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5th Annual Advances in Biomolecular Engineering Symposium

5th Annual Advances in Biomolecular Engineering Symposium

Friday, April 27, 2012

The New York Academy of Sciences

Presented By


Biomolecular Engineering aims to predictably design and engineer biomolecules or bio-inspired molecules for therapeutics, biocatalysts, protein-based biosensors, and other novel functions. The Fifth Annual Advances in Biomolecular Engineering Symposium will emphasize the design of oligosaccharides and proteins for materials and energy applications.

Specifically the symposium will focus on the following areas: (1) synthetic and biosynthetic methods to prepare oligosaccharides, and the role of these macromolecules in materials science and glycobiology, (2) rational design and self-assembly of periodically sequenced polypeptides and proteins, and (3) physical and electronic properties of bio-inspired molecules.

Reception to follow.

Image Citation: López CA, de Vries AH, Marrink SJ (2011) Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction. PLoS Comput Biol 7(3): e1002020. doi:10.1371/journal.pcbi.1002020

Registration Pricing

Student / Postdoc / Fellow Member$10
Nonmember Academia$60
Nonmember Corporate$80
Nonmember Not for Profit$60
Student / Postdoc / Fellow Nonmember$40

Silver Sponsors

  • City College of New York
  • NYU-Poly


* Presentation times are subject to change.

Friday, April 27, 2012

9:00 AM

Registration and Poster Set-up

9:50 AM

Welcome and Introduction

10:00 AM

New structures for rational protein design and engineering
Dek Woolfson, PhD, University of Bristol

10:45 AM

Protein Biomaterials and Biological Interfaces
David Kaplan, PhD, Tufts University

11:30 AM

Refreshments and Poster Viewing

11:50 AM

Preparation and applications of glycosylated polypeptides
Timothy J. Deming, PhD, University of California, Los Angeles

12:35 PM

Artificial cellulosomes for enhanced biomass processing
Wilfred Chen PhD, University of Delaware

1:20 PM

Lunch Break and Poster Viewing

2:30 PM

Analyzing the Glycome Using Systems Approaches
Lara K. Mahal, PhD, New York University

3:15 PM

Simplicity in Action: Designed Proteins for Solar Energy Conversion
Ronald Koder, PhD, The City College of New York, CUNY

4:00 PM

Closing Remarks

4:10 PM

Refreshments and Poster Session

5:00 PM

End of Meeting



Jin Ryoun Kim, PhD


Jin Ryoun Kim is an assistant professor in Chemical and Biological Engineering at Polytechnic Institute of NYU. He earned a Bachelor of Science and a Master of Science in Chemical Engineering from Seoul National University in 1997 and 1999, respectively and a PhD in Chemical and Biological Engineering from the University of Wisconsin-Madison in 2004. He worked as a postdoctoral researcher at Johns Hopkins University in 2004-2006. His research on the creation of interactive protein domain assemblies has been supported by the Alzheimer's Association and NSF.

Ronald Koder, PhD

The City College of New York

Ronald Koder obtained his undergraduate degree in Chemistry from the University of Missouri at Columbia in 1992, performing his thesis research in enzyme kinetics with Peter Tipton. After a brief period as a synthetic organic chemist at Monsanto Co. in St. Louis, he went on to do his graduate work in Biophysics at Johns Hopkins University with Anne-Frances Miller, performing the first structural and enzymological analysis of bacterial nitroreductases now used in several forms of chemotherapy, achieving his PhD in 2000. He subsequently began his postdoctoral work in the Department of Biochemistry and Biophysics at the University of Pennsylvania with P. Leslie Dutton and A. Joshua Wand, working on the de novo design and NMR analysis of artificial hemoglobin proteins. In 2006, he moved to the faculty of the Department of Physics at the City College of New York and continued his work in Biological Design, expanding his interests to the design of protein networks useful in solar energy conversion, biometamaterials, and artificial blood substitutes. In 2011 he was named the Peace Assistant Professor of Physics at the City College of New York.

Jin Montclare, PhD


Dr. Jin Kim Montclare received her undergraduate BS degree in Chemistry from Fordham University, in 1997. She then went to Yale University as a NSF predoctoral fellow and earned her PhD in Bioorganic Chemistry in 2003. After an NIH postdoctoral fellowship at California Institute of Technology from 2003–2005 in the Division of Chemistry and Chemical Engineering, she began her academic career as an assistant professor in the Department of Chemical and Biological Sciences at the Polytechnic Institute of New York University. She also has an adjunct position at SUNY Downstate Medical School in Department of Biochemistry. Her research is in the area of biopolymer synthesis with a particular focus on engineering protein-based materials as well as artificial proteins bearing unnatural amino acids.

Raymond Tu, PhD

The City College of New York

Raymond S. Tu is an Assistant Professor in Chemical Engineering at The City College of The City University of New York. He received his BS in Chemical Engineering from The University of Florida, and his PhD in chemical engineering from the University of California – Santa Barbara in 2004. At Santa Barbara, he studied with Matthew Tirrell examining the design and self-assembly of peptide functionalized molecular architectures. He completed a post-doctoral fellowship in 2005 at Georgia Institute of Technology investigating rheological properties of biologically functionalized polymer-based materials. The focus of his research program at CUNY is the synthesis of surface-active molecular building blocks, which are derived from the combination of elements that direct interfacial assembly with components responsible for selective binding. This methodology is proving to be an effective tool for engineering complex composite materials that contain structures with multiple length-scales. The research in his group has been supported by AFOSR, NSF, NSF-PREM, DOE and industry.

Vikas Nanda, PhD

Rutgers University

Dr. Nanda earned his bachelor of science degree in biology at Caltech in 1995 and his PhD in biochemistry in 2001 at Johns Hopkins University. He developed tools for computational protein engineering as a post-doctoral researcher at the University of Pennsylvania with Dr. William F. DeGrado from 2000 to 2005, after which he joined the faculty of the biochemistry department at Robert Wood Johnson Medical School. He conducts his research on computational protein design at the Center for Advanced Biotechnology and Medicine (CABM), an interdisciplinary collaboration between Robert Wood Johnson Medical School and Rutgers University.


Wilfred Chen, PhD

The University of Delaware

Wilfred Chen joined the University of Delaware on January 1, 2011, as the Gore Professor of Chemical Engineering. He obtained his BS from UCLA in 1988 and his PhD from Caltech in 1993, both in Chemical Engineering. After a one-year postdoc in Switzerland, he joined UC, Riverside in 1994. He was Professor of Chemical and Environmental Engineering and the holder of the Presidential Chair until 2010. His research interests are in biomolecular engineering, biofuel production, viral infection, and nano-biotechnology. Chen has published more than 190 journal papers and delivered over 50 invited lectures. He serves on the editorial board for eight scientific publications. He is a fellow of the American Association for the Advancement of Science (AAAS) and the American Institute for Medical and Biological Engineering (AIMBE).

Tim Deming, PhD

University of California, Los Angeles

Timothy J. Deming received a BS in Chemistry from the University of California, Irvine in 1989, and graduated with a PhD in Chemistry from the University of California, Berkeley, under Bruce Novak, in 1993. After an NIH postdoctoral fellowship at the University of Massachusetts, Amherst, with David Tirrell, he joined the faculty in the Materials Department at the University of California, Santa Barbara in 1995. Here he held a joint appointment in the Materials Department and Chemistry Departments where he was promoted to Associate Professor in 1999 and Full Professor in 2003. His appointment is now as Professor of Bioengineering and Professor of Chemistry and Biochemistry at the University of California, Los Angeles. He also served as Chairman of the Bioengineering Department at UCLA from 2006 to 2011. He is a leader in the fields of polypeptide synthesis, self-assembly of block copolypeptides, and biological activity of polypeptides, for which he has received awards from the National Science Foundation, the Office of Naval Research, The Arnold and Mabel Beckman Foundation, the Alfred P. Sloan Foundation, the Camille and Henry Dreyfus Foundation, the Materials Research Society, and the IUPAC Macromolecular Division. He was recently named a Fellow of the American Institute of Medical and Biological Engineering.

David Kaplan, PhD

Tufts University

David Kaplan holds an Endowed Chair, the Stern Family Professor of Engineering, at Tufts University. He is Professor & Chair of the Department of Biomedical Engineering and also holds faculty appointments in the School of Medicine, the School of Dental Medicine, Department of Chemistry and the Department of Chemical and Biological Engineering. His research focus is on biopolymer engineering to understand structure-function relationships, with emphasis on studies related to self-assembly, biomaterials engineering and functional tissue engineering. He has published over 400 papers and edited eight books. He directs the NIH P41 Tissue Engineering Resource Center (TERC) that involves Tufts University and Columbia University. He serves of the editorial boards of numerous journals and is Associate Editor for the journal Biomacromolecules. He has received a number of awards for teaching, was Elected Fellow American Institute of Medical and Biological Engineering and received the Columbus Discovery Medal and Society for Biomaterials Clemson Award for contributions to the literature.

Ronald Koder, PhD

The City College of New York

Lara Mahal, PhD

New York University

Lara K. Mahal is an Associate Professor of Chemistry in the Biomedical Chemistry Institute at New York University. She is well known for lectin microarray technology and has received numerous awards for her work. These include the NIH Directorʼs New Innovator Award, NSF CAREER Award, Sloan Foundation Fellowship and Arnold and Mabel Beckman Foundation Fellowship. Professor Mahal graduated with highest honors from the University of California at Santa Cruz (B.A.). She then went to the University of California at Berkeley to earn her Ph.D. and moved to New York City as a Jane Coffins Child Postdoctoral Fellow at Memorial Sloan Kettering Cancer Research Center. She began her academic career at the University of Texas at Austin in 2003, was tenured in 2009 and moved to the new Biomedical Chemistry Institute in the Chemistry Department at NYU in 2009 to pursue her interests in collaborative biomedical research involving glycans.

Dek Woolfson, PhD

Bristol University

Dek Woolfson took his first degree in Chemistry at the University of Oxford in 1987. He then did a PhD at the University of Cambridge (1987 - 1992), followed by post-doctoral research at University College London and the University of California, Berkeley. After 9 years as Lecturer through to Professor of Biochemistry at the University of Sussex (1996 - 2005), he moved to the University of Bristol to take up a joint chair in Chemistry and Biochemistry. His research has always been at the interface between chemistry and biology, applying chemical methods and principles to understand biological systems. Specifically, his group is interested in the challenge of rational protein design, and in how this can be applied in synthetic biology and bionanotechnology.


Silver Sponsors

  • City College of New York
  • NYU-Poly

Academy Friend

Wyatt Technology Corporation


Rational Peptide Design in Synthetic Biology and Materials Science
Dek Woolfson, PhD, University of Bristol

The rational, de novo design of peptides and proteins of prescribed structure and function represents a formidable challenge in modern structural molecular biology. Nevertheless, tackling this challenge, which is known as the inverse protein-folding problem, allows us to test directly our understanding of sequence-to-structure relationships in proteins, and presents routes to new protein structures with potential utility in a number of applications areas. We are taking what might be termed a synthetic-biology approach to protein design;1 that is, we are attempting to construct a toolkit of rationally designed peptides that fold independently, are well characterised, and can be used in a plug-and-play fashion as modules in various different contexts. Our initial focus has been on designing a set of α-helical coiled-coil modules of specified oligomer states, stabilities and partner preferences. We are applying these to address problems in chemical and synthetic biology and in materials science.
I shall begin this talk with an overview of coiled-coil structure and assembly, and describe how we can design specific coiled-coil structures from first principles. Next I will illustrate how a Basis Set of coiled coils can be used to direct the assembly of bacterial collagen molecules,2 engineer new proteins with central functionalizable channels,3 and to design and assemble bio-inspired hydrogel materials with potential applications in 3D cell culture and tissue engineering.4
(1) Bromley, E. H. C.; Channon, K.; Moutevelis, E.; Woolfson, D. N. ACS Chem. Biol. 3, 38. (2008)
(2) Yoshizumi, A.; Fletcher, J. M.; Yu, Z. X.; Persikov, A. V.; Bartlett, G. J.; Boyle, A. L.; Vincent, T. L.; Woolfson, D. N.; Brodsky, B. J. Biol. Chem. 286, 17512, (2011)
(3) Zaccai, N. R.; Chi, B.; Thomson, A. R.; Boyle, A. L.; Bartlett, G. J.; Bruning, M.; Linden, N.; Sessions, R. B.; Booth, P. J.; Brady, R. L.; Woolfson, D. N. Nat. Chem. Biol. 7, 935, (2011)
(4) Banwell, E. F.; Abelardo, E. S.; Adams, D. J.; Birchall, M. A.; Corrigan, A.; Donald, A. M.; Kirkland, M.; Serpell, L. C.; Butler, M. F.; Woolfson, D. N. Nat. Mater. 8, 596 (2009)

Protein Biomaterials and Biological Interfaces
David Kaplan, PhD, Tufts University

Protein polymers, such as elastins and silks, provide a versatile and tunable biomaterials platform for the detailed study of structure-function relationships in terms of material properties and with respect to cell or tissues responses. Our research focus has primarily been with these types of proteins and the exploration of modes to manipulate protein chemistry and processing to impact assembly of these proteins into functional biomaterial systems with control of structure and morphology. Genetic engineering, chemical modifications and aqueous-based processing are exploited toward these goals. Insights into these proteins has led to robust biomaterial systems with which to study cell and tissue functions, to establish new and unexpected interfaces to electronics and optics and to generate and exploit in vitro tissue 3D human systems for the study of development, disease and for drug screening.

Preparation and Applications of Glycosylated Polypeptides
Timothy J. Deming, PhD, University of California, Los Angeles

We have prepared new glycosylated alpha-amino acid-N-carboxyanhydrides (NCAs) that undergo living polymerization using transition metal initiation to give well-defined, high molecular weight homoglycopolypeptides and block and statistical glycocopolypeptides. Use of these building blocks solves many long standing problems in the direct synthesis of glycopolypeptides from NCAs that relate to monomer synthesis, purification, and polymerization, and is advantageous in that high molecular weight polypeptides with 100% glycosylation are easily obtained. These water soluble glycopolypeptides have potential to impart functionality and improve biocompatibility in copolypeptide materials, such as hydrogels for tissue engineering and vesicles for drug delivery, as well as for preparation of structurally defined sugar presenting polymers for glycomics research. Preparation of these materials and some applications will be presented.

Artificial Cellulosomes for Enhanced Biomass Processing
Wilfred Chen, PhD, University of Delaware

Biocatalysis, especially multi-enzyme systems, has been receiving more attention for the production of chemicals such as biofuels. Cellulosome, a cell-bound multi-enzyme complex can be described as one of nature's most elaborate and highly efficient biocatalysts for the deconstruction of cellulose and hemicelluloses. Enzyme assembly occurred via the highly specific cohesin and dockerin interaction, resulting in synergistic biomass deconstruction based on spatial proximity and enzyme-substrate targeting. However, due to potential metabolic burdens and protein folding problems, artificial cellulosomes with higher enzyme loadings has not been realized. Our lab has been investigating several different approaches for the functional assembly of more complex cellulosome structures. In this talk, I will highlight our recent efforts in this area by investigating the effect of enzyme density, enzyme ordering, and enzyme proximity on the synergism of cellulose hydrolysis and ethanol production.

Analyzing the Glycome Using Systems Approaches
Lara K. Mahal, PhD, New York University

Glycosylation, which creates a diverse array of carbohydrate epitopes attached to cell surface proteins and lipids, is an inherently complex system that is poorly understood. Carbohydrates play crucial roles in a diverse array of medically relevant biological processes from viral pathogenesis to tumor cell metastasis and stem cell differentiation. Systems-based approaches to biology, in which large datasets are analyzed using bioinformatic algorithms, provide an important avenue for exploring the mechanics of complex systems that cannot be predicted a-priori. Application of such approaches to glycosylation however has been limited due to the lack of methodology for high-throughput analysis of carbohydrates (glycomics). Recent work in my laboratory on lectin microarray technology has begun to address the analytical problems inherent in glycomics and thus pave the way for systematic analysis of the glycome.

Simplicity in Action: Designed Proteins for Solar Energy Conversion
Ronald Koder, PhD, The City College of New York

Evolution's 'frozen accidents' at the protein scale frequently result in overly complicated systems of limited stability and robustness to re-engineering. The synthetic biology community has developed the concept of 'integrated modular assembly' as a simple basis for constructing molecular devices which perform or extend biological function. The basis for this approach is the 'biobrick', small protein domains which are clean, stable, and practical as a starting point for the design of larger functional assemblies. Here we discuss our efforts in the creation of a phthalocyanine-based 'Photosynthetic Charge separation Triad', or PCT Biobrick, capable of holding the minimal cofactor elements which can transform photonic energy into vectorial electron transfer at the correct distances and orientations with respect to each other. These domains will be modularly attached via molecular Lego to other designed or natural protein domains and act as centers for light-activated electron extraction and/or injection. We are coupling these materials to novel metamaterial electrodes which hold great promise as solid-state light harvesting and distribution materials in multi-junction biofuel-generating solar energy nanodevices.

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