COMPARATIVE MOLECULAR DYNAMIC SIMULATIONS OF 2 HELICAL- AMPS FOUND IN ...

79 Pages·2015·12.9 MB·English

COMPARATIVE MOLECULAR DYNAMIC SIMULATIONS OF 2 HELICAL-
AMPS FOUND IN SNAKES ATRA-1 AND ATRA-2
by
Amr Zein Al-Abideen Majul
A Thesis
Submitted to the
Graduate Faculty
of
George Mason University
In Partial fulfillment of
The Requirements for the Degree
of
Master of Science
Chemistry
Committee:
Dr. Barney Bishop, Thesis Director
Dr. Amarda Shehu, Committee Member
Dr. Paige, Committee Member
Dr. John Schreifels, Director,
School of Chemistry and Biochemistry
Dr. Peggy Agouris, Dean,
College of Science
Date: Summer Semester 2015
George Mason University
Fairfax, VA
Comparative Molecular Dynamic Simulations of 2 helical-AMPS found in snakes,
ATRA-1 and ATRA-2
A thesis submitted in partial fulfillment of the requirements for the degree of
Master of Science at George Mason University
By
Amr Zein Al-Abideen Majul
Bachelor of Science
George Mason University, 2007
Director: Dr. Barney Bishop, Professor
Department of Chemistry and Biochemistry
Summer Semester 2015
George Mason University
Fairfax, VA
Copyright (cid:13)c 2015 by Amr Zein Al-Abideen Majul
All Rights Reserved
ii
Dedication
I dedicate this thesis to my mother, Lubna Z. Dabbagh, who single handedly made all
things possible, and provided me the best life one could hope for.
iii
Acknowledgments
I would like to give thanks to my adviser Dr. Bishop whose advice kept me going when I
was stuck, and has been patient with a process that took entirely too long. I would like to
thankDr. Shehuforprovidingtheresourcesandexpertisethatmadeallthispossible, and
Dr. Paige for providing me with the last minute insight that filled the holes in this work.
I would like to thank all my fellow members at the Shehu Lab and Chemistry Department
who have lent me aid. A special thanks to Dan Veltri who provided invaluable simulating
discourse and help, Brian Olson who was always available to answer my simple computer
science questions, and Corina Miss Math who spent hours working through many an
equation with me, especially the matrix algebra of Singular Value Decomposition.
iv
Table of Contents
Page
List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 Problem Statement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Thesis outline and structure . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2 Background Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.1 On Cationic Anti-Microbial Peptdes (CAMPs) and Cathelicidins . . . . . 4
2.2 CAMP modes of action and mechanism . . . . . . . . . . . . . . . . . . . 5
2.2.1 Barrel-Stave and Toroidal Pore Models. . . . . . . . . . . . . . . . 6
2.2.2 Carpet Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2.3 Macropinocytosis, an energy dependent Model . . . . . . . . . . . 8
2.3 Molecular Dynamics Introduction, Methods and Theory. . . . . . . . . . . 9
2.3.1 Basic Principles of Molecular Mechanics . . . . . . . . . . . . . . . 10
2.3.2 On Forcefields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.3.3 On Parameterization . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.4 Secondary Structure Classification . . . . . . . . . . . . . . . . . . . . . . 14
2.4.1 Ramachandran plots . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.4.2 XTLSSTR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.4.3 Salt Bridges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.5 Use of SVD in Plane Fitting . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.6 Lipid Order Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.7 The MMGBSA method to calculate Free Energy of Binding . . . . . . . . 23
2.8 Radius of Gyration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.9 Related Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.1 Simulation Program and Parameters . . . . . . . . . . . . . . . . . . . . . 27
v
3.2 Peptide-lipid systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
4.1 Peptide Insertion into the Lipid bilayer . . . . . . . . . . . . . . . . . . . . 36
4.1.1 Peptide Insertion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
4.1.2 Electrostatic and hydrophobic interactions of specific amino acids. 39
4.2 Energy Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
4.2.1 Free energy change . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
4.3 Structural Conformations of ATRA-1 and ATRA-2 . . . . . . . . . . . . 49
4.3.1 Xtlsstr Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
4.3.2 phi-psi Angles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
4.3.3 Radius of Gyration . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
4.4 Order Parameter Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
5 Disc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
5.0.1 Further Work and Direction . . . . . . . . . . . . . . . . . . . . . . 63
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
vi
List of Figures
Figure Page
2.1 Ramachandran definitions example plots . . . . . . . . . . . . . . . . . . . 17
2.2 Thermodynamic Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3.1 Lipid Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3.2 Initial peptide-lipid system example . . . . . . . . . . . . . . . . . . . . . 31
3.3 ATRA-1 vs ATRA-2 Initial setup . . . . . . . . . . . . . . . . . . . . . . 32
4.1 ATRA-1 Snapshots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
4.2 ATRA-2 Snapshots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
4.3 ATRA-1 arginine nitrogen atom snapshot illustrating Salt bridge . . . . . 37
4.4 Peptide insertion into the membrane . . . . . . . . . . . . . . . . . . . . . 38
4.5 ATRA-1 N hydrophilic residues . . . . . . . . . . . . . . . . . . . . . . . . 41
4.6 ATRA-1 N hydrophobic residues . . . . . . . . . . . . . . . . . . . . . . . 42
4.7 ATRA-2 hydrophilic residues . . . . . . . . . . . . . . . . . . . . . . . . . 44
4.8 ATRA-2 hydrophobic residues . . . . . . . . . . . . . . . . . . . . . . . . 45
4.9 Electrostatic Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
4.10 VdW Interactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
4.11 Ramachandran plots of phi-psi angles for entire simulation for each system 51
4.12 Ramachandran plots from 0-5ns for each system . . . . . . . . . . . . . . 52
4.13 Radius of gyration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
4.14 Order Parameters for lipids forming salt bridges. . . . . . . . . . . . . . . 54
4.15 Complete Lipid Bilayer Order Parameters . . . . . . . . . . . . . . . . . . 56
4.16 60ns O.P comparison . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
4.17 60-70ns O.P comparison . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
vii
Abstract
COMPARATIVE MOLECULAR DYNAMIC SIMULATIONS OF 2 HELICAL-AMPS
FOUND IN SNAKES, ATRA-1 AND ATRA-2
Amr Zein Al-Abideen Majul, M.S.
George Mason University, 2015
Thesis Director: Dr. Barney Bishop
This thesis proposes the use of Molecular Dynamic (MD) simulations to study the
two synthetic cationic antimicrobial peptides (CAMPs), ATRA-1 and ATRA-2. The pep-
tides are based off a natural antimicrobial peptide found in the elapid snake Naja Atra
[de Latour et al., 2010]. Natural AMPs can potentially serve as templates for engineer-
ing novel antibiotics. MD simulations provide a valuable resource to supplement existing
experimental and database-aided prediction data. Specifically the interaction of the two
aforementioned peptides with a model lipid bilayer membrane is studied. The antimi-
crobial potencies between the peptides differ appreciably, yet their amino acid sequences
differ from each other at only 2 positions. This thesis proposes the use of MD to run
simulations to extract qualitative and quantitative information on each peptide. Most
other similar computational studies on peptides are done on a single type of peptide.
Simulations comparing ATRA-1 and ATRA-2 are analysed in this thesis, focusing on on
finding various physical and chemical parameters that differentiate the two peptides. The
simulations employ all atom explicit models, with a realistic non-anchored membrane. In
addition, the feasibility of using MD simulations to predict and rank the effectiveness of
proposed rationally designed novel antimicrobial peptides will be evaluated.
Chapter 1: Introduction
Antimicrobial peptides (AMPs) are naturally occurring peptides reported in virtually
all organisms, including bacteria, fungi, plants and animals, and represent an ancient
defensive strategy against infection [Juba et al., 2013]. Cationic antimicrobial peptides
(CAMPs) are a class of antimicrobial peptides that are an important component of innate
immunity in higher organisms. CAMPs are generally small peptides ranging from 10-
50 amino acids that have an overall positive charge. They are further loosely grouped
into families based on structural and functional characteristics, for example magainins,
β-defensins and cathelicidins [Boman, 2003].
The two peptides used in this study, ATRA-1 and ATRA-2 are synthetic peptides
inspired by a CAMP, identified in the venom glands of the Chinese cobra, Naja Atra.
This peptide belongs to the cathelicidin family of vertebrate CAMPs. It contains a semi-
conserved repeated 11-residue pattern (KR(F/A)KKFFKK(L/P)K), termed the ATRA
motif. The ATRA motif present in the Naja Atra peptide serves as a template for the
design of the peptides, ATRA-1 and ATRA-2, which are experimentally tested to probe
the differences in how their respective sequences impact their performance. ATRA-1
and ATRA-2 are 11 residue long, having amino acids sequences of KRAKKFFKKLK
and KRFKKFFKKPK respectively. Differing in only two positions, their bactericidal
potencies has been reported to differ significantly [Juba et al., 2013].
This thesis uses Molecular Dynamics to study the two Atra peptides and their interac-
tion with a model membrane. Simulations of various configurations of the aforementioned
peptideswithlipidsareperformedtostudythem, usingallexplicitatomisticmodels, such
as realistic non-coarse grained membranes, to allow a mathematically rigorous calculation
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