Albany 2019: 20th Conversation - Details

category image Albany 2019
Conversation 20
June 11-15 2019
Adenine Press (2019)

Topics, Speakers, Chairs and Guests

Posted on March 28 2019

Arrival and Departures

For the Albany 2019 Conversation, the delegates arrive on Tuesday June 11th, that evening there is a wine and cheese reception; and poster presenters can put up their posters starting Tuesday June 11th afternoon.

The lectures start on June 12th Wednesday morning at 8:00 AM.
Lectures end by noon on Saturday June 15th.

You can start Departure on June 15th afternoon.

A Link to detailed schedule of lectures and events is posted below to download.

The 20th Conversation, June 11-15, 2019 will be held at the State University of New York, Albany, NY 12222 USA. Participants will arrive on Tuesday June 11th; there is a reception that evening. The scientific program starts Wednesday morning June 12th and will end after lunch on Saturday June 15th 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.

Ramaswamy H. Sarma, Department of Chemistry
State University of New York, Albany NY 12222 USA


Complete Logistics: Everything You Wanted to know: 20th Conversation
Detailed Daily Program of Speakers and Events
Abstracts: Requirements & Deadlines
Registration, Meals and Accommodation
Young Scientists Speaker Program
Financial Assistance
Book of Abstracts: Online

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

joachim-135x195.gifEvenings With Nobel Laureates
The Albany Conversation traditionally holds evening lectures in areas of fundamental interest to life sciences. For Albany 2019, the 20th Conversation, Nobel Laureate Joachim Frank , Professor, Columbia Univ., will deliver the keynote address on June 14, 2019 at 5;30 PM on the topic "The Structure and Dynamics of Biomolecules in Their Native States". Single-particle cryogenic electron microscopy (cryo-EM) has opened the door toward a characterization of structure and dynamics of molecules in their native, hydrated state, at resolutions matching those obtained by X-ray crystallography. The "resolution revolution" following the advent of commercial direct electron detectors in 2012 broadens the range of molecules for which atomic structures can be determined. One of the significant advantages of single-particle cryo-EM compared to X-ray crystallography stems from the fact that multiple, functionally relevant structures can be retrieved all at once from the same sample, even from a continuum of states. The impact of these new developments on Molecular Medicine is expected to be far-reaching.

em-comb.png Cryo-Electron Microscopy
At the Univ. of California, Los Angeles, Tamir Gonen’s laboratory studies the structures of membrane proteins that are important in maintaining homeostasis in the brain. Understanding structure (and hence function) requires scientists to build an atomic- resolution map of every atom in the protein of interest, that is, an atomic structural model of the protein of interest captured in various functional states. In 2013 Tamir unveiled the method MicroED, electron diffraction of microscopic crystals, and demonstrated that it was feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (cryoEM). The cryoEM is used in diffraction mode for structural analysis of proteins of interest using vanishingly small crystals that are a billion times smaller in volume than what is normally used for other structural biology methods like X-ray crystallography. Sriram Subramaniam of the National Institutes of Health, dwells on the recent breakthroughs in the field of cryoEM for determination of the structures of a variety of medically important macromolecular assemblies. The prospect that the determination of protein structures at atomic resolution will no longer be limited by size, or by the need for crystallization represents a significant and exciting horizon in structural biology. In his lecture, Sriram will discuss the broader context of the development of cryoEM methods for studying protein complexes, viruses and cells, and provide an overview of current progress and future directions as they relate to the development of improved therapeutic agents. Lynn Zechiedrich, Baylor College of Medicine, uses individual purified DNA minicircle topoisomers of a few hundred base pairs to understand how DNA supercoiling affects DNA structure and how the supercoiling-dependent structures affect DNA activities. Using a combination of cryo-electron microscopy and electron cryotomography, she and her research team discovered that DNA topoisomers of defined supercoiling adopt a reproducibly wide yet unique distribution of three-dimensional conformations, providing possible structural explanations for enzyme recognition. Ying Lu, Harvard Medical School, uses cryoEM to study conformational diversity of the proteasome. The 26S proteasome mediates ubiquitin-dependent protein degradation in all eukaryotic species. Lu and his associates aim to understand how ubiquitylated substrates are recognized and processively degraded by the proteasome. Modern cryoEM technology and classification algorithms identify multiple conformations of the proteasomes, and provide important insights into these questions. Using single particle cryo-electron microscopy, Moran Shalev-Benami, Weizmann Institute of Science, and her colleagues have unveiled the near atomic resolution structures of several challenging macromolecular complexes involved in the function and development of the central nervous system along with large ribosomal assemblies derived from eukaryotic pathogens. In her talk, Moran will describe a few recent examples of these studies highlighting the strength of cryoEM for the mechanistic understanding of macromolecules structure and function.

pro-dy-comb.pngProtein Dynamics in the Living Cytoplasm
In the last Conversation, the 19th, Nobel Laureate Martin Karplus dwelled on the importance of protein motions to understand their function, and traced his discovery of MD simulations in 1977 to fathom protein dynamics within a single molecule. Now we are in a position to talk about the motion and foldings within protein clusters in the crowded confinement of a living cell. Evan T. Powers, The Scripps Research Institute, will describe his research, carried out collaboratively with Lila Gierasch, Univ. of Massachusetts Amherst, combining computational and experimental approaches to understand how the protein homeostasis network of the E. coli cytoplasm maintains the health of its proteome. This work has revealed how the coordinated action of this network facilitates the folding of proteins of different biophysical properties and minimizes protein aggregation. Gary Pielak, Univ. of North Carolina, Chapel Hill, takes up the question of protein biophysics in living cells employing innovative methods that have been developed to monitor protein stability in living cells and under physiologically-relevant conditions in vitro. Through this work, we now know that protein stability is not the same in cells as it is in buffer, and recent efforts are leading to similar conclusions about the stability of protein complexes. Gary will discuss the origin of these effects and how classical theory needs to be modified to account for them. Martin Gruebele, University of Illinois, will describe how the quinary interactions, sticking and crowding affect protein folding and protein-protein interactions in the cytoplasm. Trends from conflicting pressures of sticking and crowding will be unraveled by comparing in-cell with in vitro experiments, and new techniques to examine protein-protein interaction dynamics and thermodynamics inside cells reveal important differences from in vitro assays. Systems range from metabolic enzymes, to loose protein clusters, to the spliceosome. Yuji Sugita, RIKEN, Japan, discusses protein structure-dynamics-function relationships in cellular environments investigated by MD simulations. It has been shown that non-specific interaction play important roles on protein stability, diffusion and protein-ligand interactions in macromolecular crowding environments.

idp-comb.pngIntrinsically Disordered Proteins: Evolution and Function
Carl Woese, Francis Crick, and many others have suggested that the genetic code evolved from a simpler precursor having far fewer amino acids. From the analysis of the work of many researchers, Edward Trifonov developed a consensus temporal order of addition of amino acids to the original genetic code. The analysis of Trifonov’s original amino acids and his temporal order of addition by Keith Dunker and his associates at Indiana Univ, School of Medicine, suggests that the first proteins on earth were intrinsically disordered and that the addition of the later amino acids enabled the formation of structured proteins, especially enzymes. Laboratory experiments provide support for these ideas. Daniel Jarosz, Stanford, remembers the past through the new form of protein-based inheritance. In his talk, Daniel will present an emerging role for intrinsically disordered proteins in promoting the emergence and inheritance of biological traits. He will also discuss the impact of this mode of inheritance on development, disease, and evolution. Sara Bondos, Texas A & M Univ., discusses regulation of protein function via structure-disorder interactions, which in the the Hox transcription factor family enables similar regions of the developing organism to acquire unique fates.  Specific intramolecular interactions between the intrinsically disordered regions of Hox proteins and their highly conserved DNA binding homeodomains diversify the function within this critical protein family. Nicolas Fawzi, Brown University, leads a team using NMR spectroscopy, molecular simulation, microscopy, and cell assays to probe disordered protein domain assembly and function. Disordered domains of RNA binding proteins aggregate in several neurodegenerative diseases and mediate formation of functional, liquid, membraneless organelles. Nick's group probes the structure of these proteins (including TDP-43, FUS, hnRNPA2) within in vitro models of these organelles, the mechanistic structural changes due to disease-causing mutations, the ability of post-translational modification to alter assembly. Elisar Barbar, Oregon State University, uses a combination of biophysical methods, structural analysis by NMR and single particle electron microscopy, and cellular transcription assays, to develop a model that proposes a concerted role of intrinsic disorder and multivalency in regulating LC8 transcription. Barbar discusses how transcription factor ASCIZ binds to multiple LC8 dimers simultaneously in both a positively and negatively cooperative fashion, enabling the formation of a dynamic equilibrium of complexes, of which low occupancy intermediates are highly populated. These observations support a novel model of autoregulation, whereby ASCIZ engages in a dynamic equilibrium of multivalent interactions that tune the level of ASCIZ transcriptional activity. Zachary Wood, University of Georgia, studies the biophysics of allostery. His most recent work shows that an intrinsically disordered (ID) peptide segment can alter the energy landscape of a folded protein to favor an allosteric response. This effect does not depend on the sequence or charge of the ID segment. Using a combination of transient state kinetics, hydrogen-deuterium exchange mass spectrometry, thermal denaturation studies, computer simulation and crystal structure analysis, they showed that the shift in the conformational ensemble originates from the entropic cost of attaching an ID segment to a folded protein. Thus, the persistence of intrinsic disorder in the proteome may reflect the evolution of low complexity structural elements that can harvest entropy to tune protein function.

chromatin-1-comb.png Rules of Life; and Session-I: Nucleosomes, Chromatin and Higher Order Chromosome Organization - I
Manju Hingorani, Professor of Molecular Biology and Biochemistry, Wesleyan Univ., and Program Director of Molecular and Cellular Biosciences at NSF, will speak on Understanding the Rules of Life, which is one of NSF’s ten big ideas that will be supported in the coming years. The Conversation will provide quiet rooms for continued dialog after Manju’s lecture. We hope that this will be very helpful to many of the young scientists such as doctoral students, post-docs and assistant professors, in addition to the seasoned researchers.
Positioning of DNA in nucleosomes can modulate DNA accessibility, which affects binding of histone modifiers and chromatin remodelers. The molecular modeling of variant nucleosomes is a challenging task since it requires modeling of a variant histone octamer and finding the correct rotational and translational positioning of DNA with respect to the histone octamer. Anna Panchenko, NIH, dwells on integrative approaches to determine the DNA positioning in nucleosomes at single base-pair resolution and to model variant nucleosomes by combining experimental data with computational techniques. Vlad Cojocaru, MPI, Munster, Germany, will present his recent efforts to explore how nucleosome dynamics modulate the binding of linker histones and transcription factors to nucleosomes. First, Vlad will show how a combination of Brownian and molecular dynamics simulations revealed an ensemble of geometries for the complex between the nucleosome core particle and linker histones. Second, he will reveal the structural basis for the binding of the pioneer transcription factor Oct4 to nucleosomes. Oct4 is a master regulator of stem cell pluripotency and is critical for cell fate transitions such as the induction of pluripotency in somatic cells. Lois Pollack, Cornell Univ., will discuss new methods to investigate the dynamic structures of DNA within nucleosome core particles. She will describe studies that examine the role of histone variants or DNA sequence on nucleosome conformation, and others that exploit triggers of conformational change ranging from the biophysical (salt) to the biological (chromatin remodelers).Beat Fierz, Ecole Polytechnique Fédérale de Lausanne, will describe his latest research to unravel how multivalent effector proteins control the structure and function of post-translationally modified chromatin. This research is based on protein chemistry methods to synthesize modified chromatin fibers, combined with single-molecule methods to directly detect chromatin conformational dynamics. He will further demonstrate mechanisms of how structural motions in chromatin fibers enable invasion of transcription factors to enable gene transcription.

chromosome-comb.pngNucleosomes, Chromatin and Higher Order Chromosome Organization - II
Under the title “The 'Self-stirred’ Genome: Bulk and Surface dynamics of the Chromatin Globule”, Alexandra Zidovska, New York Univ., uses approaches from soft matter physics and polymer physics to study chromatin, the functional form of DNA in cells, particularly its organization and dynamics in eukaryotic cell nuclei. Recently, she developed an approach, displacement correlation spectroscopy (DCS) based on time-resolved image correlation analysis, to map chromatin dynamics simultaneously across the whole nucleus in cultured human cells. This is unprecedented, as previously only movement of single genes or foci was tracked. Using DCS she discovered that chromatin dynamics is coherent at the scale of microns and seconds, which paints a new physical picture of chromatin organization, and opens new avenues in chromatin research. Alexandra will discuss the non-equilibrium chromatin dynamics, both in bulk and at the surface of the chromatin globule. Leonid Mirny is working to understand the human genome in 3D with his team at MIT in collaboration with the Dekker Lab at Univ. of Massachusetts Medical School. Using new data uncovered via Chromosome Conformation Capture (Hi-C) technology and computer simulations, the collaborators explore how the genome is organized inside a cell. Xiaowei Zhuang, Harvard Univ., will talk on in situ chromosome and transcriptome imaging in single cells. Alexander Grosberg, New York Univ., is looking at possible polymer models to study the genome. Genome folding is a complex multifaceted problem.  But one way or another, the chromatin fiber is a long polymer, and so some polymer models are bound to be necessary to understand the genome.  What are these useful models may still be an open question, but one still can discuss some of the candidates. 

r-loops-comb.pngR Loops and Genome Dynamics
Recent results on mechanisms of R-loop induced chromosome fragility, and implications for genome instability and repeat expansion diseases will be presented by Catherine Freudenreich of Tufts Univ. Stable R-loops have been shown to form at G-rich repeats and induce chromosome breaks and repeat length changes. At the human Ig locus in mammalian B cells the breaks are caused by the RAG endonuclease. However, the mechanisms causing R-loop dependent breaks and repeat instability in other types of repeat sequences are less well understood. Catherine’s lab recently identified cytosine deamination followed by base excision repair (BER) as one such mechanism, with an additional (and less understood) role for the Mlh1-Mlh3 nuclease. Lee Zou, Harvard Medical School, will talk about how aberrant R loop accumulation occurs in cancer cells, and how this specific vulnerability of cancer cells can be exploited in targeted therapy. Furthermore, Lee will discuss the molecular pathways that sense and respond to R loops in the human genome. Jacqueline Barlow, Univ. California, Davis, will discuss the causes and consequences of replication stress-induced fragile site breakage. Persistent R loops can act as barriers to replication fork progression, leading to replication fork collapse and DNA break formation. Dr. Barlow will discuss the impact of defective R loop removal on fragile site stability and the formation of gross chromosome rearrangements. Andrei Kuzminov, University of Illinois at Urbana-Champaign, will consider possible types of R-lesions (the DNA lesions that have integral RNA parts) on the basis of experiments with mutants deficient in removal of both R-loops and single ribonucleotides from DNA. Diverse evidence points to the critical importance of R-loops for R-lesion formation, but could R-loops be R-lesions themselves? Andrei will argue that, in contrast to R-loops, in which RNA invades homologous DNA duplex without forming covalent bonds, R-lesions have ribonucleotides integrated into DNA strands.

segence-comb.pngBiopolymer Sequence: Detection, Structural Dynamics and Evolution
Nanopore sequencing is a single molecule characterization method, allowing direct sequencing of stretches ranging from kilobases to even megabase long reads.  Unlike traditional sequencing-by-synthesis methods, it can distinguish covalently modified nucleotides directly through their modulation of the electrolytic current. Using this detection, Winston Timp and his associates at Johns Hopkins Univ., have explored endogenously modified bases and performed exogenous labeling to characterize the epigenome and transcriptome. Aditya Mittal, IIT, Delhi, India, presents stoichiometric constraints in protein sequences. About a decade ago, rigorous analyses of structural data of thousands of naturally occurring folded proteins yielded a surprising “margin of life” for stoichiometric composition, i.e. percentage occurrence of individual amino acids, of protein sequences. While the earlier work was based on the largest structural dataset at that time, in this work further explorations on compositional constraints for known protein sequences are presented on the largest dataset analyzed till date. The relationships between peptide-bonded pairs and triplets of amino acids, in about half-a-million protein sequences, with their various physico-chemical properties and individual proportions (of the peptide-bonded pairs and triplets) are explored. While having profound evolutionary implications towards our insights into occurrence of naturally occurring protein sequences, the results discussed also promise to serve as guide for creating stable and structurally controlled and/or “disordered” designer proteins.

npc-comb.pngNuclear Pore Complex- Transport between the Nucleus and the Cytoplasm
The nuclear pore complex (NPC) is a biological "nanomachine" that controls transport between the nucleus and the cytoplasm in eukaryotic cells. Its architecture has inspired the design of bio-mimetic nanochannels capable of molecular recognition and selective transport. Anton Zilman, Univ. of Toronto, will describe the physical underpinnings of the selective permeability and the gating strategies of the NPC and polymer-functionalized nano-channels. Tijana Jovanovic-Talisman, Beckman Research Institute, City of Hope, develops and utilizes quantitative super-resolution microscopy methods to probe the mechanism of nucleocytoplasmic transport. She employs purified NPC components and isolated nuclei to elucidate binding and diffusion of proteins that drive the transport. Roderick Y.H. Lim, Biozentrum and the Swiss Nanoscience Institute. University of Basel, Switzerland, is interested in nucleocytoplasmic transport (NCT) control. He wants to understand how nuclear pore complexes, together with the soluble NCT machinery (i.e., karyopherins; specifically importins and exportins) selectively regulate the rapid bidirectional traffic of molecular cargoes to and from the cell nucleus. Roderick’s interdisciplinary approach combines structural, biophysical and cellular experimentation with biomimetic validation to address this fundamentally unresolved question. Surprisingly, his recent findings suggest that karyopherins are key to controlling NPC function. as opposed to the accepted view that NPCs control karyopherin transport. Rob Coalson, Univ of Pittsburgh, provides a statistical mechanical model of transport receptor binding in the nuclear pore complex. Quasi-analytical statistical mechanical models are used to predict the morphology of a polymer brush in a solution filled with nanoparticles that attract monomers of the polymer.  These model calculations are calibrated via coarse-grained molecular dynamics simulations.  The models are then used to analyze interactions between natively unfolded protein filaments that line the nuclear pore complex and globular receptor proteins that ferry large biomolecular cargos through it.

antibio-comb.pngThe Molecular Basis of Antibiotic Action and Resistance
Under the title "RNA Polymerase: the Molecular Machine of Transcription", Richard H. Ebright, Rutgers Univ., will describe structural (cryo-EM, X-ray crystallography) and single-molecule (nanopore tweezers, magnetic tweezers) studies of transcription initiation, elongation, termination, and regulation. Anthony Maxwell, John Innes Centre, Norwich, UK, will discuss the DNA topoisomerases: enzymes that control the topology of DNA in all cells, and which have become key targets for antibacterial chemotherapy. Detailed structural and mechanistic understanding of these enzymes has enabled elucidation of the mode of action of known antibiotics and the development of new molecules with potential as new clinical antibacterial agents. Susan M. Rosenberg, Baylor College of Medicine, dwells on how bacteria and cancer cells regulate mutagenesis and their ability to evolve? This presentation will focus on the molecular mechanism of stress-inducible mutagenic DNA break repair in E. coli as a model for stress-inducible mutagenesis that propels infectious disease, antibiotic resistance, and other evolution. Susan considers its regulation by stress responses, demonstrates its formation of mutation hotspots near DNA breaks, and the discovery of a large gene network that underlies mutagenic break repair, most of which functions in stress sensing and signaling. She also will show that mutagenesis is induced by the antibiotic ciprofloxacin, causing resistance to other antibiotics, and demonstrate the stress-response dependent mutagenesis mechanism. Regulation of mutagenesis in time and genomic space may accelerate evolution including evolution of pathogens, cancers, and drug resistance. Chris Dowson, Univ of Warwick, UK characterizes the molecular genetic attributes which are responsible for the pathogenic properties and antibiotic resistance of a diverse range of human and animal pathogens, to understand their evolution and to open up novel therapeutic strategies. He will dwell on mechanistic and structural understanding of bacterial cell walls to combat antimicrobial resistance. Helen I. Zgurskaya, Univ. of Oklahoma, dwells on kinetic and molecular determinants of antibiotic permeation barriers. The permeability barrier of Gram-negative cell envelopes is the major obstacle in the discovery and development of new antibiotics. In Gram-negative bacteria, these difficulties are exacerbated by the synergistic interaction between two biochemically distinct phenomena, the low permeability of the outer membrane and active multidrug efflux. Helen's lab has developed an approach to separate the contributions of the two mechanisms in the activities of antibiotics and applied it in the discovery of efflux pump inhibitors and analyses of structure-activity relationships for active efflux and outer membrane permeation in different Gram-negative pathogens. Nagasuma Chandra, Indian Institute of Science, Bangalore, India, will present an interactive modeling and a novel formulation of the problem of drug resistance. A genome-scale protein-protein interaction network in Mycobacterium tuberculosis is reconstructed, which has enabled a novel formulation of the problem of drug resistance, allowing Nagasuma to identify possible routes through which drug resistance could emerge in bacteria. This is a first study of its kind in the literature and the analysis provides several testable hypotheses. Jim Spencer, Univ. of Bristol, UK, will consider how beta-lactamase enzymes enable bacterial pathogens to degrade beta-lactams, still the most widely prescribed class of antibiotics. He will describe the multiple mechanisms by which different types of beta-lactamase degrade the various beta-lactam classes and how his group and collaborators are combining experimental and computational approaches to understanding these; as well as how recent progress is extending the utility of beta-lactamase inhibitors in the face of continued emergence and evolution of beta-lactamases and their variants.

drug-comb.pngDrugs: Design and Discovery
Sichuan Xu, Yunnan Univ., Kunming, China, will talk on the subject of Dopamine Channels. The talk will consist of: (1) how to find dopamine molecular channels within dopamine receptors and (2) how to find the drugs to treat "Parkinson's Disease" based on the dopamine molecular channels. Georges Belfort, Rensselaer Polytechnic Institute, will provide evidence for the N-Terminal Hypothesis for Alzheimer’s Disease. Although the amyloid (abeta peptide, Aβ) hypothesis is 25 years old, is the dominant model of Alzheimer’s Disease (AD) pathogenesis, and currently guides the development of potential treatments, it is still controversial. From a review of the recent literature including aggregation kinetics and structural morphology, Aβ clearance, molecular simulations, long term potentiation measurements with inhibition binding, and the binding of a commercial monoclonal antibody, aducanumab, we hypothesize that the N-terminal domains of neurotoxic Aβ oligomers are implicated in causing the disease. Barry Honig, Columbia University, will discuss the application of three-dimensional protein structure to predict protein-protein and protein-ligand structures on a genome-wide scale. Protein networks and signaling pathways are constructed and described in structural terms yielding multiple potential targets for drug intervention. Drug leads are generated via structure alignment of target proteins with proteins that form a complex with small molecules where the structure is known. An integrated software package allows for the multi-directional navigation between small molecules, proteins and networks/pathways using large genomic, structural and chemical databases.Gennady Verkhivker, Chapman Univ., discusses computational modeling and engineering of allosteric regulatory mechanisms in signaling proteins: integration of multiscale simulations, network biology and machine learning. A systems-based drug discovery approach is introduced that incorporates chemical biology and network modeling for designing allosteric modulators of protein kinases and molecular chaperones. Celia Schiffer, Univ. of Massachusetts Medical School, Worcester, combines a variety of experimental and computational chemical and structural biology techniques to understand the molecular basis of drug resistance. Drug resistance occurs through evolution, limiting the effectiveness of many of our most potent drugs and impacting the lives of millions. This often happens under the selective pressure of therapy in infectious diseases and cancer due to their rapid evolution. Celia's new structure- based paradigm of drug design minimizes chances of resistance, realizing that disrupting the drug target’s activity is necessary but not sufficient for developing a robust drug that avoids resistance. Indira Ghosh, JNU, Delhi, India, addresses: the entrapment of flow of substrate to diversion pathway as a strategy to combat persistent tuberculosis. Target-based drug discovery is a dire necessity to address resistance to already known drugs in tuberculosis. Indira's in silico work deals with the identification of a novel target interaction using metabolic control analysis in shunt pathway and understanding the mechanism of protein-protein interactions to find the inhibitor for disruption of specific interactions.Richard Friesner, Columbia Univ., who has pioneered free energy simulations for drug discovery, will talk on the development and application of novel methods for ab initio electronic structure calculations, including mixed quantum mechanics/molecular mechanics (QM/MM) methods.Tali E. Haran, Technion, Haifa, Israel, will speak on the expanded repertoire of mutant p53 REs and the mechanism of gain of function in cancer. Currently, several clinical trials with p53 targeting compounds are ongoing. However, the large diversity of the p53 mutation space, necessitates an in depth knowledge of the functional impact of each cancer patient’s individual mutation. Tali will discuss her recent studies on the sequence-specificity of p53 gain-of-function mutants.

nano-comb.pngDNA: Nanotechnology
Ned Seeman, NYU, who discovered DNA nanotechnology while he was at Univ. at Albany, will chair this session and give the opening lecture on “ DNA is Not Merely the Secret of Life: Semantomorphic Chemistry in Advanced Materials”.  Björn Högberg, of the Karolinska Institute, Stockholm, Sweden, will talk about rendering polyhedral in 3D on the nanoscale using a new approach to DNA origami and how these structures can be used in experiments to decipher how nanoscale distances influence cell signaling. By using DNA origami as a platform to display other molecules, his lab is investigating how nanoscale spatial effects influence a number of different biological phenomena. Hao Yan, Arizona State Univ., addresses designer DNA architectures for programmable self-assembly. The central task of nanotechnology is to control motions and organize matter with nanometer precision.  In this talk, Hao will present his efforts in using DNA as an information-coding polymer to program and construct DNA nano-architectures with complex geometrical features. Use of designer DNA architectures as molecular sensor, actuator and scaffolds will also be discussed. Yonggang Ke, Emory Univ., will talk about a new reconfigurable DNA nanostructure design that demonstrates information propagation within the artificial molecular network, recent progress in constructing gigadalton DNA nanostructures with complex shapes, and applications in functional nanomaterials assembly.

big-data-comb.pngBig Data, Machine and Deep Learning
Gustavo Caetano-Anolles, Univ of Illinois, proposes a ‘double tale’ of accretion to rationalize the structure of biological networks. Evolutionary genomics and network biology support a ‘double tale’ of structural module creation. The theory explains the evolution of biological networks at various time frames and levels of complexity, including the emergence of metabolic networks, the rise and diversification of the proteome, the evolution of the ribosome, and the change in protein loop dynamics. Remarkably, the theory was already recounted in a ~2,000 year-old papyrus from the ancient city of Panopolis in Upper Egypt that is archived at the Univ. of Strasbourg National Library.S. Gnanakaran, Los Alamos National Laboratory, will discuss membranes and machine learning: how to optimize the transport of signals and drugs across membranes. He will discuss two examples where they have used machine learning on molecular dynamics simulations and experimental data to address the complexity of cell membranes that presents a formidable challenge to conventional biophysical approaches. Dima Kozakov, Stony Brook University, will present integrated approach, combining accurate molecular docking and powerful machine learning techniques for image recognition in application to the prediction of peptide binding to Major Histocompatibility Complex (MHC) proteins. Such computational tool is a critical component in emerging personalized medicine approaches, such as neoantigen vaccines for cancer immunotherapy. Julie Mitchell, Oak Ridge National Lab., will present several projects utilizing machine learning in predictive models for protein structure and interaction. A key benefit of such models is the ability to make predictions about energetic effects using descriptors that are not strictly physicochemical, such as shape complementary, packing density or surface area.

chair-comp-20th.pngChairs of Sessions
Manju Bansal, IISc, Bangalore, India
David Beveridge, Wesleyan Univ.
Tom Bishop, Louisiana Tech Univ.

David Cowburn, Albert Einstein
Keith Dunker, Indiana Univ. Schl of Medicine

Maxim Frank-Kamenetskii, Boston Univ.
Angel Garcia, LANL
Sarah Harris, Leeds Univ., UK

B. Jayaram, IIT Delhi, India
Luis Marky, Univ. of Nebraska Medical School
Sergei Mirkin, Tufts Univ.

Aditya Mittal, IIT, Delhi, India
Wilma Olson, Rutgers Univ.
Juan Perez, Univ. Politecnicade Catalunya, Barcelona, Spain

Ned Seeman, New York Univ.
Zippi Shakked, Weizmann Institute of Science, Rehovot, Israel

Yuji Sujita, RIKEN, Japan
Tom Tullius, Boston Univ.
Vladmir Uversky, Univ. of South Florida

Ji Hua Wang, Dezhou Univ., China
Meni Wanunu, Northeastern Univ.
Victor Zhurkin, NIH

Vsevolod Makeev, Vavilov Institute for Genetics, Moscow, Russia

Speakers, Chairs and Guests

Afek, Ariel, Duke Univ.
Alvareda Migliano, Elena, Univ. de la Republica, Salto, Uruguay
Arora, Richa, Univ. of delhi, Delhi, India
Aspuru-Guzik, Alan, Univ. of Toronto, Canada
Awan, Waqas, Univ at Albany
Bai, Zhixue, Univ at Albany
Banas, Pavel, Palacky Univ. CZ
Bansal, Manju, IISc, Bangalore, India
Bandyopadhyay, Debashree, Birla Ins.,Hyderabad, India
Barbar, Elisa, Oregon State Univ.
Barlow, Jacqueline, UC Davis
Beveridge, David, Wesleyan Univ.
Bhat, Ruchika, IIT, Delhi, India
Bilodeau, Camille, RPI
Bishop, Tom, Louisiana Tech Univ.
Bondos, Sarah E, Texas A & M
Caetano-Anolles, Gustavo, Univ. of Illinois U-C
Case, Brandon, Wesleyan Univ.
Chandra, Nagasuma, IISc, Bangalore, India
Chen, Alan, Univ at Albany
Chiranjeevi, Pasala, SVIMS Univ., Thirupathi, India
Chiu, Tus-Pei, Univ of Southern California, Los Angelis
Chu, Betty, Univ of Maryland, College Park
Coalson, Rob, Univ. of Pittsburg
Cojocaru, Vlad, MPI, Muenster, Germany
Cowburn, David, Albert Einstein
Das, Sanchaita, UC Berkeley
Degtjarik, Oksana, Weizmann Inst., Israel
Dowson, Christopher, Univ of Warwick, UK
Dunker, Keith Indiana Univ. Med. Schl.
Ebright, Richard, Rutgers Univ.
Ebrahimi, Parisa, Univ at Albany
Fang, Rui, Harvard Univ.
Fawzi, Nicolas Lux, Brown Univ.
Feig, Michael, Michgan State Univ.
Fierz, Beat, EPFL, Lausanne, Switzerland
Fonseca Guerra,Celia, VU University, The Netherlands
Frank-Kamenetskii, Maxim, Boston Univ.
Frank, Joachim, Columbia Univ. Nobel Laureate
Freudenreich, Catherine, Tufts Univ.
Friesner, Richard, Columbia Univ.
Garcia, Angel, LANL
Ghosh, Indira, JNU, Delhi, India
Gierasch,Lila, Univ. of Mass, Amherst
Goldman, Yale, Univ. of Pennsylvania
Golyshev, Victor, ICBFM SB RAS, Russia
Gonen, Tamir, UCLA
Gregurick Susan, NIH
Grosberg, Alexander, NYU
Gruebele, Martin, Univ of Illinois U-C
Haran, Tali, Technion, Israel
Harris, Sarah, Leeds UK
Haruehanroengra, Phensinee, Univ at Albany
He, Muhan, Univ at Albany
Hingorani, Manju, Wesleyan and NSF
Högberg, Björn, Karolinska Institute, Sweden
Honig, Barry, Columbia Univ.
Ignatoc, Mikhail. Stonybrook Univ.
Issar, Upasana, Univ of Delhi, Delhi, India
Jarosz, Daniel, Stanford Univ.
Jayaram, B., IIT Delhi India
Jecrosin, Anne, Univ of Mass Med Schl, Worcester
Jovanovic-Talisman, Tijana, City of Hope
Jurecka, Petr, Palacky Univ, CZ
Kaur, Simi, Univ at Albany
Ke, Yonggang, Emory Univ.
Krishnan, Yamuna, Univ of Chicago
Kührova, Petra, Palacky Univ. CZ
Kuzminov, Andrei, Univ of Illinois U-C
Lim, Roderick, Univ Basel, Switzerland
Locbaum, Gordon, Univ of Mass Med School
Lomzov, Alexander, ICBFM SB RAS, Russia
Lu, Ying, Harvard Univ.
Luan, Bai, Harvard medical School
MacArdle, Siobhan, CALTECH
Mathivanan, Johnsi, Univ at Albany
Mathulatha, Ravina, SVIMS Univ., Thirupathi, India
Marcos Robaina, Juan, Salto, Uruguay
Makeev, Vsevolod,Vavilov Inst. for Genetics, Moscow, Russia
Marky, Luis, Univ. of Nebraska Med Schl
Mathulatha, Ravina, SVIMS Univ., Thirupathi, India
Maxwell, Anthony, John Innes Centre, Norwich, UK
MacArdle, Siobhan, CALTECH
McTiernan, Jack, UC Davis
Mirkin, Sergei, Tufts Univ.
Mirny, Leonid, MIT
Mitchell, Julie. ORNL
Mittal,Aditya, IIT Delhi, India
Mondal, Anupam, JNU, New Delhi, India
Mothay, Dipti, Jain Univ., Bangalore, India
Myers, Christopher, Univ at Albany
Niv, Masha, HUJ, Israel
Olson, Wilma, Rutgers Univ.
Padhorny, Dzmitry, Stonybrook Univ.
Panchenko, Anna, NIH
Perez, Juan, Univ. Politecnicade Catalunya, Barcelona, Spain
Pielak, Gary, Univ. of North Carolina Chapel Hill
Pollack, Lois, Cornell Univ., Ithaca
Powers, Evan, The Scripps Research Institute
Premo, Aaron, Univ at Albany
Rozenberg, Haim, Weizmann Institute, Israel
Rosenberg, Susan, Baylor College of Medicine
Roukes, Michael, Caltech
Roy, Kunal, Jadvapur Univ., India
Schiffer, Celia, Univ. of Mass. Med Schl, Worcester
Seeman, Ned, NYU
Sengupta, Jayati, CSIR, IICB, Kolkata, India
Serindag, Kendar, Wesleyan Uni.
Shakked, Zippi, Weizmann Institute, Rehovot, Israel
Shalev-Benami, Moran, Weizmann Institute, Rehovot, Israel
Singh, Sanjeev, Algappa Univ, India
Spenser, Jim, Univ. Bristol, UK
Sponer, Jiri, Institute of Biophysics, Brno, Czech Republic
Stokes, Jennifer, Taylor & Francis, Oxford UK
Subramaniam, Sriram, NIH
Sudheer Kumar, Katari, SVIMS Univ., Thrupathi, India
Sujita, Yuji, RIKEN, Japan
Sudheer Kumar, Katari, SVIMS Univ., Thrupathi, India
Timp, Winston, Johns Hopkins Univ.
Tullius, Tom, Boston Univ.
Uversky, Vladmir, USF
Verkhivker, Gennady, Chapman University
Wang,JiHua, Dezhou Univ., China
Wang, Xinyu, NYU
Wanunu,Meni, Northeastern, Univ.
Wei, Guowei, Michigan State Univ.
Wood, Zachary, Univ of Georgia, Atlanta
Yan, Hao, Arizona State Univ.
Yuguang, Mu, Nanyang Technological Univ., Singapore
Zechiedrich, Lynn, Baylor College of Medicine
Zgarbova, Marie, Palacky Univ, CZ
Zgurskaya, Helen, Univ. of Oklahoma
Zhong, Aoshu, Caltech
Zhuang, Xiaowei, Harvard
Zhurkin, Victor, NIH
Zidovska, Alexandra, NYU
Zilman,Anton, Univ of Toronto
Zou, Lee, Harvard Med Schl