negative f values in the right-handed
DAla residues. Crystallographically characterized Aib
aDepartment of Physics, Indian Institute of Science, Bangalore 560
012, India. E-mail: email@example.com.; Fax: +91-80-23602602;
bMolecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012,
India. E-mail: firstname.lastname@example.org; Fax: +91-80-23600683; Tel: +91-80-
†CCDC reference number 758802. For crystallographic data in CIF or
other electronic format see DOI: 10.1039/c004577m
conformation in a 19 residue peptide.7(b) Aib-DAla segment adopting a
Type I’ b-turn conformation in an octapeptide b-hairpin.5
(a) Aib-DVal segment adopting right-handed alpha-helical (aR)
alpha-helical (aR) region of the Ramachandran plot are observed
In the case of
value of f to 60 ± 20◦. The only 4→1 hydrogen bonded b-turn
conformation sterically accessible to the Aib-DPro segment is the
Type I’ structure (idealized torsional angles for Type I’ b-turn are
fi+1= 60◦, yi+1= 30◦, fi+2= 90◦, yi+2= 0◦).
The model octapeptide, Boc-Leu-Val-Val-Aib-DPro-Leu-Val-
Val-OMe (1), forms a b-hairpin conformation in solution as
established by the presence of cross-strand nuclear Overhauser
effect and the presence of four solvent shielded NH groups.10
Single crystals of the octapeptide 1 were obtained from dimethyl-
formamide(DMF)/water solution.11Fig. 3a shows a view of the
molecular conformation of 1 in crystals. The observed hairpin
conformation is stabilized by three cross-strand hydrogen bonds
with the Aib-DPro segment adopting the anticipated Type I’ b-
turn conformation (Aib(4) : f = 56.8◦, y = 28.4◦;DPro(5) : f =
82.8◦, y = 8.0◦). Fraying of the strands is observed at the termini
with the y values for Leu(1) (f = -100.3◦, y = -16.8◦) and Val(8)
(f = -119.9◦, y = 14.0◦) deviating appreciably from the values
expected for a b-strand conformation. Val(2) (f = -136.5◦, y =
-126.2◦), Val(3) (f = -140.8◦, y = -134.3◦), Leu(6) (f = -123.1◦,
y = -136.0◦) and Val(7) (f = -79.2◦, y = -125.6◦) all adopt (f,
y) values characteristic of b-strand conformations. The crystal
structure compares very well with the structure determined by
NMR spectroscopy in solution.
The structure of 1 superposes well with that of the previously
characterized hairpin for Boc-Leu-Phe-Val-Aib-DAla-Leu-Phe-
Val-OMe (2) sequence (RMSD = 0.122 A˚, Fig. 3b).5The hairpin
DPro sidechain backbone cyclization limits the
This journal is © The Royal Society of Chemistry 2010Org. Biomol. Chem., 2010, 8, 3133–3135 | 3133
the Aib residue (blue) and the narrow region accessible to theDPro residue
(gray). The i+1 and i+2 residues of Type I’/II’ b-turns are connected by
Structural Database. Data set of 81 linear peptide sequences consisting of
164 D-amino acid residues. 11 residues lie in the aRregion.
(a) Ramachandran plot showing the sterically allowed regions for
has a pronounced right-handed twist angle (q = -55.4◦). Two
co-crystallized DMF molecules form hydrogen bonds to the NH
groups of Leu(1) and Val(7). Interestingly, if the positions of turn
residues are interchanged the resulting sequence, Boc-Leu-Val-
Val-DPro-Aib-Leu-Val-Val-OMe, forms a considerably flattened
b-hairpin (twist angle, q = -3.4◦) nucleated by a Type II’ b-turn
The packing of the flat and twisted hairpins in crystals is
somewhat different. In both the cases, the hairpins are arranged in
In the case of twisted hairpin, 1 with Aib-DPro segment, a
single intermolecular hydrogen bond is observed, whereas in the
case of flatDPro-Aib hairpin two hydrogen bonds hold adjacent
The present study provides an unambiguous structural charac-
terization of a designed peptide b-hairpin nucleated by a Type I’
b-turn. The Aib-DPro segment may be used as a conformationally
rigid template for the construction of peptide hairpins with a
considerable degree of twist between the adjacent antiparallel
strands. Such units may be useful in peptidomimetic design1e,12
and the rational design of multistranded b-sheet structures which
mimic those found in the proteins.13
This work was supported by a grant from Council of Scientific
and Industrial Research (CSIR) and Program Support in the area
are shown as dashed lines. (b) Superposition of the backbone atoms of
residues 2 to 7 of 1 (carbons in gray) and 2 (carbons in green).
(a) Molecular conformation of 1. Intramolecular hydrogen bonds
(DPro-Aib), flat hairpin. Intermolecular hydrogen bonds shown as dashed
lines. Side chains of the turn residues shown.
3134 | Org. Biomol. Chem., 2010, 8, 3133–3135 This journal is © The Royal Society of Chemistry 2010
India. U.S.R and S.A. thank University Grants Commission and
Notes and references
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Gunasekharan, C. Ramakrishnan and P. Balaram, Protein Eng., Des.
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11 Structure of 1 (C53H98N10O13) was solved using the dual space recycling
method employed in SHELXD (T. R. Schneider, G. M. Sheldrick,
Acta Cryst. D, 2002, 58, 1772). Space group P21, a = 11.0623 A˚, b =
18.7635 A˚, c = 16.6426 A˚, b = 102.369, Z/Z’=2/1, V = 3374 A˚3,
R = 9.47% and wR2= 17.34%, for 1432 reflections |Fo| > 4s(|Fo|).
The goodness-of-fit is 0.973. CCDC reference number 758802 has
crystallographic data for the paper. These data can be obtained free
of charge from The Cambridge Crystallographic Data Centre via
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This journal is © The Royal Society of Chemistry 2010 Org. Biomol. Chem., 2010, 8, 3133–3135 | 3135