BIOPHEST

2

Time Event

8:00 AM-8:55 AM Breakfast (RM. 103a, BIO5)

9:00 AM-10:30 AM Morning session #1 (Chair: Avi Leftin)

James Zook (ASU) "Structure investigation of membrane proteins through circular

dichroism and nuclear magnetic resonance."

Andrey Struts (UA) "Retinal dynamics studied by 2H NMR relaxation illuminates

rhodopsin activation mechanism."

Avigdor Leftin (UA) "Site-specific markers of phase coexistence in ternary lipid

domains revealed by separated local field 13

C NMR spectroscopy."

Liang Huang (ASU) "Detecting high-frequency oscillations by empirical mode

decomposition method."

Benjamin Heitz (UA) " Poly(lipid) bilayers: highly stable biomembranes for ion channel

screening."

Kaushik Gurunathan (ASU) "Position dependent site-exposure nucleosome dynamics by

FRET-FCS."

Marcia Levitus (ASU) "Photophysics of single-molecule fluorescent dyes: nucleobase-

dependent fluorescence of Cy3 on DNA."

K.J. Mallikarjunaiah (UA) "Equivalence of hydration and osmotic pressures for lipid

membranes established by solid-state 2H NMR."

10:30 AM-11:00AM Coffee Break

11:00 AM- 12:30PM Morning session #2 (Chair: Blake Mertz)

Sebastian A. Sandersius (ASU) "A possible role for chemotaxis in primitive streak

formation."

Wen-Xu Wang (ASU) "Role of mobility in pattern formation, sychronization and basin

of biodiversity in rock-paper-scissors game."

Adam de Graff (ASU) "Protein unfolding under force: a geometric approach."

Satish K. Singh (UA) "An analytical model of coupled receptor kinases capturing

chemotactic sensitivity and response range."

Rui Yang (ASU) "Role of intraspecific competition in coexistence of mobile populations

in spatially extended ecosystems."

Teresa Cusati (ASU) "Preliminary modeling of epithelial cells in three dimensions."

Xuan Ni (ASU) "Cyclic competition of mobile species on continuous space: pattern

formation and coexistence."

Blake Mertz (UA) "Computational insights into retinal dynamics in rhodopsin."

12:30 PM-1:30PM Lunch Break

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1:30 PM-3:15 PM Afternoon session #1 (Chair: Jacob J. Kinnun)

Mark Hunter (ASU) "First results of femtosecond protein nanocrystallography."

Daniel Farrell (ASU) "A webserver for generating stereochemically-acceptable

structural pathways in biomolecules."

Justin Spiriti (ASU) "Applications of Gaussian-mixture umbrella sampling to nucleic

acids."

Joseph Baker (UA) "Molecular dynamics simulations of drug transport through the

membrane protein EmrD."

Dmitry Matyushov (ASU) "Protein/water interface and bioenergetics."

Ashini Bolia (ASU) "A novel Protein binding approach using linear response theory."

Alexander Fuhrmann (ASU) "AFM-based force spectroscopy: new insights into ligand-

receptor interactions."

Jacob J. Kinnun (UA) "Theoretical equivalence of hydration and osmotic pressure in

membrane deformation."

Di Cao (ASU) "Electrical measurement of carbon nanotube water wetting."

3:15 PM-3:45 PM Coffee Break

3:45 PM-5:45 PM Afternoon session #2 (Chair: Brian Anderson)

Danmei Bian (ASU) "Comparing nucleation models for pathological protein

aggregation."

Stephanie Cope (ASU) ”Experimental Techniques for measuring the conformation of

intrinsically disordered proteins."

Pei Pang (ASU) "Electrochemical current measurement base on water wetting inside the

carbon nanotube."

Bennett Kalafut (UA) "Stretching poly(A) to investigate structure formation at low ionic

strength."

Olaf Schulz (ASU) "Highly localized fluorescence quenching with silicon AFM probes

on the single molecule level."

Ivan Yermolenko (ASU) "Integrin-mediated adhesion to fibrinogen studied by single cell

force spectroscopy."

Brian Anderson (UA) "The effects of PKCα phosphorylation on the extensibility of

titin’s PEVK element."

Jack Staunton (ASU) "Development of a method for quantitative mechanical

nanotomography of cells embedded in 3D matrices."

Guru Prasad Poornam (UA) "A PDB survey of crystal packing in proteins."

Minying Cai (UA) To be announced

5:45 PM-6:00 PM Closing Remarks

6:00 PM Pizza and refreshments (1702....it's the Address! 1702 Speedway Ave.)

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ABSTRACT LIST

9:00AM James Zook jdzook@asu.edu

"Structure investigation of membrane proteins through circular dichroism and nuclear

magnetic resonance." J. D. Zook, P. Fromme, B. Cherry.

Arizona State University

The 16kDa transmembrane amino acid transporter, Outer Envelope Protein (OEP16) is

recombinantly expressed and investigated through CD and NMR spectroscopy. Using

improved expression and purification techniques, it is possible to obtain the necessary

amount and concentration for NMR spectroscopy studies. This new technique also allows for

purification in several different detergent micelles. The search for optimal protein conditions

for NMR studies involves CD analysis, including secondary structure estimation as well as

melting profiles. Due to the relatively large size of OEP16 (168 residues), more specialized

techniques are required to improve resolution quality. One such technique is via partial

selective deuterium exchange as a way to observe only buried transmembrane regions. Initial

studies show that the long correlation times of the large protein-micelle complex limit certain

NMR experiments, but promise is shown with initial HNCA and NOESY-HSQC results.

9:12AM Andrey Struts struts@email.arizona.edu

"Retinal dynamics studied by 2H NMR relaxation illuminates rhodopsin activation

mechanism." Andrey V. Struts and Michael F. Brown.

Department of Chemistry, University of Arizona

Dynamics of the retinal chromophore specifically deuterated at the C5, C9, or C13 methyl

groups has been studied by 2H NMR relaxation in the Dark, Meta I, and Meta II states of

rhodopsin. Solid-state 2H NMR relaxation allows investigation of the local ps–ns timescale

motions of the retinal ligand that are linked to larger-scale µs–ms functional protein

dynamics in the Meta I–Meta II equilbrium of photoactivated rhodopsin. An activation

mechanism is suggested whereby the photonic energy is channeled by 11-cis to trans

isomerization of retinal, giving an impulse directed toward the second extracellular loop E2

by the C13-methyl group and toward helices H3 and H5 by the β-ionone ring. Sequential

breaking of two ionic locks involving the PSB and the conserved E(D)RY motif results in a

reorientation of helices H5 and H6 and formation of the activated Meta II state. [1] Struts, A.

V., et al. (2007) J. Mol. Biol. 372, 50-66.

9:24AM

Avigdor Leftin aleftin@arizona.edu

"Site-specific markers of phase coexistence in ternary lipid domains revealed by separated

local field 13

C NMR spectroscopy." Avigdor Leftin, Michael F. Brown

Department of Chemistry, University of Arizona

The propensity of functional domain formation in the membrane is determined by physical

properties including phase transition temperatures, polarities, and hydrogen-bonding abilities

of the membrane components. The canonical raft-forming membrane system is composed of

the asymmetric glycerolipid POPC, sphingomyelin, and cholesterol combined in unit

stoichiometry. To reveal site-specific interactions responsible for the phase coexistence

within this ternary membrane system, we applied solid-state 13

C magic angle spinning NMR

to record chemical shift perturbations and magnetic dipolar couplings. Measurements were

conducted on the ternary system, single lipid systems, and binary component membranes. It

could be deduced that there exists a sphingomyelin-enriched liquid-disordered phase and a

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POPC-enriched liquid-ordered phase in the membrane domain. Site-specific observations are

presented regarding changes in acyl chain packing and electrostatic perturbation.

9:36AM Liang Huang liang.huang@asu.edu

"Detecting high-frequency oscillations by empirical mode decomposition method." Liang

Huang,1,2

Xuan Ni,1 Sachin S Talathi,

3 Ying-Cheng Lai,

1 Mark Spano,

2 William L. Ditto,

2

Paul R. Carney.3

1School of Electrical, Computer and Energy Engineering, and

2School of Biological and

Health Systems Engineering, Arizona State University, 3J Crayton Pruitt Family Department

of Biomedical Engineering, University of Florida

High-Frequency Oscillations (HFOs) are believed to be able to provide insights into basic

mechanisms of epilepsy. Pathologic HFOs can be used as biomarkers for epileptogenesis and

epileptogenicity. Current automated detection of HFO employs short-time energy or line

length of the acquired data for some small frequency ranges. Here we propose a method

making use of Empirical Mode Decomposition (EMD) which decomposes a signal into

different modes in different frequency ranges. The detected HFOs by our method show clear

features of high-frequency oscillations.

9:48AM Benjamin Heitz bheitz@email.arizona.edu

"Poly(lipid) bilayers: highly stable biomembranes for ion channel screening." Benjamin A.

Heitz, Troy J. Comi, Robert P. Cordero, S. Scott Saavedra, and Craig A. Aspinwall.

Department of Chemistry and Biochemistry, University of Arizona

Highly stable suspended phospholipid bilayers (SPB) were prepared from dienoyl-

functionalized, polymerizable lipids (poly(lipid)). Poly(lipid) bilayers extended lifetimes

from several hours to upwards of 4 weeks using, bis-dienoylPC (bis-DenPC), while

maintaining ion channel (IC) functionality for one week. While loss of activity was noted,

the SPB remained intact. For ICs sensitive to membrane fluidity, binary mixtures of

poly(lipid) and fluid, non-polymerizable lipid were investigated. IC activity was maintained

in fractionally polymerized, stabilized SPBs by inducing domain formation, where ICs were

reconstituted into the fluid domains either before or after UV-irradiation, allowing UV-

sensitive ICs to be utilized. Applying various methods with poly(lipids), we have

characterized a range of model ICs towards development of ligand-gated IC based sensors

for high throughput screening applications.

10:00AM

Kaushik Gurunathan kg@asu.edu

" Position dependent site-exposure nucleosome dynamics by FRET-FCS." Kaushik

Gurunathan, Marcia Levitus.

Biodesign Institute, Arizona State University

Nucleosomes are the fundamental repeating unit of eukaryotic chromatin. Often large protein

complexes encounter a hurdle when their target DNA sites are sterically occluded inside

these nucleosomes. One of the models by which DNA sites are exposed is by spontaneous

unwrapping and rewrapping of DNA stretches and hence called Site-Exposure model. Here,

in collaboration with Widom lab, we use a FRET-FCS method to study the dynamic rates of

unwrapping and rewrapping at sites inside the nucleosomes. The system consists of labeling

the DNA with a FRET donor (Cy3) at positions along the length of the DNA, starting from

one end all the way to the center of the dyad axis, and labeling a histone protein with a FRET

acceptor (Cy5). Using FCS, we measured the relaxation time of this dynamic process which

is dominated by the re-wrapping rate of the nucleosomes. Our results show that although the

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re-wrapping rate decreases with greater lengths unwrapped, it is not as dramatic as one would

expect.

10:12AM Marcia Levitus marcia.levitus@asu.edu

"Photophysics of single-molecule fluorescent dyes: nucleobase-dependent fluorescence of

Cy3 on DNA." Claudia Perez, Billie Harvey and Marcia Levitus.

Biodesign Institute, Arizona State University

Advances in single-molecule detection allow for improved signal-to-noise measurements,

and as a consequence the field is shifting towards more quantitative applications. A

remarkable consequence of this is the increased interest among biophysicists in

understanding how the photophysical properties of fluorophores are affected by the

environment within the biomolecule. We investigated the photophysical properties of Cy3 in

DNA. The efficiency of fluorescence of Cy3 depends strongly on DNA sequence, and the

chemistry used for covalent attachment. Results can be explained in terms of a

photoisomerization mechanism that competes with fluorescence. The barrier for

isomerization depends on the ability of Cy3 to interact with DNA, which is in turn a function

of the flexibility of the biomolecule, and the presence of conjugated moieties such as purines

(A and G). DNA-interactions also limit the rotational mobility of the dye, with important

consequences in studies involving energy-transfer.

10:24AM Mallikarjunaiah Kodirampura Jayaramappa kjmarjun@email.arizona.edu

"Equivalence of hydration and osmotic pressures for lipid membranes established by solid-

state 2H NMR." K. J. Mallikarjunaiah,

µ Jacob J. Kinnun,

∆ Avigdor Leftin,

µ and Michael F.

Brownµ,∆

µDepartment of Chemistry, and

∆Department of Physics, University of Arizona

Understanding the interactions between the lipid bilayers and proteins is an important issue

of membrane biophysics and structural biology [1]. Hydration force dominates at low

hydration levels. Here, we report 2H NMR results of phospholipid membranes with hydration

pressure (dehydration) and osmotic pressure (addition of osmolyte) techniques to establish

their equivalence. These two stresses are thermodynamically equivalent, more effective than

hydrostatic pressure, because the change in chemical potential when transferring water from

the interlamellar space to the bulk water phase corresponds to the induced pressure [2]. These

findings demonstrate the applicability of solid-state 2H NMR spectroscopy with membrane

stress techniques for investigating the mechanism of pressure sensitivity of membrane

proteins. [1] Botelho et al . (2006) Biophys. J. 91:4464-4477. [2]. Mallikarjunaiah et al.

(2010) Biophys. J. 98:282a.

11:00AM

Sebastian A. Sandersius sebastian.sandersius@asu.edu

"A possible role for chemotaxis in primitive streak formation." Sebastian A. Sandersius,1

Cornelis J. Weijer,2 Timothy J. Newman.

1

1Department of Physics, Arizona State University,

2Division of Cell and Developmental

Biology, College of Life Sciences, University of Dundee

A key stage of embryo development is gastrulation, in which cell germ layers are established.

Presented here is a model used to investigate the collective cell movement which is observed

at the onset of gastrulation in the Chick embryo. In the avian embryo, gastrulation is initiated

by a cadre of cells moving coherently, bisecting the embryo, thereby forming a structure

known as the primitive streak. The mechanisms underlying primitive streak formation are the

subject of recent experimental controversy. One hypothesis is that coherent cell motion is

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driven by chemotactic response to long-range signaling gradients. We will present results

from large-scale computer simulations testing this hypothesis. In particular, we perform

simulations using the Subcellular Element Model (ScEM). We have found that, in addition to

chemotaxis, active cell migration is crucial for ``fluidizing"" the tissue thereby allowing

large-scale coherent cell movement.

11:12AM Wen-Xu Wang wenxu.wang@asu.edu

"Role of mobility in pattern formation, sychronization and basin of biodiversity in rock-

paper-scissors game." Wen-Xu Wang, Xuan Ni, Ying-Cheng Lai, and Celso Grebogi.

School of Electrical, Computer, and Energy Engineering, Arizona State University

I will talk about the general role of individual migration in species diversity in the framework

of evolutionary game. Migration is a ubiquitous, and can arise in different scales. We

consider both intra- and inter-patch migration and find that random migration among

different patches can induce species coexistence in a novel target wave pattern, where

species coexistence can emerge from either random initial configuration or a single species in

each patch. In particular, we find synchronization and lag synchronization of target waves

among different patches, depending on the intra- and inter-patch migration mobility and the

area of migration target. We have derived a theory to characterize the formation of target

waves and synchronization among patches. At last, I will talk about basins of different

waves. We will show the entangle basin structures in the phase space and the emergence of

target wave basins from extinction basins induced by the inter-patch migration.

11:24AM Adam de Graff adam.degraff@asu.edu

"Protein unfolding under force: a geometric approach." Adam de Graff, Dan Farrell, Michael

Thorpe/

Center for Biological Physics, and Department of Physics, Arizona State University

There are diverse groups of proteins in our bodies that have evolved specialized mechanical

responses under an applied load. Proteins can possess similar folds but very different

unfolding pathways because of modifications to the spatial distribution of bonds which play a

key role in dictating how stress is internally distributed. Using a simplified protein model, I

demonstrate how these large differences in the unfolding mechanism can be predicted from

the geometry of the underlying bond network. We acknowledge financial support of the

National Science Foundation grant numbers DMR-0703973 and DMS-0714953.

11:36AM

Satish K. Singh satish@email.arizona.edu

"An analytical model of coupled receptor kinases capturing chemotactic sensitivity and

response range." Satish K. Singh, William R. Montfort, and Andrew C. Hausrath.

Department of Chemistry and Biochemistry, University of Arizona

Bacteria sense and move in response to chemical substances in their environment with

exquisite sensitivity, and are able to respond over at least six orders of magnitude in ligand

concentration. This chemotactic response is mediated by receptor complexes embedded in

the periplasmic membrane. How the bacterial sensory apparatus is able to respond to retain

sensitivity to small changes over such a wide concentration range remains perplexing. Here

we present an exactly solvable model, based on the infectivity principle introduced by

Dennis Bray, of how the collective behavior of receptors in the clusters extends the response

range well beyond that of indvidual receptors. Our modified infectivity model readily

explains the long-standing paradox of uniform chemotactic amplification at different levels

of adaptation, predicts a non-linear role for infectivity in extending the range of signaling

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response and successfully captures the entire six-order response range in chemotaxis.

11:48AM Rui Yang ryang8@asu.edu

"Role of intraspecific competition in coexistence of mobile populations in spatially extended

ecosystems." Rui Yang,1 Wen-Xu Wang,

1 Ying-Cheng Lai,

1,2,3 Celso Grebogi.

3

1School of Electrical, Computer, and Energy Engineering and

2Department of Physics,

Arizona State University, 3Institute for Complex Systems and Mathematical Biology, King's

College, University of Aberdeen

Evolutionary-game based models of non-hierarchical, cyclically competing populations have

become paradigmatic for addressing the fundamental problem of species coexistence in

spatially extended ecosystems. We study the role of intraspecific competition in coexistence

with the following findings. For high individual mobility, the competition can strongly

promote coexistence. The critical value of the competition rate beyond which coexistence is

induced is found to be independent of the mobility. However, in the regime of moderate

mobility, coexistence is hampered by intraspecific competition in the sense that coexistence

would be stable in the absence of the competition. We derive a theoretical model based on

nonlinear partial differential equations to predict the critical competition rate and the

boundaries between the coexistence and extinction regions in a relevant parameter space.

12:00AM

Teresa Cusati Teresa.Cusati@asu.edu

"Preliminary modeling of epithelial cells in three dimensions." Teresa Cusati, Karl Dutson,

Sebastian Sandersius, and Timothy Newman.

Center for Biological Physics, Arizona State University

Epithelial tissue is fundamental in animal organisms, providing stabilization and selective

biochemical isolation to organ systems. Disruption of epithelial tissue is also fundamental to

cancer biology – 90% of cancers are carcinomas, which originate in epithelial tissue. We are

in the first stages of developing a model of a 3D epithelial tissue and its disruption. In order

to carry out this research work we employ the Subcellular Element Model (ScEM) as a

theoretical tool. Each cell is modeled as a collection of elastically coupled elements,

interacting via short-range potentials, and updated using over-damped Langevin dynamics. In

order to model the apical basal polarity of epithelial cells, we need to construct cells using at

least two element types, representing cortex and non-cortex regions of the cell. In this work

we discuss our preliminary efforts to model this system. This work is supported by the

Human Frontier Sciences Program, and the National Cancer Institute.

12:12AM

Xuan Ni xuan.ni@asu.edu

"Cyclic competition of mobile species on continuous space: pattern formation and

coexistence." Xuan Ni,1 Wen-Xu Wang,

2 Ying-Cheng Lai,

1,2,3 Celso Grebogi.

3

1Department of Physics, and

2School of Electrical, Computer, and Energy Engineering,

Arizona State University, 3Institute for Complex Systems and Mathematical Biology, King's

College, University of Aberdeen

We propose a model for cyclically competing species on continuous space and address the

effect of the interplay between the interaction range and mobility on coexistence. A transition

from coexistence to extinction is uncovered with a strikingly non-monotonic behavior in the

coexistence probability. About the minimum in the probability, switches between spiral and

plane-wave patterns arise. A strong mobility can either promote or hamper coexistence,

depending on the radius of the interaction range. These phenomena are absent in any lattice-

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based model, and we demonstrate that they can be explained by a theoretical framework of

nonlinear partial differential equations. Our continuous-space model is more physical and we

expect the findings to generate experimental interest.

12:24AM Blake Mertz jbmertz@email.arizona.edu

"Computational insights into retinal dynamics in rhodopsin." Blake Mertz,1 Michael Lu,

2

Scott. E. Feller,2 Michael F. Brown

1

1Department of Chemistry and Biochemistry, University of Arizona,

2Department of

Chemistry, Wabash College

Rhodopsin, a prototypical GPCR, is activated when its covalently bound ligand, retinal,

isomerizes from an 11-cis to an all-trans conformation. Fourier transform infrared (FTIR)

and 2H NMR spectroscopy has identified the importance of retinal methyl groups to

rhodopsin activation, indicating lower methyl rotation barriers than observed in previous MD

simulations [1,2,3]. We report quantum mechanical (QM) calculations of retinal model

compounds and comparison to MD simulation in vacuo. By using larger retinal fragments

and a higher level of theory, we can accurately reproduce the rotational behavior observed in

2H NMR data [3]. These results in turn should lead to the ability to begin to simulate the

coupling of small- to large-scale motions in rhodopsin activation and extend to other GPCR

systems. [1] K. Martínez-Mayorga et al. (2006) JACS 128:16502. [2] R. Vogel et al. (2006)

Biochemistry 45:1640. [3] M.F. Brown et al. (2010) BBA, 1798:177.

1:30PM

Mark Hunter mark.hunter.1@asu.edu

" First results of femtosecond protein nanocrystallography." M.S. Hunter, P. Fromme, R.A.

Kirian, R.B. Doak, U. Weierstall, J.C.H. Spence.

Arizona State University

Serial crystallography has been used to show the first proof-of-principle for femtosecond

nanocrystallography at the Linac Coherent Light Source (LCLS), a 2keV pulsed X-ray laser

at SLAC which provides 3-300 femtosecond pulses. The intensity of the X-ray pulse exceeds

3rd generation sources by 12-orders of magnitude, yet the pulses are so short that X-ray

diffraction data could be collected before the sample is destroyed. In serial crystallography,

X-ray diffraction is collected from a stream of fully hydrated protein nanocrystals in their

mother liquor. The jet introduced nanocrystals of Photosystem I, a complex membrane

protein with a mass of 1.056 MDa consisting of 36 protein subunits and 381 cofactors, to the

femtosecond X-ray beam produced at the LCLS. Individual diffraction patterns were

recorded to the detector-limited resolution of 0.9nm. This work is a large international

collaboration, involving the CAMP group from three Max Planck Institutes, ASU, the LCLS

staff and the ASG team.

1:42PM

Daniel Farrell dwf@asu.edu

"A webserver for generating stereochemically-acceptable structural pathways in

biomolecules." Daniel W. Farrell, Kirill Speranskiy, and M. F. Thorpe.

Center for Biological Physics, Arizona State University

We present the geometric targeting method for rapidly generating all-atom pathways between

two known states of a biomolecule (protein, DNA/RNA) or biomolecular complex. We also

present a new publicly-available webserver that enables users to produce and visualize

pathways. In geometric targeting, the molecule is gradually pulled towards the target state

using an RMSD constraint, while various geometric constraints are enforced to maintain

good stereochemistry. The geometric constraints maintain covalent bond distances and

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angles, keep backbone dihedral angles in allowed Ramachandran regions, avoid eclipsed

side-chain torsion angles, avoid non-bonded overlap, and maintain a set of hydrogen bonds

and hydrophobic contacts. The method does not necessarily produce the optimal pathway,

but rather a stereochemically-acceptable pathway. We acknowledge financial support of the

National Science Foundation, grant numbers DMR-0703973 and DMS-0714953.

1:54PM Justin Spiriti justin.spiriti@asu.edu

"Applications of Gaussian-mixture umbrella sampling to nucleic acids." Justin M. Spiriti,1

Arjan van der Vaart.2

1Arizona State University,

2University of South Florida

Two applications of the newly developed multi-dimensional Gaussian-mixture umbrella

sampling simulation method will be presented. The first application focuses on a Cy3-DNA

system. The fluorescent dye Cy3 is used in FRET experiments to measure distances. Our

study examined stacking interactions and linker dynamics that affect the interpretation of

FRET experiments. Using the new method, the free energy basins of the DNA/Cy3 system

were characterized in terms of five dihedral angles along the linker between Cy3 and the

DNA, and important intermediates in the unstacking of the dye were identified. The second

application describes an extension of the method to enhance the conformational sampling of

small DNA strands. We will present preliminary results of this study, along with an outline

of future work.

2:06PM

Joseph Baker baker@physics.arizona.edu

"Molecular dynamics simulations of drug transport through the membrane protein EmrD."

Joseph Baker,1 Stephen Wright,

2 Florence Tama.

3

1Department of Physics,

2Department of Physiology, and

3Department of Chemistry and

Biochemistry, University of Arizona.

In order to facilitate the transport of molecules that are unable to easily cross the semi-

permeable cellular membrane, the cell utilizes membrane embedded proteins as transport

channels. The protein, EmrD, is a multidrug transporter found in the inner cellular membrane

of Escherichia coli (E. coli) bacteria. EmrD's function facilitates the expulsion of

hydrophobic drugs, contributing to the development of bacterial drug resistance. Therefore,

the EmrD drug transport pathway is of great interest from a pharmacological perspective.

Steered Molecular Dynamics (SMD) simulations are used to study drug transport in EmrD.

SMD allows external forces to be applied to atoms in the system, and is utilized in our

simulations to steer a drug through the EmrD central channel. A summary of the EmrD

simulations conducted will be presented, highlighting details of the drug transport pathway

and protein conformational changes.

2:18PM Dmitry Matyushov dmitrym@asu.edu

"Protein/water interface and bioenergetics." Dmitry Matyushov.

Center for Biological Physics, Arizona State University

Electrostatic fluctuations within proteins are critical to their biological activity as carriers in

electron transport chains. A significant number of steps an electron within a single chain

needs to hop poses the question of how a very low loss of free energy is achieved. Numerical

simulations show that the statistics of electrostatic water fluctuations at the protein interface

is strongly non-Gaussian resulting in a gigantic width of the energy distribution. This large

width develops at the temperature of dynamical transition of the protein and disappears at

lower temperatures when electrostatic fluctuations become Gaussian.

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2:30PM Ashini Bolia abolia@asu.edu

"A novel porotein binding approach using linear response theory." Ashini Bolia, Banu

Ozkan, Z. Nevin Gerek.

Center for Biological Physics, Arizona State University

Most of the docking protocols rely on a fixed conformation of receptor or already known

bound conformation of proteins. Therefore, we propose a novel protein binding method

based upon Linear Response Theory, which predicts the ligand binding response from the

structural information of the unbound conformation of protein. For this study we selected the

PDZ domain, the most common interaction domain proteins in signaling. In our docking

methodology, we first generate an ensemble of deformed structures of unbound conformation

by perturbing every residue of the system. The ensemble of perturbed conformations are

clustered, minimized and then docked with the peptides or ligands using

ROSETTALIGAND. Our approach succeeded to predict correct poses and the affinity of

binding peptides, and the results were also in agreement with the observations from the

crystal structure. This protocol could be of great help to the medical field for the design of

new drugs and inhibitors.

2:42PM

Alexander Fuhrmann alexander.fuhrmann@asu.edu

"AFM-based force spectroscopy: New insights into ligand-receptor interactions." Alexander

Fuhrmann,1 Qiang Fu,

2 Stuart Lindsay,

2 Robert Ros

1

1Center for Biological Physics, and

2The Biodesign Institute, Arizona State University

In single molecule force spectroscopy (SMFS), a ligand attached to the AFM tip is brought

toward a sample surface coated with receptors. This will occasionally lead to the formation

of a ligand-receptor bond. After this, the tip is retracted and the force needed to break the

bond is measured. Upon repeating this experiment several times and varying the pulling

velocity, one can learn about the binding energy barriers and kinetic reaction rates.

Nevertheless, the current standard theoretical model of SMFS, and even the modifications of

the model in the recent literature, fail to fit sufficiently well the published experimental data.

I will present our experimental work on DNA base-base interactions combined with highly

sophisticated methods of data analysis and will identify where the experiments and where the

models fail. This work can help experimentalists to identify flaws in their experimental

design and select the appropriate theoretical model(s) for the investigated system.

2:54PM

Jacob J. Kinnun jkinnun@email.arizona.edu

"Theoretical equivalence of hydration and osmotic pressure in membrane deformation."

Jacob J. Kinnun,1 K. J. Mallikarjunaiah,

2 Avigdor Leftin,

2 Matthew J. Justice,

3 Adriana L.

Rogozea,3 Horia I. Petrache,

3 Michael F. Brown.

1,2

1Department of Physics,

2Department of Chemistry, University of Arizona,

3Department of

Physics, Indiana University-Purdue University

Phospholipid membranes are implicated in cellular homeostasis together with a multitude of

key biological functions. Many regulatory functions are known to be mediated through

protein-lipid interactions. An important feature of pressure-sensitive membrane proteins

(rhodopsin, mechanosensitive channels) is that their activation is coupled to membrane

tension and deformation [1,2]. Membrane deformation can be achieved through the

application of osmotic stress and stress due to dehydration. These two stresses are

thermodynamically equivalent because the change in chemical potential when transferring

water from the interlamellar space to the bulk water phase corresponds to the induced

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pressure. A simple theoretical framework based on a unified thermodynamic description is

developed. This framework is extended to predict the area compressibility of membranes. [1]

A.V. Botelho et al. (2006) Biophys. J. 91, 4464-4477. [2] S.I. Sukharev et al. (2001) Biophys.

J. 81, 917-936.

3:06PM Di Cao di.cao@asu.edu

"Electrical measurement of carbon nanotube water wetting." Di Cao, Jin He, Pei Pang, Stuart

Lindsay.

Department of Physics, and The Biodesign Institute, Arizona State University

We fabricate the device which uses CNT to collect the two reservoirs opened on PMMA.

The translocation of single-stranded DNA through single-walled carbon nanotubes (SWNT)

is detected in our device. We want to further study the effect of water wetting outside and

inside of CNT. Back gate is added to the device. For semi-conducting CNT, we get the p-

type CNT-FET gate effect. We find that adding water to unopened CNT has little effect to

the gate curve, but adding water to opened (wetting inside) of CNT increase the conductance

of CNT and flatten the gate curve.

3:45PM

Danmei Bian dbian@asu.edu

"Comparing nucleation models for pathological protein aggregation." Danmei Bian, Sara M.

Vaiana.

Center for Biological Physics, and Department of Physics, Arizona State University

Several diseases are associated with pathological aggregation of proteins forming amyloid

fibrils (Alzheimer’s, Parkinson’s, type II diabetes, etc.). The physics behind amyloid fiber

formation is not yet fully understood. It is commonly accepted that amyloid fiber formation

occurs through a nucleation process, but simple homogeneous nucleation is not sufficient to

describe the kinetics of amyloid formation. At variance with Sickle Cell Hemoglobin (HbS)

aggregation, where a complete thermodynamic and kinetic model exists (FHE double

nucleation model [1]), a quantitative model describing amyloid fiber formation is still

lacking. I will discuss a model by Knowles et al.[2] that has recently been published and

compare it to the FHE model for HbS aggregation and present some experimental techniques

and approaches we are using to study amyloid aggregation. [1] Ferrone, F.A, et al. J.Mol.

Biol. (1985) [2] Knowles, T.P.J., et al. Science (2009) 326, 1533-1537.

3:57PM

Stephanie Cope stephanie.cope@asu.edu

”Experimental Techniques for measuring the conformation of intrinsically disordered

proteins." Stephanie Cope and Sara M. Vaiana.

Center for Biological Physics, and Department of Physics, Arizona State University

Intrinsically Disordered Proteins (IDPs) are a newly identified class of proteins that lack 3-

dimensional structure yet carry out biological functions. They are estimated to comprise 50%

of mammalian proteins, becoming more populous with an organism’s complexity.[1] IDPs

are surprisingly difficult to characterize due to rapid changes in conformation. As a result not

much is known about their specific structural and dynamical properties. I will discuss some

experimental techniques and approaches we are using to study this new class of proteins and

present some preliminary data on Islet Amyloid Polypeptide, an IDP involved in type II

diabetes. [1] Mohan, A et al. Molecular Biosystems (2008) 4: 328-340.

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4:09PM Pei Pang ppang1@asu.edu

"Electrochemical current measurement base on water wetting inside the carbon nanotube."

Pei Pang, Jin He, Di Cao, Stuart Lindsay.

Department of Physics, The Biodesign Instite at Arizona State University

We demonstrate the electrical properties of field effect transistor (FET) based individual

semi-conducting single-walled carbon nanotube (SWNT) can be change to totally ON state

after the introduction of water molecules into the SWNT. Meanwhile, the CNT can be also

used as the nanoelectrodes for electrochemistry. However, we observe the electrochemical

current with the different amplitude when the electrolyte outside and inside the SWNT.

These studies demonstrate the potential of using SWNT as a model carbon nanoelectrode for

electrochemistry.

4:21PM Bennett Kalafut kalafut@physics.arizona.edu

" Stretching poly(A) to investigate structure formation at low ionic strength." Bennett

Kalafut, Koen Visscher.

Department of Physics, University of Arizona

Polyadenylic acid (poly(A)) is known to form helices due to base-stacking interactions at

ionic strengths high enough that electrostatic self-repulsion of RNA's phosphodiester

backbone can be neglected. In stretching experiments, a helix-coil transition is manifested by

a plateau in the force-extension curve at approximately 20 pN of tension. Using optical

tweezers to stretch poly(A) to 30 pN of tension, we find that this plateau is not present at low

concentration of Na+. Addition of a small amount of Mg

++ greatly enhances the transition.

4:33PM

Olaf Schulz olaf.schulz@asu.edu

"Highly localized fluorescence quenching with silicon AFM probes on the single molecule

level." Olaf Schulz,1 Marcelle Koenig,

2 Felix Koberling,

2 Robert Ros.

1

1Center for Biological Physics, Arizona State University,

2PicoQuant GmbH

The combination of atomic force microscopy (AFM) with single-molecule-sensitive confocal

fluorescence microscopy enables a fascinating investigation into the structure, dynamics and

interactions of single biomolecules or their assemblies. AFM reveals the structure of

macromolecular complexes with nanometer resolution, while fluorescence can facilitate the

identification of their constituent parts. In addition, nanophotonic effects, such as

fluorescence quenching or enhancement due to the AFM tip, can be used to increase the

optical resolution beyond the diffraction limit, thus enabling the identification of different

fluorescence labels within a macromolecular complex. Our novel setup, which is the

combination of two commercial, state-of-the-art microscopes, allows us to gather high

resolution topographic as well as optical data on timescales from sub-nanoseconds to hours.

Here, we show highly localized silicon induced quenching of the fluorescence of organic

fluorophores.

4:45PM

Ivan Yermolenko ivan.yermolenko@asu.edu

"Integrin-mediated adhesion to fibrinogen studied by single cell force spectroscopy." Ivan

Yermolenko¹, Alexander Fuhrmann², Tatiana Ugarova¹, Robert Ros²

¹Center for Metabolic Biology, School of Life Sciences, and ²Center for Biological Physics,

Department of Physics, Arizona State University

The physical properties of substrates are known to control cell adhesion and signaling via

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integrin-mediated mechanotransduction. It is well known that the plasma protein fibrinogen

is absorbed on the surface of blood clots and implanted biomaterials. The fibrinogen coating

may modify and alter adhesion of blood cells such as leukocytes and platelets. To gain an

understanding of the mechanism whereby fibrinogen matrices with different densities

influence cell adhesion we used single cell force spectroscopy. In this technique, a single cell

is attached to a tipless cantilever of the atomic force microscope and force-distance curves

for different surfaces are acquired. Cell adhesion was studied and correlated with the

physical and structural properties of fibrinogen matrices. The early cell adhesion events were

determined and detachment forces to various substrates were quantified.

4:57PM Brian Anderson briananderson13@gmail.com

"The effects of PKCα phosphorylation on the extensibility of titin’s PEVK element." Brian R. Anderson, Julius Bogomolovas, Siegfried Labeit, Henk Granzier.

Department of Physics, University of Arizona.

Posttranslational modifications, along with isoform splicing, of the giant muscle protein titin

determine the passive tension development of stretched cardiac muscle. It was recently

shown that PKCα phosphorylates two highly-conserved residues (S26 and S170) of the

PEVK region in cardiac titin, resulting in passive tension increase. To determine how each

phosphorylated residue affects myocardial stiffness, we generated three recombinant mutant

PEVK fragments (S26A, S170A and S170A/S26A), each flanked by Ig domains. Single-

molecule force spectroscopy shows that PKCα decreases the PEVK persistence length (from

0.99 nm to 0.68 nm). Before PKCα, all three mutant PEVK fragments showed at least 40%

decrease in persistence length compared to wildtype. We conclude that phosphorylation of

S26 is the primary mechanism through which PKCα modulates cardiac stiffness.

5:09PM

Jack Staunton jrstaunt@asu.edu

"Development of a method for quantitative mechanical nanotomography of cells embedded

in 3D matrices." Jack Staunton,1 Alexander Fuhrmann,

1 Olaf Schulz,

1 Sandor Kasas,

2 and

Robert Ros.1

1Center for Biological Physics, and Physical Sciences-Oncology Center, Arizona State

University, 2EPFL Laboratory of the Physics of Living Matter

Cancer development is associated with changes in the mechanical properties of cells as well

as the extracellular matrix. Few facts are known about the interplay of cells and the

extracellular matrix (ECM) on the molecular level with respect to the transformation from a

normal to a malignant cell. We are working on the development of experimental and data-

analytical methods to investigate local mechanical properties of cells embedded in 3D

matrixes using atomic force microscopy (AFM) based nanoindentation experiments.

Simultaneously with the mechanical measurements, the cells will be investigated using

confocal laser scanning microscopy (CLSM) with fluorescence life time

imaging/spectroscopy. We will present our setup and the alignment of the AFM with the

confocal volume. We will also present preliminary results comparing the Young's moduli of

the nuclei of live normal and cancer cells adhered to glass surfaces.

5:21PM

Guru Prasad Poornam guru@email.arizona.edu

"A PDB Survey of Crystal packing in proteins." Guru Prasad Poornam, Osamu Miyashita.

Department of Chemistry and Biochemistry, University of Arizona

X-ray crystallography has been the most dominant experimental technique for providing

atomic detail structures of proteins. While conformational changes are an important aspect of

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biomolecular function, understanding them from a static structure is not straightforward.

Given the inherent level of flexibility,different crystallising conditions and the packing forces

acting on it, a protein may adopt multiple conformations. Of these factors, packing plays a

vital role in protein structural stability. For example lack of relatively fixed structure at the

loop regions are prone to inefficient packing.This inefficient packing leads to disordered

regions in the structure which sometimes become ordered due to crystal contacts.

Methodology developed to understand the influence of crystal contacts in protein structural

disorder and the results will be discussed.

5:33PM Minying Cai mcai@email.arizona.edu

TO BE ANNOUNCED. Minying Cai, Victor Hruby.

Department of Chemistry and Biochemistry, University of Arizona

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Notes

We gratefully thank BIO5 and the Department of Chemistry

and Biochemistry at the University of Arizona for support of

this year's Biophest.