Biomolecular research is increasingly changing from phenomenological and descriptive to quantitative and predictive. The overall goal of the proposed research is to facilitate this paradigm shift in mechanistic studies of biomolecular recognition, which occurs at a wide range of spatial scales. Protein-ligand binding and allosteric regulation are the prototypical molecular recognition processes. Moving up the spatial scale, many intrinsically disordered proteins have now been identified, often involved in signaling or regulation by binding to their cellular targets. At the subcellular scale, exciting discoveries are being made about a membraneless form of micro-compartments, wherein specific proteins and RNAs are condensed but remain fluid. These intracellular bodies assemble reversibly in response to regulatory signals and can recognize bystander components for exclusion. High concentrations of bystander macromolecules (crowders) are always present in the cellular environments and affect all these molecular recognition processes. Irrespective of spatial scales, the fundamental basis of molecular recognition is the molecular physical properties, including molecular interactions and motions. To gain deep mechanistic knowledge on all these molecular recognition processes, the proposed research will use three complementary approaches. Theoretical models will be developed to test mechanistic hypotheses and guide experimental design and to establish the framework for relating thermodynamic and mechanistic properties to molecular physical properties. The framework will be implemented computationally, through molecular simulations and atomistic-level calculations. Experimental measurements will be made to obtain critical information, which will also serve to inspire theoretical models and validate computational results. Through the integration of the three approaches, the effects of macromolecular crowding will be characterized, such that the knowledge from dilute-solution studies can be transferred to the cellular context. The deep, quantitative understanding of biomolecular recognition to be achieved will enable accurate predictions of mechanistic properties and yield opportunities for drug design through altering mechanistic pathways.

Public Health Relevance

Molecular recognition is at the core of biology. This project will generate fundamental knowledge on molecular recognition processes occurring at a wide range of spatial scales and yield unique opportunities for drug design through altering mechanistic pathways.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Unknown (R35)
Project #
5R35GM118091-05
Application #
9904727
Study Section
Special Emphasis Panel (ZGM1)
Program Officer
Lyster, Peter
Project Start
2016-04-15
Project End
2021-03-31
Budget Start
2020-04-01
Budget End
2021-03-31
Support Year
5
Fiscal Year
2020
Total Cost
Indirect Cost
Name
University of Illinois at Chicago
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
098987217
City
Chicago
State
IL
Country
United States
Zip Code
60612
Zhou, Huan-Xiang; Pang, Xiaodong (2018) Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 118:1691-1741
Nguemaha, Valery; Qin, Sanbo; Zhou, Huan-Xiang (2018) Atomistic Modeling of Intrinsically Disordered Proteins Under Polyethylene Glycol Crowding: Quantitative Comparison with Experimental Data and Implication of Protein-Crowder Attraction. J Phys Chem B :
Hicks, Alan; Zhou, Huan-Xiang (2018) Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations. J Chem Phys 149:072313
Zhou, Huan-Xiang; Nguemaha, Valery; Mazarakos, Konstantinos et al. (2018) Why Do Disordered and Structured Proteins Behave Differently in Phase Separation? Trends Biochem Sci 43:499-516
Campitelli, Paul; Guo, Jingjing; Zhou, Huan-Xiang et al. (2018) Hinge-Shift Mechanism Modulates Allosteric Regulations in Human Pin1. J Phys Chem B 122:5623-5629
Amin, Johansen B; Leng, Xiaoling; Gochman, Aaron et al. (2018) A conserved glycine harboring disease-associated mutations permits NMDA receptor slow deactivation and high Ca2+ permeability. Nat Commun 9:3748
Nguemaha, Valery; Zhou, Huan-Xiang (2018) Liquid-Liquid Phase Separation of Patchy Particles Illuminates Diverse Effects of Regulatory Components on Protein Droplet Formation. Sci Rep 8:6728
Nguyen, Trung Hai; Zhou, Huan-Xiang; Minh, David D L (2018) Using the fast fourier transform in binding free energy calculations. J Comput Chem 39:621-636
Banks, Anthony; Qin, Sanbo; Weiss, Kevin L et al. (2018) Intrinsically Disordered Protein Exhibits Both Compaction and Expansion under Macromolecular Crowding. Biophys J 114:1067-1079
Amin, Johansen B; Salussolia, Catherine L; Chan, Kelvin et al. (2017) Divergent roles of a peripheral transmembrane segment in AMPA and NMDA receptors. J Gen Physiol 149:661-680

Showing the most recent 10 out of 21 publications