1. A Simulation-Based Investigation of Beta-Hairpin Formation by Cyclic Peptide
Khoi M. Pham, Iris W. Fu, Hung D. Nguyen
Department of Chemical Engineering and Materials Science, University Of California, Irvine
Abstract
Beta-hairpins, one of simplest secondary structures, are widely observed in globular proteins and have often been considered as nucleation sites for protein folding. Recent experimental studies have demonstrated that the turn structure consisting of two natural amino acids, D-Pro-Gly, are especially good at stabilizing beta-
hairpins1. In this work, we study an artificial turn structure known as delta-Ornithine (δOrn), an unnatural amino acid, and perform replica exchange molecular dynamics simulations (REMD) to investigate its ability to stabilize beta-hairpins. The result of a 630-ns REMD shows that in the presence of δOrn, the cyclic peptide
[δOrn-Arg-Trp-Gln-Tyr-Val-δOrn-Lys-Phe-Thr-Val-Gln] can fold into a well-defined beta-hairpin at low temperatures (<276K), indicating that δOrn turn is also an excellent structural motif that can be incorporated to stabilize beta-hairpins. In addition, we study the stability of δOrn turn as function of temperature. Our analyses
reveal that δOrn turn is only stable and able to promote beta-hairpin formation at temperatures lower than 276K. At higher temperatures, the turn becomes more flexible and adopts an extended conformation, which prevents the formation of beta-hairpins.
Introduction
 Beta-hairpin: Two antiparallel beta-strands connected by a
“hairpin” bend known as beta-turn.
 δ-Ornithine (δOrn): An unnatural amino acid whose structure is
recently studied by Nowick et al.,2 using H-NMR and NOE
techniques. Its structure is similar to L-Ornithine but the peptide
bonds occur at δCarbon instead of αCarbon in L-Ornithine.
 Peptide sequence: We study a macrocyclic beta-sheet peptide
comprised of twelve residues with two δOrn residues as the
artificial turn.
cyclo(δOrn-Arg-Trp-Gln-Tyr-Val-δOrn-Lys-Phe-Thr-Val-Gln)
α
δ
L-Orn δOrn
K F T V Q
V Y Q W R
δOδO
Methods
 Maestro: Software used to build custom residues and outputs the
coordinates of the structure in pdb format.
 Amber Tools:
 Replica Exchange Molecular Dynamics (REMD): Simulation
method that allows systems to sample and explore large
conformation space at different temperatures to overcome potential
energy barriers.
β-hairpin motif
 Antechamber: Recognizes the type of each atom in
custom residues and calculate their charges. It takes a pdb
file as the input and write out the charges of every atom in
the structure.
 xleap: A tool that constructs peptide sequences as well as
creating force field parameters needed for molecular
dynamics simulations.
 Amber force field: Amber 99SB – widely used in
molecular dynamics simulations.
PotentialEnergy
Coordinate
 In this study, we run a 630-ns
REMD with the temperature
ranging from 200K – 400K.
The result of the last 21ns (≈
3500 frames) was used for
the analysis.
References
1. Espinosa, J. and Gellman S. “A Designed Beta-Hairpin Containing a
Natural Hydrophobic Cluster”, Angewandte Chemie International
Edition. 39: 2330-2333, (2000).
2. Nowick, J. and Brower J. “A New Turn Structure for the Formation
of Beta-Hairpins in Peptides”, J Am Chem Soc. 125, (2003).
Acknowledgements
This project was funded by the Undergraduate Research Opportunities
Program and the Summer Undergraduate Research Program.
Computational resource time was provided by UCI GreenPlanet
Physical Science Cluster.
Future Work
 Investigate the conformation of δOrn turn in linear peptides
sequences to determine if the turn is widely applicable.
 Perform aggregation simulation studies on the cyclic peptides to
examine their self-assembly behavior.
 Beta-hairpin forms if either δOrn turns adopt a compact conformation (i.e., distance d(αH - pro-S) ≤ 2.5 Å and d(αH - pro-R) ≤ 4.0 Å)
Left Turn Right Turn
pro-S
pro-R
αH
αH
pro-R
pro-Sd=4.67 d=4.07
d=2.04 d=4.64 d=2.07
d=3.61
d=4.13
d=3.61
pro-R
pro-R pro-S
pro-S
αHαH
Initial Conformation
(extended conformation)
Dominant Conformation
(compact conformation) after 610 ns
Dominant Conformation
(compact conformation) after 610 ns
Initial Conformation
(extended conformation)
Distance(Å)
Distance(Å)
Distance(Å)
Distance(Å)
Time (ns) Time (ns) Time (ns) Time (ns)
d(αH - pro-S)
d(αH - pro-R)
d(αH - pro-S)
d(αH - pro-R)
Distance (Å) Distance (Å)
Quantity
Quantity
ProbabilityofCompact
Conformation(%)
ProbabilityofCompact
Conformation(%)
Temperature (K) Temperature (K)
 A network of backbone hydrogen bonds forms as the turns
fold into the compact structure, further stabilizing the beta-
hairpin structure
Initial conformation
of cyclic peptide
Dominant conformation of cyclic peptide after 610 ns (T=200K)
The formed beta-hairpin
contains the maximum of
five backbone hydrogen
bonds. As the temperature
increase, the probability of
forming four or five
hydrogen bonds decreases.
Temperature (K)
Probability(%)
Right (R)
Turn
Left (L)
Turn
Conclusions
 δOrn turns is good at stabilizing the beta-hairpin, but its
configuration is sensitive to temperature. The right turn is more
stable than the left turn due to the strong electrostatic interaction
between side chains on Arg and Gln.
 The ability for the turns to adopt the compact conformation results
in the formation of a network of backbone hydrogen bonds which
further stabilizes β-hairpin structure.
Positively Charged Polar Hydrophobic
Introduction Results and Discussion
Methods
Future Work
Acknowledgements
References
Conclusions
Abstract
L
L
R
R
 The criteria for the formation of the compact conformation (distance d(αH - pro-S) ≤ 2.5 Å and d(αH - pro-R) ≤ 4.0 Å) is observed in the distribution graphs.
 The turns lose their compact structures as the temperature increases. At the temperatures above 276K, the probability of adopting compact structure is relatively
low.
 The distance d(αH - pro-S) scatters around 2.1 Å and d(αH - pro-R) scatters around 3.8 Å, indicating the formation of the compact conformation of the turns.
δ
δ
δ δ