Alexander Grishaev

Grishaev Group

Contact

Email: agrishaev@ibbr.umd.edu

Call: (240) 314-6892

Education

  • Postdoctoral Fellow, Laboratory of Chemical Physics, NIDDK/NIH, 2001-2005
  • Ph.D., Chemistry/Biophysics, Carnegie Mellon University, 2001
  • M.S., Chemistry, University of Wisconsin-Madison, 1995
  • Diploma, Physical/Quantum Chemistry, Moscow State University, 1993

Profile

Dr. Alexander Grishaev’s laboratory focuses on integrative structural biology and deriving biomolecular structures by combining experimental data from several complementary, biophysical techniques within a computational framework that optimally restrains the conformation space. The lab’s primary experimental approaches are solution X-ray and neutron scattering, and nuclear magnetic resonance (NMR) spectroscopy. They aim to design methodologies for maximizing the information content and fidelity of interpretation of the observables attainable by these techniques. An important part of the Grishaev lab’s work is mining information in structural databases to improve force fields for protein/RNA/DNA structure refinement. The group focuses on systems characterized by a low density of experimental restraints, such as flexibly linked multi-domain or disordered proteins, amyloid fibrils, protein complexes, and RNA constructs.

CURRENT RESEARCH

Using wide-angle solution X-ray scattering to define biomolecular structure and dynamics

Solution X-ray scattering instrument at IBBR includes robotic sample handling and automated setup of the experimental configurations.

The Grishaev lab develops methods for improving both the speed and the accuracy of modeling solution X-ray scattering data from atomic coordinates to facilitate their integration into structure refinement of intrinsically disordered and flexibly linked multi-domain proteins, RNA, DNA, and lipid or detergent-based nanoparticles. The lab’s ultimate goal is to determine the structures of proteins and RNA as multi-state conformational ensembles, which they view as the next frontier of structural biology. Model improvements are underpinned by high-fidelity molecular dynamics simulations in explicit solvent and structural database analysis, allowing formulation of detailed, experimentally verifiable, multi-dimensional hydration maps and motional models of biomolecules. Infrastructure support for this work comes from state-of-the-art facilities including in-house small- and wide-angle X-ray scattering (SAXS/WAXS) instrumentation, synchrotron beamlines for both non-resonant and anomalous scattering experiments, local neutron scattering facilities at NIST, and a high-performance computing cluster at IBBR. The Grishaev group’s strategy of jointly using wide-angle solution scattering data, NMR, and advanced simulation techniques aims to maximize the density of the experimental observables while limiting the expansion of the number of degrees of freedom to minimize data over-fitting. The group also develops novel scattering approaches -- including high-contrast heavy atoms labels and anisotropic alignment -- to increase the information content of scattering data.

Improving the accuracy of NMR-determined biomolecular structures via better force fields and advanced simulation techniques

NMR is an important component of the lab’s workflow and their efforts include increasing the impact of NMR restraints, such as residual dipolar couplings and chemical shifts. They develop both novel empirical energy terms and codes for better use of NMR and SAXS data, with applications to structure refinement packages, such as Xplor-NIH, CNS, and Amber. They also develop and apply metrics for both empirical protein and RNA structure validation and experimental cross-validation as sensitive and objective gauges of the coordinates’ accuracy.

Examples of using SAXS and NMR data to define biomolecular structure. Left: Overlay of SAXS data for GC-rich (blue) and AT-rich (red) B-DNA constructs differing in both structure and conformational fluctuations, compared with the predictions from the NMR-only fitted structure ensembles, illustrating the added information content of scattering data. Center: First hydration shells surrounding UUCG tetraloop RNA (right), and B-DNA (left) generated using structural database statistics. Right: Orientations of the normals to the planes of the aromatic rings relative to the axes of the alignment tensor obtained by fitting NMR residual chemical shift anisotropy (rCSA) data for axially symmetric (left) and fully rhombic (right) CSA tensors.

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Publications
2022
Conformational Heterogeneity of UCAAUC RNA Oligonucleotide from Molecular Dynamics Simulations, SAXS, and NMR experiments.
2021
Ionization and structural properties of mRNA lipid nanoparticles influence expression in intramuscular and intravascular administration.
2020
Structural Characterization and Modeling of a Respiratory Syncytial Virus Fusion Glycoprotein Nanoparticle Vaccine in Solution.
Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR.
HIV-1 gp120-CD4-Induced Antibody Complex Elicits CD4 Binding Site-Specific Antibody Response in Mice.
Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a di-heptamer macromolecular assembly.
2019
Accuracy of MD solvent models in RNA structure refinement assessed via liquid-crystal NMR and spin relaxation data.
Maximizing accuracy of RNA structure in refinement against residual dipolar couplings.
Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level.
2018
Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".
PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer.
A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity.
2017
Hybrid Applications of Solution Scattering to Aid Structural Biology.
Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins.
Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity.
2016
Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment.
Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.
Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering.
2015
Side Chain Conformational Distributions of a Small Protein Derived from Model-Free Analysis of a Large Set of Residual Dipolar Couplings.
Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering.