User:Shulin Zhuang

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  • Shulin Zhuang
  • College of Enviromental and resources,Zhejiang University, China
  • Email:shulin.zhuang@gmail.com
I apply both computational methods and experimental methods to study the interactions of
proteins and ligands.

Highlights

1. Solid background in computational structural biology, single-molecule biophysics, chemistry, protein engineering and molecular biology, especially skilled in single-molecule biophysics, biomolecular structure & function and computational structural biology.

2. Thorough knowledge in drug design & discovery, protein design.

3. Extensive experience in biophysics: AFM, CD, Fluorescence, Stop-Flow, FPLC.

4. Strong skills in using computational soft: Amber, NAMD, Groamcs, Autodock, Dock, Sybyl, Modeller, Rosetta

Education

  • June 2010 ~ present: researcher, College of Environmental and Resources, Zhejiang University.
  • September 2007 ~ May 2010: Postdoctoral fellow, Department of Chemistry, University of British Columbia.
 During this period, I perform both molecular biology experiment and computational biology work

in biophysics research field to enhance protein mechanical properties.

  • March 2004 ~ March 2007: Ph.D., Chemical Biology major, Department of Chemistry, Zhejiang University, China.
 During this period, I use molecular modeling such as molecular dynamics, molecular docking

and QSAR for drug design & discovery and the study of protein-ligand interactions.

  • September 2001 ~ February 2004: M.S., Organic Chemistry major, Department of Chemistry, Zhejiang University, China.
 During this period, I have studied genomics and bioinformatics in Beijing Genomics Institute

for four months and spent one year in James D.Watson Institue of Genome Sciences, Zhejiang University to complete the master thesis.

  • September 1999 ~ July 2001: B.S., Chemistry Department, Qufu Normal University, China.
  • September 1997 ~ July 1999: junior college student, Chemical education major, Linyi Normal University, China.

Research Experiences

September 2007 ~ Present:

I. Experimental project

1.Mapping unfolding pathway of TNfn3 by AFM

2.Mechanism–based design of TNfn3 mutants with higher mechanical property

3.Mechanical study of Top7 with bihistidine engineering method

4.Single molecule force spectroscopy study of GB1 and Gc3b4 mutant

Using single molecule atomic force spectroscopy and protein engineering to study the mechanical properties of GB1, Gc3b4 and their mutants.


Methods: PCR, Electrophoresis, poly-protein building, protein expression and purification, AFM, CD, Fluorescence.


II. Computational project

1.Force-unfolding pathway study of GB1 and its two mutants:

2.Mechanical unfolding study of TNfn3

3.Project in plan: Biomolecular design of proteins to enhance binding affinity

Explore the “hot spots” of the protein complex using Alanine-scanning and computationally design proteins to enhance the binding affinity.

Methods: constant velocity SMD, constant force SMD, conventional molecular dynamics simulations, principal component analysis, MM-PBSA, Alanine-scanning


March 2004 ~ March 2007:

1. “Unfolding of Macrophage Migration Inhibitory Factor(MIF) Domain with Steered Molecular Dynamics”.

2. “Molecular Dynamics Simulation and Free Energy Calculations of Macrophage Migration Inhibitory Factor(MIF)-inhibitor Complexes”

Methods: molecular dynamics simulations, molecular docking, steered molecular dynamics, locally enhanced sampling, MM-PBSA, QSAR

Doctoral thesis: “Molecular dynamics simulation of the interaction between macrophage migration inhibitory factor and small molecules”


January 2003 ~ February 2004:

“Screening for the molecular pathogenesis of autosomal dominant congenital stationary night blindness”, as a graduate student, hosted by Dr. Songnian hu at James D.Watson Institue of Genome Sciences of Zhejinag University, Hangzhou Genomics Institute

Methods: PCR, DNA sequencing

Master thesis: “Study of five point mutations and rhodopsin gene in a large Chinese family with autosomal dominant congenital stationary night blindness”


August 2002 ~ December 2002:

Attend the project of “The Genome Sequencing of Oryza sativa”, hosted by Dr. Songnian hu et al. at Beijing Genomics Institute.

Skills

Experimental skills: DNA/RNA extract, PCR, Electrophoresis, protein expression and purification, AFM, CD, Stop Flow,FPLC, SPR

Computational skills:

Operating Systems Linux, Unix, Windows
Methods Molecular Dynamics Simulations, Steered Molecular Dynamics,

Molecular Docking, QSAR, Homology Modelling, Binding free energy calculation

Software Amber, NAMD, Gromacs, Dock, AutoDock, VMD, MMTSB, Modeller, Sybyl, Gaussian, Rosetta
Language Python, Tcl

Publications

  1. Shulin Zhuang, Qing Peng, Yi Cao, Hongbin Li. Modulating the Mechanical Stability of Extracellular Matrix Protein Tenascin-C in a Controlled and Reversible Fashion. J. Mol. Biol. 2009, 390(4), 820-829 [1]
  2. Qing Peng, Shulin Zhuang, Meijia Wang, Yi Cao, Yuanai Khor and Hongbin Li. Mechanical design of the third FnIII domain of tenascin-C. J. MoL. Biol. 2009, 386, 1327-1342 [2]
  3. Yi Cao, Teri Yoo, Shulin Zhuang, Hongbin Li. Protein–protein interaction regulates proteins’ mechanical stability. J. MoL. Biol. 2008, 378, 1132-1141 [3]
  4. Shulin Zhuang, Jianwei Zou, Yongjun Jiang, Xiang Mao, Bing Zhang, Haichun Liu, Qingsen Yu. Some Insights into the Stereochemistry of Inhibition of Macrophage Migration Inhibitory Factor with 2-Fluoro-p-hydroxycinnamate and Its Analogues from Molecular Dynamics Simulations. J. Med.Chem. 2005,48, 7208-7214 [4]
  5. Xiaoling Liu, Shulin Zhuang, Songnian Hu, Feng Zhang, Bing Lin, Xu Li, D. Xu, Shi-Han Chen. A Dominant Form of Congenital Stationary Night Blindness (adCSNB) in A Llarge Chinese Family. Ann. Hum. Genet. 2005, 69, 315-321 [5]
  6. Jun Yu, Jun Wang, Wei Lin, Songgang Li …… Shulin Zhuang(the 61rst author)…… et al. The Genomes of Oryza sativa: A History of Duplications. PLoS Biol. 2005, 3(2), e38(0001-0016) [6]
  7. Shulin Zhuang, Jianwei Zou, Chunlong Peng, Xiaoling Liu, Shihan Chen, Fangliang Huang, Songnian Hu,Qingsen Yu. Exclusion of the association of five known mutations with congenital stationary nyctalopia in a large Chinese family. Journal of Zhejiang University(medical sciences), 2005, 34(3), 255-259 [7]
  8. Shulin Zhuang, Qingsen Yu, Jianwei Zou, Yongjun Jiang, Yadong Chen, Huaxing Zhang, Haixiao Jin, Haichun Liu, Na Zhang. A Study of the Interaction of Cinnamate Analogues with Macrophage Migration Inhibitory Factor (MIF) and P1G Mutant from Molecular Dynamics Simulations. J. Mol. Struct.(THEOCHEM). 2006, 763,97-101 [8]
  9. Na Zhang, Yongjun Jiang, Jianwei Zou, Shulin Zhuang, Haixiao Jin , Qingsen Yu. Insights into unbinding mechanisms upon two mutations investigated by molecular dynamics study of GSK3β-axin complex: Role of packing hydrophobic residues. Proteins. 2007, 67(4), 941-949 [9]
  10. Bing Zhang, Vincent B. C. Tan, Kian Meng Lim, Tong Earn Tay, Shulin Zhuang. Study of the inhibition of cyclin-dependent kinases with roscovitine and indirubin-3’-oxime from molecular dynamics simulations. J. Mol. Model. 2006, 13(1), 79-89 [10]

Usefull links

1. Protocol online:http://www.protocol-online.org/

2. Protein Design and Protein Folding:http://www.proteindesign.com/

3. Human Proteome Folding Project:http://en.wikipedia.org/wiki/Human_Proteome_Folding_Project

4. Protein Folding Database:http://www.foldeomics.org/pfd/public_html/index.php

5. Refolding protocols:http://refold.med.monash.edu.au/