The New York Structural Biology Discussion Group 11th Winter Meeting

Organizers

Iban Ubarretxena, PhD

Mount Sinai School of Medicine

John Hunt, PhD

Columbia University

David Jeruzalmi, PhD

City College of New York

David Jeruzalmi is a Professor of Biochemistry & Chemistry at City College of New York. He and his research group have a long standing interest in proteins that do interesting things with DNA. He obtained his PhD from Yale University for work with Professor Thomas Steitz. After completing post-Doctoral training at The Rockefeller University with Professor John Kuriyan and Professor Mike O’Donnell, he started his independent research career in the Department of Molecular and Cellular Biology at Harvard University. In 2012, Professor Jeruzalmi returned to New York City and moved his lab to City College of New York.

Sonya Dougal, PhD

The New York Academy of Sciences

Speakers

David Eliezer, PhD

Weill Cornell Medical College

Andras Fiser, PhD

Albert Einstein College of Medicine

Andras Fiser, PhD is a professor in the Department of Systems and Computational Biology, Department of Biochemistry and a faculty member of the Cancer Center at the Albert Einstein College of Medicine in New York, USA. Dr. Fiser’s research group is a computational structural biology laboratory with strong collaborations to a number of experimental labs in structural biology, neuroscience and immunology. The research themes of the lab include understanding the protein structural adaptation during evolution and its application in homology, ab initio, and hybrid modeling, and in protein design; exploring the molecular level mechanism of recognition among Immunoglobulin Superfamily receptor-ligand proteins at the immunological synapse; and modeling gene regulation in disease. Dr. Fiser is an author of over 100 peer-reviewed publications and 10 reviews and book chapters.

Ruben Gonzalez, PhD

Columbia University

Balasubramanian Harish, PhD

Princeton University

B. Harish has obtained an Integrated Master’s degree in Chemistry from IIT Bombay, Mumbai in India. He completed his PhD from Princeton in Prof. Jannette Carey’s lab. Harish is interested in the structure and dynamics of proteins. By using information from NMR and crystal structures as inputs for molecular dynamics simulations, his work has uncovered multiple conformations in dynamic systems, focusing on E. coli protein tryptophan repressor as a model system.

Ron Koder, PhD

City College of New York

Ronald Koder was named the James L. Peace chair in Physics at the City College of New York in 2012. He received his PhD in Biophysics at the Johns Hopkins University in 2000 where he investigated the structure and mechanism of the prodrug-activating flavoenzyme nitroreductase in the lab of Anne-Frances Miller. As a postdoctoral fellow in Biophysics at the University of Pennsylvania School of Medicine, he worked on the design and optimization of artificial oxygen transport proteins in the labs of P. Leslie Dutton and A. Joshua Wand.  Since starting at City College in 2006, he has focused on protein design projects in solar biofuels, enzymatic chemotherapies, and biological sensing.

Filippo Mancia, PhD

Columbia University

Filippo Mancia is an Assistant Professor in the Department of Physiology & Cellular Biophysics at Columbia University. He is a structural biologist with experience in x-ray crystallography and in production and characterization of membrane proteins for structural studies. He has also been a key member of the New York Consortium of Membrane Protein Structure (NYCOMPS), where he has played a pivotal role in the design, development, implementation and optimization of the high-throughput cloning and protein production platform for prokaryotic membrane proteins successfully functioning at the NYCOMPS center. The main research focus of his lab is on membrane protein – lipid interactions, both in terms of enzymes, which process lipid substrates, and of transporters, which mediate cellular uptake of lipidic substrates.

Smita Patel, PhD

Rutgers University

Smita Patel is a Professor in the Department of Biochemistry and Molecular Biology at the Robert Wood Johnson Medical School of the Rutgers University in New Jersey. Dr. Patel earned her PhD from Tufts University in Chemistry from David Walt's (co-founder of Illumina) lab, where fluorescent-based technology was developed for next generation sequencing. She conducted post-doctoral research at the Penn State University in Kenneth Johnson’s lab, world expert in rapid kinetic methods (President of KinTek Corp). Her current NIH funded research investigates the mechanisms of helicases and polymerases in DNA replication and transcription, and the role of RIG-I helicase as an innate immune receptor. The Patel lab studies how molecular motors move on nucleic acids using the energy from NTP hydrolysis. The unifying approach is quantitative characterization of enzymatic reactions using transient state kinetics, single molecule kinetics, computational kinetic modeling, and crystallography. Integration of structural and functional studies allows development of a complete mechanistic picture. The elegantly simple T7 enzymes allows the lab to probe the structure and mechanism of replisome with unprecedented temporal and spatial resolution, to develop new biophysical tools, and to propose new mechanisms that serve as a basis for our current studies of human mitochondrial DNA replication and transcription mechanisms.

Stefano Piana-Agostinetti, PhD

D.E. Shaw Research

Stefano Piana holds a BS in chemistry and a PhD in Condensed Matter Physics.  In his early post-doc research at ETH and EPFL (Switzerland), he had used QM, QM/MM and classical molecular dynamics simulations to study catalysis; subsequently, he held a research position at Curtin University in Perth (Australia) where he used simulations to study interfacial processes including crystal growth from solution.  Since 2007 he has been a research scientist at D.E. Shaw research where he develops methods and models for the simulation of proteins and nucleic acids. His most recent work has been focused on providing an accurate description of disordered and partially ordered states.

Betsy Speltz

Yale University

Betsy is a graduate student at Yale University in the laboratory of Dr. Lynne Regan. She plans to start a postdoctoral position in the summer at the University of Washington under Dr. Jesse Zalatan. Her research focuses on the rational and combinatorial design of orthogonal protein-protein interactions. She is also interested in using these interactions for many applications in biochemistry and synthetic biology. In her future work, she plans to use this knowledge to design more complex protein assemblies as a means to both understand complex biochemical processes and also to manipulate these processes for applications in biotechnology.

Corey Wilson, PhD

Yale University