Yiqin Gao
Cheung Kong Professor (PI)

  • E-mail:gaoyq@pku.edu.cn
  • Tel:+86-10-62752431
    Office:C208, Chemistry Building, PKU
    Mailing Address:College of Chemistry and Molecular Engineering, Peking University, Beijing, China 100871
  • B.S. in Chemistry, Sichuan University, China,1993
    M.S. in Chemistry, Institute of Chemistry, Chinese Academy of Sciences, 1996.
    Ph.D in Chemistry, California Institute of Technology, June 2001.

    Professional Experiences

  • 2015-present, Dean, College of Chemistry and Molecular Engineering, Peking Universtiy

    2013-present, BIOPIC, Peking University,Principal Investigator

    2010-present, College of Chemistry and Molecular Engineering, Peking University,Cheung Kong Professor

    2005-2010, Department of Chemistry, Texas A&M University,Assistant Professor

    2002-2004, Harvard University, Postdoctoral Research Fellow

    2001-2002, California Institute of Technology, Postdoctoral Research Fellow
    Research Interests

  • Gao lab is doing research in the fields of theoretical/computational chemistry and biophysical chemistry. We are developing efficient computational methods and statistical mechanics tools to study the conformations of biological molecules in aqueous solutions, mechanisms of enzymatic reactions, and the solvation effects in chemical reactions. Progress has been made in various aspects of chemical rate theories and computational methods. Through theoretical studies, we successfully explained the unconventional isotopic effects in ozone formation, built a self-consistent structure-based model for both ATP hydrolysis and synthesis by F1Fo-ATPase, developed a highly efficient sampling method in both configuration and reactive trajectory spaces, and used these simulations to make predictions on the folding mechanisms of a variety of proteins and polypeptides including their co-solvent effects. Making use of molecular dynamics simulations and statistical mechanics, we provided a simple theoretical model to explain the effects of inorganic salts and small organic molecules on protein structures and various water properties. Many of these predictions have been verified by experimental studies of different research groups. Our current research effort includes further development of sampling methods in QM/MM calculations with the focus on applications to enzymatic reactions, protein/ligand binding, solvation effects in solution and interfacial chemical reactions. We are also developing enhanced sampling method in ab initio and path integral molecular dynamics. The lab is working on the simulation/theoretical studies of the following systems: (1) solvation effects in DNA and protein structure formation in aqueous solutions (2) chaperon/membrane protein interactions (3) allosteric effects in DNA and proteins, sequence and chemical modification effects (4) dynamics and spectra calculations for aqueous solutions (5) theory of self-assembly; structure and formation pathways of molecular clusters.
    Awards and Honors

  • 2012 Innovation Research Team, Ministry of Education
    2011 NSFC Outstanding Young Investigator Award
    2008 Changjiang Scholar
    2006 Searle Scholar
    2004 Camille and Henry Dreyfus New Faculty Award
    2001 Milton and Francis Clauser Prize for the Best Doctoral Thesis, Caltech

    Selected Publication

    15. Zhang L, Xie WJ, Liu S, Meng L, Gu C and Gao YQ. DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells. Biophys J. 2017;113:1395-1404.

    14. Hou GL, Liu CW, Li RZ, Xu HG, Gao YQ and Zheng WJ. Emergence of Solvent-Separated Na(+)-Cl(-) Ion Pair in Salt Water: Photoelectron Spectroscopy and Theoretical Calculations. J Phys Chem Lett. 2017;8:13-20.

    13. Kan Z, Zhu Q, Yang L, Huang Z, Jin B and Ma J. Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method. J Phys Chem B. 2017;121:4319-4332.

    12. Zhang J, Zhang Z, Yang YI, Liu S, Yang L and Gao YQ. Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories. ACS Cent Sci. 2017;3:407-414.

    11. Zhang Z, Xie WJ, Yang YI, Sun G and Gao YQ. Simulation Studies of the Self-Assembly of Halogen-Bonded Sierpiński Triangle Fractals. Acta Physico-Chimica Sinca. 2017;33:539-547.

    10. Che X, Du XX, Cai X, Zhang J, Xie WJ, Long Z, Ye ZY, Zhang H, Yang L, Su XD and Gao YQ. Single Mutations Reshape the Structural Correlation Network of the DMXAA-Human STING Complex. J Phys Chem B. 2017;121:2073-2082.

    9. Xie WJ, Meng L, Liu S, Zhang L, Cai X and Gao YQ. Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle. Sci Rep. 2017;7:2818.

    8. Structural Flexibility and Conformation Features of Cyclic Dinucleotides in Aqueous Solutions, X. Che, J. Zhang, Y.Y. Zhu, L.J. Yang, H. Quan, Y.Q. Gao*, J. Phys. Chem. B 120, 2670-2680 (2016).

    7. From Thermodynamics to Kinetics: Enhanced Sampling of Rare Events, L. Yang, C.W. Liu, Q. Shao, J. Zhang, Y.Q. Gao*, Acc. Chem. Res 48, 947–955 (2015).

    6. Tautomerization-dependent Recognition and Excision of Oxidation Damage in Base-excision DNA Repair, C.X. Zhu, J. Zhang, L. Lu, C.X. Zhu, L. Lu, J. Zhang, Z. Yue, J. Song, S. Zong, M.H. Liu, O.G. Stoviceke, Y.Q. Gao*, C.Q. Yi*, Proc. Natl. Acad. Sci. U S A (accepted).

    5. Microsolvation of LiI and CsI in water: Anion photoelectron spectroscopy and ab initio calculations, Y. Li, C.W. Liu, Y.Q. Gao, H. Jiang, W. J. Zheng, J. Am. Chem. Soc. 135, 5190-5199 (2013).

    4. Probing Allostery Through DNA, S. Kim, E. Broströmer, D. Xing, J. Jin, S. Chong, H. Ge, S. Wang, C. Gu, L. Yang,Y. Q. Gao, X. Su, Y. Sun, X. S. Xie Science 339, 816-819 (2013).

    3. From Protein Denaturant to Protectant: Comparative Molecular Dynamics Study of Alcohol/protein Interactions, Q. Shao, Y.B Fan, L.J. Yang, Y.Q. Gao, J. Chem. Phys. 136, 115101 (2012).

    2. The binding change mechanism of F1-ATPase revisited, Y. Q. Gao, W. Yang, and M. Karplus, Cell 123, 195-205 (2005).

    1. Strange and unconventional isotopic effect in ozone formation, Y. Q. Gao and R. A. Marcus, Science 293, 259-263 (2001).