Matching Items (2)
Description
Contrary to the traditional structure-function paradigm for proteins, intrinsically disorderedproteins (IDPs) and regions (IDRs) are highly disordered sequences that lack a fixed
crystal structure yet perform various biological activities such as cell signaling, regulation,
and recognition. The interactions of these disordered regions with water molecules are essential
in the conformational distribution. Hence, exploring their solvation thermodynamics
is crucial for understanding their functions, which are challenging to study experimentally.
In this thesis, classical Molecular Dynamics (MD), 3D-Two Phase Thermodynamics (3D-
2PT), and umbrella sampling have been employed to gain insights into the behaviors of
intrinsically disordered proteins (IDPs) and water.
In the first project, local and total solvation thermodynamics around the K-18 domain
of the intrinsically disordered protein Tau were compared, and simulated with four pairs
of modified and standard force fields. In empirical force fields, an imbalance between
intramolecular protein interactions and protein-water interactions often leads to collapsed
IDP structures in simulations. To counter this, various methods have been devised to refine
protein-water interaction models. This research applied both standard and adapted force
fields in simulations, scrutinizing the effects of each adjustment on solvation free energy.
In the second project, the MD-based 3D-2PT analysis was utilized to examine variations
in local entropy and number density of bulk water in response to an electric field, focusing
on the vicinity of reference water molecules.
In the third project, various peptide sequences were examined to quantify the free energy
involved when specific sequences, known as alpha-MoRFs (alpha-Molecular Recognition
Features), transition from intrinsically disordered states to structured secondary motifs
like the alpha-helix. The low folding free energy penalty of these sequences can be exploited
to design peptide-based or small-molecule drugs. Upon binding to alpha-MoRFs,
these drugs can stabilize the helix structure through a binding-induced folding mechanism.
Alpha-MoRFs were juxtaposed with entirely disordered sequences from known proteins,
with findings benchmarked against leading structure prediction models. Additionally, the
binding free energies of various alpha-MoRFs in their folded conformation were assessed
to discern if experimental binding free energies reflect the separate contributions of folding
and binding, as obtained from umbrella sampling simulations.
ContributorsMaiti, Sthitadhi (Author) / Heyden, Matthias (Thesis advisor) / Ozkan, S. Banu (Committee member) / Sulc, Petr (Committee member) / Arizona State University (Publisher)
Created2024
Description
In a typical living cell, millions to billions of proteins—nanomachines that fluctuate and cycle among many conformational states—convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics (EqMD) can capture atomistic detail and solute-solvent interactions, but even microseconds of sampling attainable nowadays still falls orders of magnitude short of transition timescales, especially for large systems, rendering observations of such "rare events" difficult or effectively impossible.
Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)—an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project—developing a hybrid atomistic-continuum method—is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.
Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)—an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project—developing a hybrid atomistic-continuum method—is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.
ContributorsSeyler, Sean L (Author) / Beckstein, Oliver (Thesis advisor) / Chamberlin, Ralph (Committee member) / Matyushov, Dmitry (Committee member) / Thorpe, Michael F (Committee member) / Vaiana, Sara (Committee member) / Arizona State University (Publisher)
Created2017