Thermodynamics of Antimicrobial Lipopeptides Interaction with Lipid Membranes

306 Pages·2015·12.13 MB·English

Thermodynamics of Antimicrobial Lipopeptides
Interaction with Lipid Membranes
by
Dejun Lin
Submitted in Partial Fulfillment
of the
Requirements for the Degree
Doctor of Philosophy
Supervised by
Professor Alan Grossfield
Department of Biochemistry and Biophysics
School of Medicine and Dentistry
University of Rochester
Rochester, New York
2016
ii
Dedication
Tothelovingmemoryofmyfather.
Tomymotherforherlove,supportandencouragement.
iii
Biographical Sketch
Dejun Lin attended Nankai University in Tianjin, China during 2006 and 2010
and earned his Bachelor of Science degree in Biological Sciences in May of 2010.
He entered the Biophysics, Structural and Computational Biology program at the
University of Rochester in September 2010. He joined the lab of Dr. Alan Gross-
field, completing his Master of Science degree in Biophysics in 2013. He was
funded by the Leon L. Miller Graduate Fellowship in 2011 and The Elon Hunting-
ton Hooker Graduate Fellowship from 2014 to 2015. He was awarded the Student
Seminar Award in Biophysics in 2012 and 2014, Elena Gilde Grossfield presen-
tation award in 2013 and Graduate Student Society poster competition award in
2014.
Publications
• Lin, D., 2015. Generalized and efficient algorithm for computing mul-
tipole energies and gradients based on Cartesian tensors. J. Chem.
Phys. 143:114115. http://scitation.aip.org/content/aip/
journal/jcp/143/11/10.1063/1.4930984.
• Lin,D.,andA.Grossfield. Coarsed-grainedmembraneforcefieldbasedonGay-
Berne potential and electric multipoles. In Q. Cui, M. Meuwly, and P. Ren,
editors, Many-Body Effects and Electrostatics in Biomolecules, Pan Stanford
Publishing,chapter14. Inpress.
• Lin, D., and A. Grossfield, 2015. Thermodynamics of Micelle Formation
and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity. Bio-
iv
phys. J. 109:750–759. http://www.sciencedirect.com/science/
article/pii/S0006349515007171.
• Lin, D., and A. Grossfield, 2014. Thermodynamics of Antimicrobial Lipopep-
tide Binding to Membranes: Origins of Affinity and Selectivity. Bio-
phys.J.107:1862–1872. http://www.sciencedirect.com/science/
article/pii/S000634951400928X.
• Horn, J. N., J. D. Sengillo, D. Lin, T. D. Romo, and A. Grossfield, 2012.
Characterization of a potent antimicrobial lipopeptide via coarse-grained mole-
cular dynamics. Biochim. Biophys. Acta, Biomembr. 1818:212–218. http:
//dx.doi.org/10.1016/j.bbamem.2011.07.025.
• Zhang, W., W. Peng, M. Zhao, D. Lin, Z. Zeng, W. Zhou, and M. Bart-
lam, 2011. Expression, purification and preliminary crystallographic analy-
sis of human thyroid hormone responsive protein. Acta Crystallogr Sect F
Struct Biol Cryst Commun 67:941–946. http://dx.doi.org/10.1107/
S1744309111021099.
v
Acknowledgments
First and foremost, I must thank Alan Grossfield for his guidance and continuous
support. I have a big appetite for scientific methods and Alan never suppresses it
but he indulges it. I also like the fights we have had about doing things differently;
they’re like diets of the mind, keeping my head clear. Alan always encourages
attending conferences, presenting our work and learning from others. I greatly
appreciatetheseopportunitiesandImustthankAlanformakingthemhappen. The
ideasbehindsomeofmythesisworkswereinspiredbytheconversationsIhadwith
otherscientistsduringtheseconferences.
I must acknowledge the enormous help from Tod Romo. I was completely new
to computational research when I joined the lab and Tod has been effectively my
thesisadvisor oncomputation. I’m alwaysgrateful forthenumerous conversations
withhimaboutscienceandprogramdesignandthecountlesshands-onC++tutori-
als.
Josh Horn and Nick Leioatts provided a lot of scientific insights in developing
myresearchprojects. Theyalwaysgaveconstructivecriticismformypresentations
andwritings. Ialsoenjoyedthetimeplayingsoccerwiththem.
vi
My thesis committee members, Dr. Mark Dumont, Dr. David Mathews and Dr.
Martin Pavelka, were always helpful in providing directions and unique perspec-
tives regarding my research. I’m also grateful for their encouragement and advice
onpursuingmycareergoal.
Thanks to the Health Sciences Center for Computational Innovation (HSCCI)
and the Center for Integrated Research Computing (CIRC) at the University of
Rochester for providing computational resources for this work. Special thanks go
to Harry Stern and Carl Schmidtmann for their help in debugging my computer
programs.
IwanttothankmyfriendsYongchunZhang,ShihaoXuandHeFangforhelping
my beginning in a foreign country. Adapting to the new environment was not as
difficultasIhadimaginedbecauseoftheirhelp.
Finally, I’d like to acknowledge all the fellow students and colleagues in the
UniversityofRochesterwhosharedinterestindiscussingmyresearchprojectsand
scienceingeneral. Ithasalwaysbeenajoyworkinginthiscommunity.
vii
Abstract
The increasing number of antibiotic-resistant strains has been a severe medical
problem in the 21st century. This necessitates the development of new antibiotics
that operate via mechanisms that are less likely to incur evolved resistance. One
class of promising candidates is antimicrobial lipopeptides (AMLPs) which are
short peptides conjugated to a hydrophobic acyl chain. Experiments have demon-
stratedtheseAMLPs’activitiesbothinvivoandinvitro,whichcorrelatewiththeir
abilities to permeabilize model membranes. This leads to the fundamental hy-
pothesis that these AMLPs act by preferentially perturbing microbial membranes.
To understand their mechanisms of membrane interaction, we ran long time-scale
molecular dynamics simulations to quantitatively examine their interactions with
model membrane bilayers. We used a coarse-grained method and enhanced sam-
pling algorithms to uncover the thermodynamics governing these AMLPs’ binding
to membranes. In Chapter 2, we calculate AMLP’s membrane binding free energy
andshow thatthe hydrophobicacyl chainis mainlyresponsible forAMLPs’ mem-
brane affinity, while the peptide portion determines the membrane selectivity. In
Chapter3,weintroduceanovelreactioncoordinatebasedonhydrophobiccontacts
and apply it to explore the thermodynamics of oligomerization of these AMLPs.
viii
It was found that their oligomerization is polydisperse. Moreover, we discovered
that the AMLP oligomers bind to membranes via mechanisms distinct from the
monomericcases;whilethebindingisthermodynamicallyfavorable,ithastoover-
comesignificantfreeenergybarriersandtheheightofthesebarriersdependsonthe
membrane composition. This suggests that these AMLPs’ selectivity towards the
microbial membranes is driven by both thermodynamics and kinetics. This novel
mechanism highlights the importance of AMLPs’ oligomerization in solution to
their antimicrobial activity. To further our understanding of lipopeptide-membrane
interaction,acoarse-grainedmodeloflipidsisintroducedinChapter4withthegoal
of achieving better representation of electrostatics and molecular shape than com-
mon coarse-grained models while retaining most of their computational efficiency.
Along the same line, an efficient algorithm is developed to calculate electric mul-
tipole interactions, which can be applied to the new coarse-grained model. This
algorithmisintroducedinChapter5.
ix
Contributors and Funding Sources
ThisworkhasbeensupervisedbyadissertationcommitteeconsistingofProfessors
Alan Grossfield (advisor), Mark Dumont of the Department of Biochemistry and
Biophysics, Dave Matthews of the Department of Biochemistry and Biophysics,
and Martin Pavelka of the Department of Microbiology and Immunology. The
committee chair is Ignacio Franco of the Department of Chemistry. All work for
thedissertationwascompletedindependentlybythestudent.
The computer simulations in Chapters 2, 3 and 4 were done on University of
Rochester’s BlueHive linux cluster and BlueGene/Q supercomputer maintained by
the Health Sciences Center for Computational Innovation (HSCCI) and the Center
forIntegratedResearchComputing(CIRC).
This work is partially funded by grant GM095496 from the the U.S. National
InstituteofHealthawardedtoDr. AlanGrossfield,theLeonL.MillerGraduateFel-
lowshipandtheElonHuntingtonHookerGraduateFellowshipfromtheUniversity
ofRochester.
x
Table of Contents
Dedication ii
BiographicalSketch iii
Acknowledgments v
Abstract vii
ContributorsandFundingSources ix
ListofTables xx
ListofFigures xxi
1 Introduction 1
1.1 ProblemsofAntimicrobialResistance . . . . . . . . . . . . . . . . 1
1.1.1 AntimicrobialResistanceIsInevitable . . . . . . . . . . . . 3
1.1.2 ThePressingNeedforNewAntimicrobialDrugs . . . . . . 6
1.2 Antimicrobial Peptides and Lipopeptides Are Novel Antimicrobial
DrugCandidates . . . . . . . . . . . . . . . . . . . . . . . . . . . 7