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Albany 2015: Conversation 19

category image Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2014)

Topics, Speakers, Chairs and Guests

The 19th Conversation, June 9-13, 2015 will be held at the State University of New York, Albany, NY 12222 USA. Participants will arrive on Tuesday June 9th, there is a reception that evening. The scientific program starts Wednesday morning June 10th and will end after lunch on Saturday June 13th at 2:00 PM. The conference will have roughly 50 lectures by leading scientists, in addition to several short lectures by young scientists who will be selected from abstracts submitted for poster + young scientist lecture presentations. We will have on display, throughout the conference, some 250 posters. We anticipate about 400 participants with diverse background from over 20 countries for these continuing conversations.

Young Scientists Lecture Program
The Organizing Committee has left 5.5 hrs of the Conversation time for the young scientists lecture program. Extraordinarily talented young professional researchers, at the rank of assistant professors, post-doctoral fellows and doctoral students, will be selected from the abstracts submitted for lecture + poster presentations to provide oral presentations which will be sandwiched between those by senior scientists. Go to link below.

Director
Ramaswamy H. Sarma, Department of Chemistry
State University of New York, Albany NY 12222 USA
ph: 518-456-9362; fx: 518-452-4955; email:rhs07@albany.edu

download_book_of_abstracts-2015.pdf
Complete Logistics: Everything You Wanted to know: 19th Conversation
Complete Logistics: Light Web PDF Download
Complete Logistics: Print PDF Download
After Deadline Presenting Posters & Short Orals
Detailed Daily Program of Speakers and Events
Abstracts: Requirements & Deadlines
Registration, Meals and Accommodation
Young Scientists Speaker Program
Financial Assistance
Albany 2015: The 19th Conversation Poster
Albany 2015: Book of Abstracts



Sponsored by:
University at Albany (pending)

    Department of Chemistry
    Department of Biology
    Office of the Dean, Arts and Sciences
    Office of the Vice President for Research
National Science Foundation (pending)
JBSD and
Adenine Press



sharp-web.gifEvenings With Nobel Laureates
The Albany Conversation traditionally holds evening lectures in areas of fundamental interest to life sciences. For Albany 2015, the 19th Conversation, Nobel Laureate Phillip A. Sharp, Institute Professor, Koch Institute for Integrative Cancer Research, MIT will deliver the keynote address on Thursday June 11 2015 at 8:00 PM on the topic The 21st Century opened with a revolution in RNA Biology. The discoveries of RNA interference and the evolutionary conservation of microRNAs at the turn of the century heralded a revolution in RNA Biology and the development of important innovations. Of particular note is the emerging understanding of the wide- ranging roles of non-coding RNAs. Long non-coding RNAs probably regulate the expression of genes through both cis and trans mechanisms and provide organization to the nucleus. Small non-coding RNAs channel gene expression to specific states and suppress transposon elements. Excitingly, these insights and others are now being translated into new treatments for diseases and control of plant pathogens.

karplus-web.gifOn Wednesday, June 10 2015, at 8:00 PM, Nobel Laureate Martin Karplus will show a video of his Nobel Lecture. The Nobel Lecture (35 minutes) traces the development of molecular dynamics simulations from early trajectory studies of the H+H2 -> H2-H exchange reaction to their present application to biomolecules. The importance of the realization that classical mechanics is sufficient for studying the motion of atoms at ambient temperatures is emphasized. To illustrate biomolecular applications, a recent film recalling the first molecular dynamics simulations of a protein is shown and the mechanism by which kinesin walks on microtubules is described. The remaining 25 minutes will be spent on the theme "What Does the Future Hold". Here Martin will discuss the future of simulations with a prediction of what will be possible when.

Martin used to be a frequent guest of the Albany Conversation in the early 1980's. Back in 1981, Sir David Phillips in the Conversation Halls in Albany declared that the period in which rigid brass models of double-helical DNA and a variety of protein molecules dominating the scene and much of that thinking is coming to an end. Thanks to the very first molecular dynamics simulation of a biomolecule, BPTI, in 1977 by McCammon, Gelin and Karplus, and the hydrogen-deuterium exchange studies by Walter Englander. And Sir David noted voices crying in the wilderness about enzyme molecules changing shapes, and people protesting like Galileo "but they do move" and the message going out from this meeting is that they indeed do. That happened in Albany 33 years ago. We have lived through interesting times. We hope that we will visit some of these times with Martin in 2015. You can download the remarks by Sir David made in 1981, and a pdf of the Martins biography. We strongly recommend that you read the biography. The biography is an arresting story of an eight-year old Austrian Jewish lad, very disillusioned and unhappy that his non-Jewish friends are deliberately avoiding him, escaping with his parents from the Nazis in 1938, arriving at the Statue of Liberty, and living quiet among Boston Brahmins, cautiously not revealing he is a German speaking Jewish boy, and this extraordinary journey finally exploding and establishing the discipline of computational structural biology.

We will celebrate the crowning achievements of computational structural biology and its triumph in 2013 with the Nobel Prize in Chemistry for Martin Karplus, Michael Levitt, and Arieh Warshel by its extensive coverage during the Albany 2015 deliberations. We describe eight such sessions later.

hingorani-preush-comb.gifNSF and NIH present grant opportunities and strategies
Dr. Manju Hingorani, Ph.D. Professor of Molecular Biology and Biochemistry, Wesleyan Univ., and also program director of Molecular and Cellular Biosciences at NSF, and Dr. Peter Preusch, Ph.D, Chief of the Biophysics Branch in the Division of Cell Biology and Biophysics, NIGMS, NIH, will speak about funding opportunities and strategies at their respective institutions. The Conversation will provide quiet rooms for continued dialog after their lectures. This should be a very rewarding experience to many of the young scientists such as doctoral students, post-docs and assistant professors, in addition to the seasoned researchers.

exciting-comb.gifExciting Developments in Structural Biology
A ubiquitous phenomenon is transcriptional bursting in bacteria, and it has been shown that transcription of highly expressed genes occur in stochastic bursts. But their origin has not been understood yet. Sunney Xie, Harvard, has for the first time unraveled the mechanism by developing a high-throughput, in vitro, single-molecule assay to follow transcription on individual DNA templates in real time. He showed that positive supercoiling buildup on a DNA segment by transcription slows down transcription elongation and eventually stops transcription initiation. Transcription can be resumed upon gyrase binding to the DNA segment. He proves that transcriptional bursting of highly expressed genes in bacteria is primarily caused by reversible gyrase dissociation from and rebinding to a DNA segment, changing the supercoiling level of the segment. In the next step of life, translation, polypeptides are manufactured; and Bernd Bukau, Univ. of Heidelberg, Germany, will provide insights into the complex life of nascent polypeptides. Multiple finely regulated mechanisms involving the ribosome as hub ensure that nascent polypeptide chains are enzymatically processed, targeted to membranes and folded to native structure. Current knowledge and emerging concepts underlying the critical interplay between translation and protein maturation are presented. Eric Greene, Columbia University, will describe research efforts seeking to understand how proteins locate specific target sites within DNA. This research is based upon real-time single-molecule imaging technology and utilizes a unique experimental platform called DNA curtains. Eric will also describe the DNA curtains technology and its application to a variety of biochemical problems related to protein-nucleic acid interactions. Hashim Al-Hashimi, Duke Univ., shows using NMR relaxation dispersion experiments that canonical and non-canonical base pairs in DNA and RNA duplexes exist in dynamic equilibrium with alternative forms that change the chemical presentation of the genetic code. Hashim discusses how these alternative base pairs underlie the basic mechanisms of RNA switches, DNA damage induction and repair, spontaneous mutations, sequence-specific DNA recognition and signaling. Michael Weiss, Case Western Reserve University, will focus on the structure and evolution of insulin and the insulin receptor. Recent progress in understanding how the hormone binds to its receptor rationalizes sites of mutations in these proteins causing diabetes mellitus and provides a new foundation for the design of therapeutic insulin analogs.

optogenetics-comb.gif Optogenetics
Sensitivity of biological molecules to light is the underpinning of optogenetics; there is a huge breakthrough happening now on the interface between structural biology, light sensitivity, neuroscience and ultra fast reactions. Ed Boyden, MIT, will talk about new tools for mapping, recording, and controlling the brain, both to reveal how cells of the brain work together in circuits to generate complex behaviors and decisions, as well as to reveal the underlying fundamental mechanisms, and potential treatments for neural disorders. These tools range from optogenetics, molecules that make neurons sensitive to being activated by light, to robotic methods for analyzing neural activity, to new kinds of microscopes that offer ultra-high-speed and precise neural imaging. Xue Han, Boston Univ., will continue to elaborate on the molecular tools for analyzing neural circuit dynamics. Keith Moffat, University of Chicago, will present time-resolved crystallography using synchrotron and free electron laser X-ray sources, on time scales from seconds to 100 picoseconds and approaching femtoseconds. Initiation of ultra fast reactions typically requires light-sensitive systems in which reaction can be initiated by a visible laser pulse - but clearly, not all interesting biological systems are light-sensitive. This raises the question: how can sensitivity to light be conferred on otherwise light-inert systems, by optogenetic approaches? Shigehiko Hayashi, Kyoto Univ., Japan will present theoretical analyses of functional properties of retinal binding proteins employed in optogenetics as well as computational design of their mutational variants with new functionality. Various computational approaches including quantum chemistry, molecular dynamics simulations, and statistical integral equation theory are utilized in combinatorial ways to examine molecular mechanisms underlying functional properties such as color tuning, light-gating/switching, and ion transport, and to model mutational variants based on the mechanisms elucidated.

crispr-comb.gifCRISPR: Structural Biology & Biochemistry
Hong Li of Florida State Univ., opens the session. Many bacteria and archaea encode a small RNA-mediated adaptive immunity system called CRISPR-Cas that conceptually parallels the RNA interference system in eukaryotes. The inner workings of the CRISPR-Cas immunity are as interesting to the field of molecular biology as they are to the field of translational medicine. Three-dimensional structures of several CRISPR-Cas components have been resolved by both X-ray crystallographic and electron microscopic techniques. The results reveal biochemical mechanisms of nucleic acid recognition and cleavage and surprising links among distantly related proteins and protein-RNA complexes. Blake Wiedenheft of Montana State University takes up phage infection of bacteria. Viruses that infect bacteria are the most abundant biological entities on earth and the selective pressures imposed by these pervasive predators have a profound impact on the composition and the behavior of microbial communities in every ecological setting. Blake aims to understand the mechanisms that bacteria use to defend themselves from phage infection and counter mechanisms that phages use to subvert these immune systems. Eugene Koonin, NIH, will lecture on the origin and evolution of adaptive immunity systems. Comparative genomics reveals unexpected, striking parallels between the evolutionary scenarios inferred for adaptive immunity systems in animals and prokaryotes. Both the vertebrate adaptive immunity that is centered on V(D)J recombination and the CRISPR-Cas mechanism of adaptive immunity in archaea and bacteria appear to have evolved through integration of distinct transposable elements into innate immunity loci in the respective genomes. This unexpected parallelism reveals general principles of Lamarckian evolution and also explains the remarkable efficiency of adaptive immunity systems as tools of molecular biology. In fact, Konstantin Severinov, Rutgers Univ., advocates that CRISPR/Cas spacer acquisition is one of the very rare truly Lamarckian biological processes known. How do bacteria ensure that they acquire spacers from foreign DNA and avoid autoimmunity mediated by CRISPR spacers acquired from their own DNA. Konstantin will discuss molecular mechanism responsible for adaptive behaviour of CRISPR/Cas and discrimination of self and non-self in these systems.

rna-comb-photo.gifRNA: Localization, Catalysis & Structure
Even though bacteria have no subcellular organelles similar to eukaryotic cells, they have an elaborate internal organization to manage the flow of genetic information. Natalia Broude, Boston Univ., elaborates on this flow of genetic information by following the localization and dynamics of bacterial RNAs, and by developing several methods to label RNA in live E. coli cells. David Lilley, Univ. of Dundee, UK, presents a unified model of RNA catalysis. RNA catalyses two of the most important reactions in the cell, and probably a great deal more at an early stage of life's development on the planet. David is engaged in combined crystallographic and mechanistic studies of the origins of chemical catalysis in ribozymes, revealing their surprising catalytic power. He presents a unified model of general acid-base catalysis in the nucleolytic ribozymes, yet with interesting differences between the various members of the group. Alan Chen, University at Albany, discusses recent advances in de-novo folding of small RNAs using all-atom molecular dynamics simulations. Alan finds that the predictive accuracy of such models is greatly increased when the underlying molecular mechanics model is extensively calibrated against thermodynamic and kinetic measurements of mono and di-nucleotides in solution. Manju Bansal, Indian Institute of Science, Bangalore India, dwells on the nucleo-cytoplasmic transport of tRNA by Exportin-t. Export of mature, fully processed tRNA molecules from nucleus to cytoplasm is carried out by Exportin-t (Xpot) protein in mammals, which is formed by repeating motifs of 35-40 amino acids, called HEAT repeats. MD studies have been carried out for a range of molecular complexes including free Xpot protein and intermediate state complexes, bound either to Ran or tRNA and various molecular determinants responsible for cargo binding and conformational change after tRNA release have been identified. The energetics of intermediate complexes were also studied, in order to rationalize the differential binding affinities of Xpot in presence or absence of its specific cargo and directionality of the overall transport process.

dna-damage-comb.gifDNA: Damage, Repair, Self-assembly and Recombination
Threats of RNA contamination of DNA, and consequent DNA damage will be discussed by Scott Williams of NIH. More than 1,000,000 ribonucleotides enter and exit the genome each mammalian cell cycle and these numbers exceed, by 1-2 orders of magnitude, all other known DNA damage events combined. Yet, possible functions of ribonucleotides, their impact on genome integrity, and cellular factors required for coping with ribonucleotides are largely unknown. Scott will describe cellular RNA-DNA damage response factors acting to process intermediates arising from ribonucleotide-triggered DNA damage, and molecular mechanisms of inactivation of such repair factors (eg. Aprataxin) in neurological disease. Sarah Delaney, Brown University, will discuss base excision repair (BER) of DNA and how this process, which typically helps to maintain genetic stability by repairing DNA damage, can be detrimental when it occurs in triplet repeat DNA and causes expansion of the repeat DNA. Non-homologous end joining (NHEJ) is the major pathway for repair of DNA double-strand breaks (DSBs) in human cells. The current integration of structures by combined methods is resolving puzzles regarding the mechanisms, coordination and regulation of NHEJ steps. Michal Hammel, LBL, Univ. of California, Berkeley will present structural results suggesting that the NHEJ system forms a flexing scaffold with the DNA-PKcs HEAT repeats acting as compressible macromolecular springs suitable to store and release conformational energy to apply forces to regulate NHEJ complexes and the DNA substrate for DNA end protection, processing, and ligation. Mara Prentiss, Harvard University, examines Homologous Recombination (HR) from the standpoint of self-assembly. Self-assembly is an important feature of living beings, and the promise of artificial self-assembly has been a main driver of nanotechnology research. HR is an example of natural self-assembly which occurs in all organisms during double strand break repair in eukaryotes and during meiotic recombination. Recent results, at the Prentiss laboratory, have revealed new information about structure/function relationships occurring during RecA mediated HR leading to a new detailed model of HR. Mara's thesis is that the basic features revealed by the new results must constitute the core underpinning of any complex self-assembling system, including protein folding. Chantal Prevost, IBPC, Paris, France, provides structural insights into the proposed mechanism of HR. The recognition and strand exchange process central to HR involves structural transitions for the nucleic acid component, which goes from a B-DNA form outside the recombinase filament to a stretched/unwound form when incorporated within this filament. This distorted form has long been thought to be a key issue for the HR mechanism. Chantal will discuss the main features of the DNA structural transition within the proposed model for the HR mechanism. The recombinase filament itself can change the internal arrangement of its monomers upon ATP hydrolysis, thus modifying its helical form. Chantal will discuss these transitions in the light of a new model for the HR mechanism.

dna-nano-comb.gifDNA: Nanotechnology
Molecular self-assembly with DNA provides a route for placing molecules and constraining their fluctuations in user defined ways which opens attractive avenues for scientific and technological exploration. Hendrik Dietz,TUM, will talk about new concepts for designing complex and dynamic objects from DNA. He will discuss phenomena that occur during self-assembly of such objects, and he will report on a series of DNA-based scientific instruments that offer unprecedented precision in space and time in their respective fields of application. Peng Yin, Harvard University, will describe DNA bricks as a general framework for constructing nanostructures with prescribed molecular geometry and kinetics. By interfacing these DNA structures with technologically relevant functional molecules, Peng's lab has developed diverse applications in digital fabrication of inorganic materials, bioimaging (in particular highly multiplexed super-resolution imaging), and biosensing. Lulu Qian, California Institute of Technology, will talk about robust and systematic molecular engineering with synthetic DNA strand displacement circuits, and how these DNA circuit components can be used to create DNA robots for prototyping complex nanomechanical tasks performed using simple and composable molecular building blocks. One example system is to demonstrate a DNA robot that can search through a maze, identifying a direct path from the entrance to the exit, and to evaluate the robustness of the robot by testing it against a variety of nanoscale mazes with increasing complexity.

dna-theory-comb.gifComputational Structural Biology I: DNA
Jiri Sponer, Institute of Biophysics, Brno, Czech Republic, will summarize recent advances of large-scale quantum-mechanical (QM) computations of biomolecular systems, specifically of nucleic acids. These computations allow accurate structure-energy analysis of small but complete biomolecular building blocks (such as RNA motifs, B-DNA fragments or quadruplex DNA stems) that can complement classical molecular dynamics (MD) simulation studies. Advantages and limitations of such computations will be explained, and their synergy with force field computations will be demonstrated. Combining force field computations with large-scale QM computations can provide a truly multi-scale modelling of nucleic acids. Celia Fonseca Guerra, VU University, The Netherlands, applies high-end QM studies to explore the fidelity of the DNA replication mechanism. She employs Dispersion-corrected Density Functional Theory computations to reveal key factors behind the intrinsic affinity of a DNA template-primer complex to select the correct nucleotide. Sarah Harris, University of Leeds, UK, uses high- performance supercomputing to comprehend the role played by DNA supercoiling and topology in bacterial gene regulation. Using computer simulations of complex DNA topologies she aims to understand the information content of genomes from a biophysical, as well as a biochemical point of view.

dna-protein-comb.gifComputational Structural Biology II: DNA-Protein Complexes
Protein-nucleic complexes are at the very core of life being involved in fundamental biological processes. Michael Feig, Univ. of Michigan, will elaborate on the mechanistic details of two specific processes, transcription by RNA polymerase and DNA mismatch recognition by MutS and homologs, from a dynamics perspective using results from recent computer simulations. In his presentation, Koby Levy, Weizmann Institute of Science, Israel, brings up protein sliding that occurs on both double- and single-stranded DNA, and discusses the molecular features of proteins and of the nucleic acids that allow fast dynamics and high affinity binding. Remo Rohs, Univ. of Southern California, then takes up the computational modeling of transcription factor binding specificities using DNA structure. Quantitative predictions of binding specificities from genome-wide datasets are an important step towards properly understanding gene regulatory mechanisms. Based on a first large-scale benchmark study for many different families of transcription factors, Remo demonstrates that the availability of DNA shape information on a high-throughput basis enabled the integration of DNA structural features in the accurate modeling of DNA binding specificities. Remo shows that using statistical machine learning, structural features that are key for protein-DNA recognition can be identified from sequence when a structure is unavailable. This advance changes our ability to derive key structural features from hundreds of thousands of sequences and suggests a much needed integration of genomics and structural biology.

ligand-binding-comb.gifComputational Structural Biology III: Ligand Binding Effects
Binding of proteins to ligands such as small molecule drugs, inhibitors and peptides unleash a variety of structural events. Jeffrey Skolnick, Georgia Institute of Technology, addresses the intrinsic ability of protein structures to exhibit the geometric and sequence properties required for ligand binding without evolutionary selection. This is demonstrated by the coincidence of the properties of pockets in native, single domain proteins with those in computationally generated, compact homopolypeptide, artificial, ART structures. The library of native pockets is covered by a remarkably small number of representative pockets (~400), with virtually every native pocket having a statistically significant match in the ART library, suggesting that the library is complete. Finally, Jeff presents examples of experimental validation of promising small molecule hits that exploits the degeneracy of ligand binding pockets. Ian Thorpe, Univ. of Maryland, takes up the RNA-dependent RNA polymerase from the Hepatitis C virus which is a validated drug target and contains several distinct allosteric sites. However, the mechanisms by which allosteric inhibitors reduce activity of the polymerase are not fully understood. Using molecular simulations, Ian provides evidence that allosteric inhibitors alter the distribution of conformations sampled by the enzyme in ways that can account for their inhibitory action. Ora Schueler-Furman, Hebrew University in Jerusalem, Israel, addresses the regulatory protein interactions that are mediated by short linear peptides. Ora is interested in the development of tools to model the structure and binding specificity of these interactions, and to integrate these models with other experimental and computational approaches to obtain a detailed view of these individual interactions and their context.

protein-design-comb.gifComputational Structural Biology IV: Design and Engineering
Teresa Head-Gordon, Univ. of California, Berkeley will describe her theoretical work in quantifying protein statistical and dynamical motions that correlate with enzyme performance of de novo enzymes and the possibility of incorporating fluctuations and dynamics into the early stages of enzyme design. N. Srinivasan, Indian Institute of Science, Bangalore, India will describe a method to design protein-like artificial sequences to fill-in void and sparse regions in protein sequence space. He will also demonstrate the tremendous power of these artificial protein sequences in aiding recognition of relationships between natural proteins which are enormously diverged in evolution.

mole-simu-biology-comb.gifComputational Structural Biology V: Molecular Simulations
There are biological events which we cannot physically see at the molecular level such as activation of enzymes, energy landscapes and so on. But we get fired up and ready to go by visualizing them via simulations. Rommie Amaro, UCSD, will discuss emerging techniques that allow us to model and predict biological phenomena across diverse scales of biological organization. Rommie will also cover the latest advances at the intersection of biophysics and computer-aided drug design, including how novel computational approaches are enabling the discovery of new small molecule compounds. Vijay Pande, Stanford, uses novel computational methods to simulate millisecond dynamics of kinases and GPCRs, shedding light on the conformational change associated with activation, with implications for next generation rational drug design against these targets. Carol Post, Purdue Univ., uses molecular dynamics simulations combined with NMR spectroscopy to gain insights into the transition pathway for conformational activation of Src kinases. While this transition pathway has features that appear to be common across the kinome, substrate recognition was found recently to differ within the one and only family of tyrosine kinases in the kinome. It was also discovered that the unique allosteric mechanism for controlling the interaction of Syk with membrane receptors defies entropy/enthalpy compensation; phosphorylation of Syk alters binding entropy with little affect on enthalpy. Sandor Vajda, Boston Univ., explores the energy landscape of encounter complexes in the process of protein-protein association. Projecting the nonlinear manifold describing the relative orientation of two solid bodies onto a Euclidean space and determining the shape of low energy regions by principal component analysis show that the energy surface is canyon-like, with a smooth funnel within a two-dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition.

mmmm-comb.gifComputational Structural Biology VI: Molecular Magic, Machines and Motors
Jose Onuchic, Rice Univ., advocates the thesis that biological machines are fundamentally different from conventional heat engines or machines in the macroscopic world because biomolecules fluctuate via thermal motion and their dynamics is diffusive. One of the key features of biological machines is the conformational changes triggered by the thermal noise under weak environmental perturbation. Therefore one can explain how they behave using ideas borrowed from the energy landscape theory of protein folding and polymer dynamics. This new view allows us to envisage the dynamics of molecular motors from the structural perspective and it provides the means to make several quantitative predictions that can be tested by experiments. Dave Thirumalai, Univ. of Maryland will lecture on the cargo transporter machine Myosin V which takes 36 nm steps as it walks hand-over-hand on filamentous actin burning one ATP molecule in the process. Dave has created a theory, which quantitatively predicts all the experimental observables for this motor. The theory also allows him to understand the design principles of Myosin V. The Na+,K+-ATPase pump which is ubiquitous to all animal cells will be the subject of presentation by Benoit Roux, Univ. of Chicago. It resides in the plasma membrane and is a major player in keeping the physiological K+ and Na+ concentration gradient across the cell membrane in check. It works via a ping-pong mechanism making iterative conformational transitions between the inward-facing (E1) and outward-facing (E2) states. The E1 state binds three Na+ from the intracellular side and transports them to the extracellular cell matrix and the E2 state binds two K+ from the extracellular side to import them into the cell. Although the rough scheme of the pumping cycle is known, the transition mechanisms between the conformational states and why a given state preferentially binds K+ or Na+, both monovalent cations, is not understood. Using molecular dynamics simulation techniques, Benoit seeks to explain the origin of the ion binding specificity associated with different conformational states. By integrating experiments and molecular dynamics simulations, Huan-Xing Zhou, Florida State Univ., has developed functional mechanisms of ion channels, and refined and remodeled channel structures in different functional states. Huan-Xing has also explored the conformational space of the pore-lining helices in channels, and developed general rules for gating motions. Finally in this session of molecular magic, machines and motors, Moitrayee Bhattcharyya, Univ. of California, Berkeley, talks about neuronal signaling and synapses. Ca2+/Calmodulin dependent kinase II plays a pivotal role in neuronal signaling by mediating downstream phosphorylation, which results in enhancement of synaptic strength. One puzzling feature of this protein is activation mediated subunit exchange, the mechanisms of which are complex. Moitrayees presentation will focus on understanding the mechanistic underpinnings of this phenomenon using experimental and theoretical approaches.

shekhar-etc-comb.gifComputational Structural Biology VII: Solution & Ion Environment
It is all well known that the structural dynamics of biological macromolecules is driven by their solution and ionic environment. How about their structure as they move from the water surface to the bulk water? Shekhar Garde, RPI, here on the Renselear Hills on the Hudson, focuses on understanding the role of water in biological self-assembly and interactions, and specifically on the fundamental understanding of hydrophobic and ionic interactions in water. He will discuss new methods to characterize hydrophobicity of proteins and interfaces using molecular modeling and simulation methods. He will also highlight how assembly at soft aqueous interfaces differs from that in bulk water, and its implications on biology and materials science. David Case, Rutgers, will discuss what can be learned about nucleic acids from simulations of X-ray diffraction in crystals and from small- and wide-angle X-ray scattering in solution. Such studies emphasize the water and ion environment, including counts of excess ions and water around both single and double-stranded samples, and the relatively weak contacts that stabilize crystal lattices. Progress towards improved methods for crystallographic refinement will also be discussed. Juan Perez, Univ. Politecnicade Catalunya, Barcelona, Spain, takes up the landscape of peptides which are flexible molecules in solution due to a fast exchange between different conformations at room temperature. The conformational profile is a balance between the intrinsic conformational features of the sequence and the interaction with the solvent in such a way that the conformational landscape is modified depending on the solvent used. Juan provides insights into the behavior of peptides in solution through the analysis of molecular simulations, and the assessment of the bioactive conformation and the way ligands bind to a receptor.

protein-domain-comb.gifComputational Structural Biology VIII: Protein- Repeats, Swaps, Evolution
Oxana Galzitskaya, Institute of Protein Research, Moscow, Russia, will talk about homorepeats in proteomes. Eukaryotic and bacterial proteomes contain proteins bearing simple amino acid motifs including homorepeats consisting of a single multiple of repeat amino acid. Functional importance of many homorepeats remains unclear. The occurrence of various lengths of homorepeats (single-amino-acid tandem repeats) in proteins and the relationship of these tandem repeats to such properties as amyloidogenic or aggregation has been considered across 122 eukaryotic and bacterial proteomes. R. Sowdhamini, National Center for Biological Sciences, Bangalore, India, expounds on this aggregation in proteins, domain swaping and their inherent sequence characteristics as protein aggregation being a serious observation associated with neurodegenerative diseases. Banu Ozkan, Arizona State University, examines the classical view of one sequence-one structure-one function paradigm (the Pauling and Landsteiner proposal). This view is being now extended to a new dimension: an ensemble of conformations in equilibrium that can evolve new functions. Banu elaborates on the thesis that the protein conformational dynamics is the mechanism that evolution uses to alter the function. She will present her current results on the critical role of conformational dynamics and allostery on the evolution of three different protein families.

chair-comp-19th-correct.gifChairs of Sessions
Paul Agris, Univ. at Albany
David Beveridge, Wesleyan
Tom Bishop, Louisiana Tech Univesity






Samir Brahmachari, CSIR, Delhi, India
Angel Garcia, RPI
Indira Ghosh, JNU, Delhi, India





Maxim Frank-Kamenetskii, Boston Univ.
Tali Haran, Technion, Israel
Udo Heinemann, MDC, Berlin Germany






Neville Kallenbach, NYU
Luis Marky, Univ of Nebraska Medical School
Tony Maxwell, John Innes Centre, Norwich UK







Aditya Mittal, IIT-Delhi, India
Wilma Olson, Rutgers
Ned Seeman, NYU







Zippi Shakked, Weizmann Institute of Science, Rehovot, Israel
Vladimir Teif, DKFZ, Heidelberg, Germany
Edward Trifonov, Univ. of Haifa, Haifa, Israel





Tom Tullius, Boston Univ.
Saraswathi Vishveshwara, IISc, Bangalore, India
Mike Weiss, Case Western Reserv.






Victor Zhurkin, NIH



Speakers, Chairs and Guests
Agris, Paul, Univ. at Albany
Agudelo, Juliana, Univ. at Albany
Al-Hashimi, Hashim, Duke Univ.
Alvareda, Elena, UdelaR Univ., Montevideo, Uruguay
Aytenfisu, Asaminew H., Univ of Rochester Med. School
Amaro, Rommie, UCSD
Ashalatha Sreshty Mamidi, IISc, Bangalore, India
Auffinger, Pascal, IBMC-Starsboug, France
Bai, Yawen, NIH,
Balcioglu, Mustafa, Univ. at Albany
Bansal, Manju, Indian Institute of Science, Bangalore India
Barthwal, Ritu, IIT Roorkee, India
Bell, Janeen, Univ. at Albany
Belotserkovskii, Boris, Stanford University
Beveridge, David, Wesleyan
Bhattcharyya, Moitrayee, Univ. of California, Berkeley
Bishop, Tom, Louisiana Tech
Borkar, Aditi, Univ. of Cambridge, UK
Boyden, Ed, MIT
Brahmachari, Samir, CSIR, Delhi, India
Broude, Natalia, Boston Univ.
Brunelle, Erica, Univ. at Albany
Buening, Penny, Northeastern Univ.
Bukau, Bernd, Univ. of Heidelberg, Germany
Case, David, Rutgers Univ.
Chen, Alan, University at Albany
Chilka, Pallavi, IIT Gandhi Nagar India
Chiu, Tsu-Pei, Univ. of Southern California
Chung, Aram, RPI
Cleaver, James, Taylor & Francis, UK
Clubotaru, Mihai, IFIN-HH, Romania
Deeva, Anna, Siberian Federal Univ., Russia
Delaney, Sarah, Brown University
D'Ascenzo, Luigi, IBMC-Strabourg
D'Esposito, Rebecca, Univ. at Albany
Dietz,Hendrik, TUM, Germany
Di Felice, Rosa, Univ. of Southern California
Doyle, Shannon, NIH
Dupureur, Cynthia, Univ. of Missouri St Louis
Dutta, Mary, Tezpur University, India
Eisenstein, Miriam, Weizmann, Israel
Elbahnsi, Ahmad, University of Cergy, France
Endutkin, Anton, ICBFM SB RAS, Novosibirsk, Russia
Ermolenko, Dmitri, Univ. of Rochester
Fedorova, Olga, ICBFM SB RAS, Novosibirsk, Russia
Feig, Michael, Univ. of Michigan
Feld, Geoffrey, NIH/NIEHS
Fonseca Guerra, Celia, VU University, The Netherlands
Frank-Kamenetskii, Maxim, Boston Univ.
Frohlich, Kyla, Univ. at Albany
Galindo, Rodringo, Univ. of Utah
Galzitskaya, Oxana, Institute of Protein Research, Moscow, Russia
Gasper, Paul, Univ. at Albany
Garcia, Angel, RPI
Garde, Shekhar, RPI
Ge, Xiaoxia, CCNY.CUNY
George, Justin, Univ. at Albany
Ghosh, Indira, JNU, Delhi, India
Ghosh, Soma, Sastra Univ, Tanjavur, India (Oom Namashivaya!)
Greene, Eric, Columbia University
Gupta, Asmita, IISc., Bangalore, India
Gupta, Goutam, Los Alamos National Laboratory
Gutierrez, Cristina, Columbia Univ.
Halamek, Jan, Univ. at Albany
Hammel, Michal, LBL, Univ. of California, Berkeley
Han, Haixiang, Univ. at Albany
Han, Sue, Boston Univ.
Hall, David, Boston University
Hao, Yudong, New York University
Haran, Tali, Technion, Israel
Harris, Sarah, University of Leeds, UK
Haruehanroengra, Phensinee, Univ. at Alabany
Hayashi, Shigehiko, Kyoto Univ., Japan
He, Muhan, Univ. at Albany
Head-Gordon, Teresa, Univ. of California, Berkeley
Heinemann, Udo, MDC, Berlin Germany
Hema, Kanipakam, SVIMS University, Tirupati, India
Hernandez, Carina, New York University
Hingorani, Manju, National Science Foundation
Hizir, Mustafa Salih, Univ. at Albany
Hosur, M. V., TMC/ACTREC, Kharghar, India
Hosur, Ramakrishna V., TIFR, Mumbai, India
Huynh, Crystal, Univ. at Albany
Huynh, Loan, Univ. at Albany
Ivanov, Ivaylo, Georgia State Univ.
Kallenbach, Neville, NYU
Karplus, Martin, Harvard Univ., Nobel Laureate
Kaur, Divneet, CSIR-IGIB, delhi, India
Kayedkhordeh, Mohammad, Univ. of Rochesr
Khan, Taushif, JNU, Delhi, India
Khrameeva, Ekaterina, Skolkovo Institute, Moscow, Russia
Kompanichenko, Vladimir, RAS, Birobidzhan. Russia
Kononova, Olga, Univ of Mass
Koonin, Eugene, NIH
Kravats, Andrea, NIH
Kuhrova, Petra, Palacky Univ., CZ
Kumar, Padmapriya, IIT Roorkee, India
Kurita, Noriyuki, Toyohashi Univ. of Technology, Japan
Kuznetsov, Nikita, ICBFM SB RAS, Russia
Lachke, Salil, Univ. of Delaware
Lahri, Sudipta, Wesleyan
Lakhani, Bharat, Wesleyan
Lama, Dilrag, A-STAR, Singapore
Levi, mariana,, Northeastern Univ.
Levy, Koby, Weizmann Institute of Science, Israel
Li, Hong, Florida State Univ.
Li, Timothy, Northeastern Univ.
Li, Wen, Columbia Univ.
Liu, Shu-Qu, Yunnan University, Kunming, China
Lilley, David, Univ. of Dundee, UK
Liu, Fei, Yale Univ.
Liu, Juan, Wesleyan Univ.
Lomzov, Alexander, ICBFM SB RAS, Russia
Lukin, Mark, Stony Brook Univ.
Lynch, Janet, Univ. at Albany
Malde, Apesh, University of Queensland, Australia
Mailloux, Shay, Univ. at Albany
Makeev, Vsevolod, Vavilov Inst., RAS, Moscow, Russia
Marky, Luis, Univ of Nebraska Medical School
Martin, Craig T., Univ. of Mass., Amhearst
Marx, Kenneth A, Univ. of Mass
Maxwell, Tony, John Innes Centre, Norwich UK
Mehrotra, Prachi. IISc., Bangalore, India
Mienda, Bashir, Universiti Teknologi, Malaysia
Mink, Michael, Sirga Advanced Biopharma
Mitra, Chanchal, Univ. of Hyderabad, India
Mittal, Aditya, IIT-Delhi, India
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Mohan, Suma, Sastra Univ., Tanjavur, India (Oom Namashivaya!)
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Nangia, Shika, Syracuse Univ.
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Norouzi, Davood, NIH
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Olson, Wilma, Rutgers
Olusanya, O, Univ. of Benin, Nigeria
Onuchic, Jose, Rice Univ.
Ortiz, Julio, MPI Munich, Germany
Ozkan, Banu, Arizona State University
Pande, Vijay, Stanford
Pasquali, Samuela, Univ. of Paris, France
Patel, Saumya, Gujarat Univ., India
Patlolla, Reathap Reddy, IIT, Gandhi Nagar, India
Perez, Juan, Univ. Politecnicade Catalunya, Barcelona, Spain
Petr, Jurecka, Palacky Univ., CZ
Popov, Aleksandr, ICBFM SB RAS, Russia
Porrini, Massimiliano, Inserm, Bordeaux Univ., France
Post, Carol, Purdue Univ.
Pradhan, Dibyabhaba, ICMR, New Delhi, India
Pradeep, Natarajan, SVIMS University, Tirupati, India
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Prevost, Chantal, IBPC, Paris, France
Protopopova, Anna, SRI PCM, Moscow, Russia
Qian, Lulu, California Institute of Technology
Qu, Guosheny, Univ. at Albany
Rana, Muhit, Univ. at Albany
Ranganathan, Sri, Univ. at Albany
Rao, Satyanarayan, USC
Reiling, Calliste, Univ. of Nebraska Medical School
Robertson, Neil, Univ. at Albany
Rohs, Remo, Univ. of Southern California
Roux, Benoit, Univ. of Chicago
Rouzina, Ioulia, Univ. of Minnesota
Royzen, Maksim, University at Albany
Ruan, Zheng, Univ. of Georgia
Ryasik, Arten, ICB, RAS, Moscow, Russia
Sagendorf, Jared, Univ. of Southern Califonia
Sarachan, Kathryn, Univ. at Albany
Sayahi, Halimah, Univ. at Albany
Schueler-Furman, Ora, Hebrew University, Jerusalem, Israel
Scimeni, Annalisa, Univ. at Albany
Seeman, Ned, NYU
Seniya, Chandrabhan, Univ. of Warwick UK
Serwer, Philip, Univ of Texas HSC San Antonio
Setaro, Angelo, Univ. at Albany
Severinov, Konstantin, Rutgers Univ.
Sha, Roujie, New York University
Shakked, Zippi, Weizmann Institute of Science, Rehovot, Israel
Shanker, Sudhanshu, JNU, Delhi, India
Sharp, Phillip, MIT, Nobel Laureate
Shaytan, Alexey, NIH
Singh, Himanshu, AIIMS, Delhi, India
Singh, Poonam, Central Drug Institute, Lucknow, India
Singh, Sanjeev Kumar, Alagappa Univ., India
Skolnick, Jeffrey, Georgia Institute of Technology
Shub, David, Univ. at Albany
Sloma, Michael, Univ. of Rochester
Spasic, Aleksandar, Univ. of Rochester Med. School
Sorokin, Anatoly, Pushchino, Moscow, Russia
Sowdhamini, R., NCBS, Bangalore, India
Sponer, Jiri, Institute of Biophysics, Brno, Czech Republic
Srinivasan, N., Indian Institute of Science, Bangalore, India
Staroselets, Yaroslav, ICBFM, SB RAS, Novosibirsk, Russia
Su, Jenney, Univ. at Albany
Sun, Ming, Columbia Univ.
Sun, Hongying, Univ. of Rochestr
Swargam, Sandeep, SVIMS University, Tirupati, India
Tan, Zhen, Univ. of Rochestr
Tandon, Vibha, JNU, Delhi, India
Teif, Vladmir, DKFZ, Heidelberg, Germany
Thirumalai, Dave, Univ. of Maryland
Thorpe, Ian, Univ. of Maryland
Tjahjono, Daryono, Bandung Institute of Technology, Indonesia
Todd, Gabrielle, Univ. at Albany
Trifonov, Edward, Univ. of Haifa, Haifa, Israel
Tullius, Tom, Boston Univ.
Vajda, Sandor, Boston Univ.
Vangaveti, Sweta, Univ. at Albany
Vishveshwara, Saraswathi, IISc, Bangalore, India
Vologodskii, Alex, New York Univ.
Vyas, Pratic, Technion, Israel
Wang, Jun, Univ. at Albany
Wang, Rui, Univ. at Albany
Wang, Zhang, Univ. at Albany
Watson, Catherine, Univ. of Manchester, UK
Weiss, Michael, Case Western Reserve University
Whitford, Paul, Northeastern Univ.
Wiedenheft, Blake, Montana State University
Williams, Aled, Univ. of Manchester, UK
Williams, Mark, Northeastern University
Williams, Scott, NIH
Xie, Sunney, Harvard Univ.
Yang, Darren, Harvard
Yang, Lin, USC
Yigit, Mehmet, Univ. at Albany
Yin, Peng, Harvard University
Zgabova, Marie, Palacky Univ., CZ
Zhou, Huan-Xing, Florida State Univ.
Zhou, Zheng, Univ. at Albany
Zhurkin, Victor, NIH