A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

Nguyen, Crystal N.; Yamazaki, Takeshi; Kovalenko, Andriy; Case, David A.; Gilson, Michael K.; Kurtzman, Tom; Luchko, Tyler

doi:10.1371/journal.pone.0219473

Cited by 29 publications

(45 citation statements)

References 52 publications

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“…Molecular reconstruction of thermodynamic maps of water entities were depicted additively by combining oxygen and hydrogen against a solute. Solute-solvent interaction description was calculated by 3D-RISM (three-dimensional reference interaction site model with Universal Correlation, UC) ( Luchko et al, 2010 ; Nguyen et al, 2019 ). The displacement of water molecules favorably modulates the free energy of protein-ligand complex binding.…”

Section: Introductionmentioning

confidence: 99%

Distribution and Function of Glycosaminoglycans and Proteoglycans in the Development, Homeostasis and Pathology of the Ocular Surface

Puri

Coulson-Thomas

Gesteira

et al. 2020

Front. Cell Dev. Biol.

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The ocular surface, which forms the interface between the eye and the external environment, includes the cornea, corneoscleral limbus, the conjunctiva and the accessory glands that produce the tear film. Glycosaminoglycans (GAGs) and proteoglycans (PGs) have been shown to play important roles in the development, hemostasis and pathology of the ocular surface. Herein we review the current literature related to the distribution and function of GAGs and PGs within the ocular surface, with focus on the cornea. The unique organization of ECM components within the cornea is essential for the maintenance of corneal transparency and function. Many studies have described the importance of GAGs within the epithelial and stromal compartment, while very few studies have analyzed the ECM of the endothelial layer. Importantly, GAGs have been shown to be essential for maintaining corneal homeostasis, epithelial cell differentiation and wound healing, and, more recently, a role has been suggested for the ECM in regulating limbal stem cells, corneal innervation, corneal inflammation, corneal angiogenesis and lymphangiogenesis. Reports have also associated genetic defects of the ECM to corneal pathologies. Thus, we also highlight the role of different GAGs and PGs in ocular surface homeostasis, as well as in pathology.

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Section: Introductionmentioning

confidence: 99%

Distribution and Function of Glycosaminoglycans and Proteoglycans in the Development, Homeostasis and Pathology of the Ocular Surface

Puri

Coulson-Thomas

Gesteira

et al. 2020

Front. Cell Dev. Biol.

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“…Some examples of successful applications of the 3D-RISM-KH theory in exploiting the explicit role of water maps are reported for in-drug design and protein aggregation studies [ 82 , 83 , 84 ]. A very recent modification of the 3D-RISM theory in mapping solvation sites in enzyme active site was reported by Nguyen et al [ 85 ]. This new development extended the GIST (grid inhomogeneous solvation theory) based mapping technique in to the 3D-RISM grids.…”

Section: Binding Site Mappingmentioning

confidence: 99%

Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory

Roy

Kovalenko

2021

IJMS

Self Cite

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The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand binding, and structure-function related solvation properties. Upon coupling the 3D-RISM-KH theory with a novel multiple time-step molecular dynamic (MD) of the solute biomolecule stabilized by the optimized isokinetic Nosé–Hoover chain thermostat driven by effective solvation forces obtained from 3D-RISM-KH and extrapolated forward by generalized solvation force extrapolation (GSFE), gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties were obtained in this new quasidynamics protocol. The multiscale OIN/GSFE/3D-RISM-KH algorithm was implemented in the Amber package and well documented for fully flexible model of alanine dipeptide, miniprotein 1L2Y, and protein G in aqueous solution, with a solvent sampling rate ~150 times faster than a standard MD simulation in explicit water. Further acceleration in computation can be achieved by modifying the extent of solvation layers considered in the calculation, as well as by modifying existing closure relations. This enhanced simulation technique has proven applications in protein-ligand binding energy calculations, ligand/solvent binding site prediction, molecular solvation energy calculations, etc. Applications of the RISM-KH theory in molecular simulation are discussed in this work.

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“…[ 464 ] Using 3D‐RISM, they can predict properties of the solute molecules, such as solvation free energy, enthalpy and entropy, [ 465 ] hydrophobicity, [ 466 ] protein‐drug binding affinities, [ 467 ] and the distribution of water and ions around solutes. [ 468–471 ]…”

Section: Overview Of Mercury Faculty Research Effortsmentioning

confidence: 99%

Twenty years of exceptional success: The molecular education and research consortium in undergraduate computational chemistry (MERCURY)

Shields

2020

Int J of Quantum Chemistry

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The molecular education and research consortium in undergraduate computational chemistry (MERCURY) consortium, established in 2000, has contributed greatly to the scientific development of faculty and undergraduates. The MERCURY faculty peer-reviewed publication rate from 2001 to 2019 of 1.7 papers/faculty/year is 3.4 times the rate of the physical science faculty at primarily undergraduate institutions. We have worked with over 1000 students on research projects since 2001, and 75% of our undergraduate research students have been under-represented in chemistry, either female or students of color. Approximately half of our alumni attend graduate school for the purpose of obtaining advanced degrees in STEM fields, and two-thirds are female and/or students of color. We have had more than 1600 attendees at 18 MERCURY conferences, including 111 invited speakers, 61 of whom have been female and/or faculty of color. In this paper, the research accomplishments, transformational outcomes, and scientific productivity of the MERCURY faculty are highlighted.

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A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

Cited by 29 publications

References 52 publications

Distribution and Function of Glycosaminoglycans and Proteoglycans in the Development, Homeostasis and Pathology of the Ocular Surface

Distribution and Function of Glycosaminoglycans and Proteoglycans in the Development, Homeostasis and Pathology of the Ocular Surface

Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory

Twenty years of exceptional success: The molecular education and research consortium in undergraduate computational chemistry (MERCURY)

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