Biography

Education:

BS (Chemistry), Peking University

MS (Physical Chemistry), Peking University

PhD (Computational Chemistry), Emory University

Research Expertise

Computational Chemistry / Aromatic Foldamer / Computer Aided Molecular Design / Protein-Protein Interaction

My research interests are the development and application of computational methods to gain molecular insight into mechanisms of chemical reactions, to obtain structural and dynamical properties of biological/biomedical and foldamer (biomimetic or other novel scaffold) systems. Our long-term goal is to apply the scientific discoveries in the invention of new therapeutics or novel material. Specifically, we use various computational methods, such as quantum mechanical (QM) methods, all-atom molecular dynamics (MD) simulations, and coarse grain MD simulations, to study a variety of systems/processes, such as aromatic oligoamide (arylamide) foldamers, protein-protein interactions, protein-foldamer interactions. Recent research projects include:

• Development of computational tools for accurate prediction of structure, mechanism and solution dynamics of aromatic foldamers (NSF funded)
• Mechanistic studies of functional arylamide foldamers, ex. handedness inversion and induction mechanisms of helical aromatic foldamers
• Design of arylamide receptors for carbohydrate recognition (NIH funded)
• Helical arylamide foldamers for selective water transport (NSF funded)
• Prediction of binding strength and sequence optimization of arylamide foldamers binding with proteins
• MD investigation of RAF kinases activation/inhibition

Member of:

American Chemical Society

Recent Publications:

1. “Accessing Improbable Foldamer Shapes with Strained Macrocycles” K. Urushibara; Y. Ferrand; Z. Liu; K. Katagiri; M. Kawahata; E. Morvan; R. D'Elia; V. Pophristic; A. Tanatani; I. Huc, Eur. J. 2021, 27,11205-11215.
2. “Analyses of the oncogenic BRAF^D594G variant reveal a kinase-independent function of BRAF in activating MAPK signaling”, N. J. Cope; B. Novak; Z. Liu; M. Cavallo; A. Y. Gunderwala; M. Connolly; Z. Wang, Biol. Chem. 2020, 295(8), 2407-2420.
3. “Aquafoldmer-Based Aquaporin-like Synthetic Water Channel”, Shen; R. Ye; A. Romanies; A. Roy; F. Chen; C. Ren; Z. Liu; H. Zeng, J. Am. Chem. Soc. 2020, 142(22), 10050-10058.
4. “Biochemical Characterization of Full-Length Oncogenic BRAF^V600E together with Molecular Dynamics Simulations Provide Insight into the Activation and Inhibition Mechanisms of RAF Kinases.” N. Cope, B. Novak, C. Candelora, K. Wong, M. Cavallo, A. Gunderwala, Z. Liu, Y. Li, Z. Wang, ChemBioChem 2019, 20(22), 2850-2861.
5. “Frustrated helicity: joining the diverging ends of a stable aromatic amide helix to form a fluxional macrocycle”, K. Urushibara; Y. Ferrand; Z. Liu; H. Masu; V. Pophristic; Tanatani; I. Huc, Angew. Chem. Int. Ed. 2018, 57, 1-6.
6. “Molecular dynamics study of homo-oligomeric ion-channels: Structures of the surrounding lipids and dynamics of water movement”, T. H. Nguyen; C. C. Moore; P. B. Moore; Z. Liu, AIMS Biophys. 2018, 5(1), 50-76.
7. “UV and Thermo Controllable Azobenzene-Decorated Polycarbodiimide Molecular Springs", D. Siriwardane; O. Kulikov; B. Batchelor; Z. Liu; J. M. Cue; S. Nielsen; B. M. Novak, Macromolecules, 2018, 51 (10), pp 3722–3730
8. “Computational prediction and rationalization, and experimental validation of handedness induction in helical aromatic oligoamide foldamers”, Z. Liu; X. Hu; A. M. Abramyan; Á. Mészáros; M. Csékei; A. Kotschy; I. Huc; V. Pophristic, Eur. J. 2017, 23, 3605-3615. Featured on the inside cover of the journal
9. “Helix handedness inversion in arylamide foldamers: elucidation and free energy profile of a hopping mechanism”, Abramyan; Z. Liu; V. Pophristic, Chem. Commun. 2016, 52, 669-672. Featured on the inside cover of the journal
10. “Helical arylamide foldamers: structure prediction by molecular dynamics simulations”; Z. Liu; A. Abramyan; V. Pophristic, New J. Chem. 2015, 39, 3229-3240. Featured on the inside cover of the journal