Annual Report 2011 - Center for Advanced Biotechnology and ...

Dr. Vikas Nanda
CABM Resident Faculty Member
Associate Professor
Department of Biochemistry
UMDNJ-Robert Wood Johnson
Medical School
Dr. Fei Xu
Research Associate
Dr. Agustina
Rodriguez-Granillo
Research Assistant
Dr. James Stapleton
Postdoctoral Fellow
Dr. Isaac John Khan
Postdoctoral Assoc.
Dr. Avanish Parmar
Postdoctoral Assoc.
Sumana Giddu
Research Teaching Spec.
Teresita Silva
Research Teaching Spec.
Daniel Hsieh
Graduate Student
Protein Design and Evolution Laboratory
Dr. Vikas Nanda joined CABM in September of 2005 after studying as an
NIH National Research Service Award postdoctoral fellow in the laboratory
of Dr. William DeGrado at the Department of Biochemistry and Biophysics
at the University of Pennsylvania School of Medicine. His research focused
on studying the molecular basis of transmembrane interactions among
integrins involved in regulation of platelet hemostasis. Prior to that, Dr.
Nanda received his doctorate in Biochemistry from Johns Hopkins
University. His laboratory is supported by federal grants including a recent
highly competitive NIH New Innovator Award.
.
Our group is interested in constructing new proteins for applications in biomedical
research, nanotechnology and as tools for understanding how proteins fold and
evolve. Significant progress has been made in the last decade using sophisticated
computer programs to design proteins with novel folds and functions. We maintain
and develop the software package, protCAD (protein computer aided molecular
design), which has been applied to protein design, structure prediction and docking
of protein ligand complexes.
Computational Design of an Extracellular Matrix
The extracellular matrix (ECM) is a complex network of collagens, laminins,
fibronectins and proteoglycans that provides a surface upon which cells can adhere,
differentiate and proliferate. Defects in the ECM are the underlying cause of a wide
spectrum of diseases. The ECM mediates endothelial cell polarity and under normal
conditions can suppress pre-oncogenic transitions to a neoplastic state. We are
constructing artificial, de novo collagen-based matrices using a hierarchic
computational approach. These matrices will be physically characterized in the
laboratory and used to probe the role of chemical and spatial organization in the
ECM on the tumor forming potential of adhered cells. Successfully designed
matrices will be applied to engineering safer artificial tissues.
Rational Design of Enhanced Peptide Therapeutics
Peptides are an emergent and important class of therapeutics with over forty
compounds on the market and nearly 700 more in clinical or pre-clinical trials.
During the development of peptide drugs, D-enantiomers of amino acids are
frequently incorporated to improve pharmacokinetic and pharmacodynamics
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