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Education
Master
of Pharmacology, 2001
Shanghai
Institute of Materia Medica, Chinese Academy of Sciences
Bachelor
of Biology, 1998
Research
Interest
From September 1998 to July 2001, I was a MS student of Pharmacology in Shanghai Institute of Materia Medica, Chinese Academy of Sciences, where I did research on opioid receptors' structure and function. Chimeric opioid receptors were used to identify the specific binding domain and the signal transduction function of µ- and kappa- opioid receptors for all kinds of ligands, which would be helpful in designing and inventing sub-type opioid receptor specific drugs. We also applied SF9 insect cells in a highly efficient protein express system to collect enough µ-opioid receptor through Ni affinity chromatography and study its structure and function. Since X-ray crystal structure of human opioid receptors were not available at that time and even now, we constructed a 3-D structural model of human kappa-opioid receptor by homology modeling and studied its interaction mechanism with the a subunit of G-protein.
From September 1998 to July 2001, I was a MS student of Pharmacology in Shanghai Institute of Materia Medica, Chinese Academy of Sciences, where I did research on opioid receptors' structure and function. Chimeric opioid receptors were used to identify the specific binding domain and the signal transduction function of µ- and kappa- opioid receptors for all kinds of ligands, which would be helpful in designing and inventing sub-type opioid receptor specific drugs. We also applied SF9 insect cells in a highly efficient protein express system to collect enough µ-opioid receptor through Ni affinity chromatography and study its structure and function. Since X-ray crystal structure of human opioid receptors were not available at that time and even now, we constructed a 3-D structural model of human kappa-opioid receptor by homology modeling and studied its interaction mechanism with the a subunit of G-protein. From Aug 2002 to now, I am a Ph.D student at the Dept. of Biochemistry, Biophysics and Molecular Biology in Iowa State University and work with Dr. Jernigan on the field of bioinformatics and computational biology. We are interested in studying and estimating statistical potential energies at coarse grain level of protein structures. Atomic force field potentials used in molecular dynamic simulation produced some excellent results for predicting small proteins’ structure, but were very expensive in computing time. It is always our goal to derive precise statistical potential energies for use in protein structure prediction. We have developed a new scheme to derive four-body contact potentials with the intention of devising a way to consider protein interactions as being more cooperative. In this new scheme, we focus on the interactions between backbones and side chain. We are also interested in using elastic network models (ENM) to study the relationship between proteins’ fluctuations and contact potential energies. ENM are popular for studying protein’s dynamics and many papers have been published to demonstrate that ENM are successful in explaining experimental results in terms of theoretical data, such as free energy change associated with Hydrogen exchange (HX), the deformation of bound and unbound structures, etc. However, we don’t know the internal relationship between the entropy and free energy change calculated by ENM, and contact potential energies we have studied. This issue is interesting and promising.
Work
Experience
From Aug 2001 to Aug 2002, I worked in the department of research and development in the Jianfeng Pharmaceutical Company, China. My job mainly focused on supervising and coordinating a Phase I clinical trial of a kind of anti-HSV new drug and a Phase II clinical trial of Gatifloxacin, an antibiotic.
Teaching
Experience
Teaching assistant for BBMB301 and BBMB404.
Skills
Familiar with C++, Perl, Matlab, R.
Publications
- Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan. Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys. (accepted, Proteins, 2006).
- Taner, S.T., Feng, Y, Garcia, J.V., Kloczkowski, A., Jernigan, R.L. The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. J. Chem. Theory Comput., 2 (3), 696 -704, 2006.
- Feng Y, Chen LW, Zhou DH, Chen J, Xu XJ, Chi ZQ. Analysis of binding domain and function of chimeric mu/kappa opioid receptors to ohmefentanyl stereoisomers. Acta Pharmacol Sin. Nov;22(11):981-5, 2001
- Chen Li-Wei, Feng Ya-Ping, Zhou De-He, Xu Xue-Jun, Chen Jie, Wei Qiang, and Chi Zhi-Qiang. One-Step Affinity Purification of Human Mu-Opioid Receptor Overexpressed in Baculovirus System. Protein and Peptide Letters, 8(4):265-272, 2001
- Xuhu Wan, Huang Xiao-Qin, Zhou De-He, Jiang Hua-Liang, Feng Ya-Ping, Chen Kai-Xian, and Chi Zhi-Qiang Molecular Modeling of Kappa Opioid Receptor-Gi Protein Recognition. Protein and Peptide Letters, 7(6):403-409, 2000.
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Copyright 2007. All
rights reserved.