Mechanism of Solvent Control of Protein Dynamics

Mukherjee, Saumyak; Mondal, Sayantan; Bagchi, Biman

doi:10.1103/physrevlett.122.058101

Cited by 46 publications

(69 citation statements)

References 64 publications

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“…In addition to the static orientations of water molecules, their dynamics are crucial for protein functions (21,23,24,28): Highly mobile water molecules are molecular lubricants, which are essential for the conformational mobility required for optimal catalysis (48,49). Here, we determine the residence time of the nearest water molecules for different types of amino acids by following recent work (50).…”

Section: Petase Surface Domains Distinctly Govern the Orientation Andmentioning

confidence: 99%

“…Unfortunately, the existing experimental techniques are currently limited in their capability to quantify such local hydration on a protein surface (23)(24)(25). Atomistic computer simulations have used nonpolarizable potentials to study average water orientation (21,26,27) and dynamics (21,23,24,28) as a function of the distance from a protein's surface. However, a lack of atomic polarizability in these potentials raises concerns regarding the accurate description of protein solubility and molecular recognition in that the relative permittivities of proteins (27,29) are much lower than that of bulk water.…”

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confidence: 99%

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Water follows polar and nonpolar protein surface domains

Qiao

Jiménez-Ángeles

Nguyen

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

100

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The conformation of water around proteins is of paramount importance, as it determines protein interactions. Although the average water properties around the surface of proteins have been provided experimentally and computationally, protein surfaces are highly heterogeneous. Therefore, it is crucial to determine the correlations of water to the local distributions of polar and nonpolar protein surface domains to understand functions such as aggregation, mutations, and delivery. By using atomistic simulations, we investigate the orientation and dynamics of water molecules next to 4 types of protein surface domains: negatively charged, positively charged, and charge-neutral polar and nonpolar amino acids. The negatively charged amino acids orient around 98% of the neighboring water dipoles toward the protein surface, and such correlation persists up to around 16 Å from the protein surface. The positively charged amino acids orient around 94% of the nearest water dipoles against the protein surface, and the correlation persists up to around 12 Å. The charge-neutral polar and nonpolar amino acids are also orienting the water neighbors in a quantitatively weaker manner. A similar trend was observed in the residence time of the nearest water neighbors. These findings hold true for 3 technically important enzymes (PETase, cytochrome P450, and organophosphorus hydrolase). Our results demonstrate that the water−amino acid degree of correlation follows the same trend as the amino acid contribution in proteins solubility, namely, the negatively charged amino acids are the most beneficial for protein solubility, then the positively charged amino acids, and finally the charge-neutral amino acids.

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Section: Petase Surface Domains Distinctly Govern the Orientation Andmentioning

confidence: 99%

mentioning

confidence: 99%

Water follows polar and nonpolar protein surface domains

Qiao

Jiménez-Ángeles

Nguyen

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

100

View full text Add to dashboard Cite

show abstract

“…The surrounding of protein in the cellular environment consists mainly of water molecules along with ions and other important co‐factors. The water molecules in the immediate vicinity of protein influence the dynamics and function of proteins . These surrounding water molecules are known to form a hydration layer.…”

Section: Introductionmentioning

confidence: 99%

Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

et al. 2020

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Urea at sufficiently high concentration unfolds the secondary structure of proteins leading to denaturation. In contrast, choline chloride (ChCl) and urea, in 1 : 2 molar ratio, form a deep eutectic mixture, a liquid at room temperature, protecting proteins from denaturation. In order to get a microscopic picture of this phenomenon, we perform extensive all‐atom molecular dynamics simulations on a model protein, HP‐36. Based on our calculation of Kirkwood‐Buff integrals, we analyze the relative accumulation of urea and ChCl around the protein. Additional insights are drawn from the translational and rotational dynamics of solvent molecules and hydrogen bond auto‐correlation functions. In the presence of urea, water shows slow subdiffusive dynamics around the protein owing to a strong interaction of water with the backbone atoms. Urea also shows subdiffusive motion. The addition of ChCl further slows down the dynamics of urea, restricting its accumulation around the protein backbone. Adding to this, choline cations in the first solvation shell of the protein show the strongest subdiffusive behavior. In other words, ChCl acts as a nano‐crowder by excluding urea from the protein backbone and thereby slowing down the dynamics of water around the protein. This prevents the protein from denaturation and makes it structurally rigid, which is supported by the smaller radius of gyration and root mean square deviation values of HP‐36.

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“…For UN, the values of D e and β of the Morse function fitted from DFT-PBE1 results are 5.08 eV and 1.79Å − 1 , respectively. us, ω e � 816.72 cm − 1 after substituting the β and D e values into equation (3). en, the anharmonicity constant χ e � 0.004983 from equation (4), and χ e ω e � 4.07 cm − 1 .…”

Section: Journal Of Chemistrymentioning

confidence: 99%

“…e properties and phenomena in materials typically occur at multiple time and length scales. erefore, to investigate the dynamic behaviors and the time evolution processes, one should resort to the molecular dynamics simulations instead of the first principles [3]. As an alternative solution, molecular dynamics simulation with a molecular force field is a practical method to calculate the dynamic property of the condensed materials [4].…”

Section: Introductionmentioning

confidence: 99%

Potential Functions and Thermodynamic Properties of UC, UN, and UH

Tang

Wang

Xia

et al. 2020

Journal of Chemistry

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Potential energy surface scanning for UC, UN, and UH was performed by configuration interaction (CI), coupled cluster singles and doubles (CCSD) excitation, quadratic configuration interaction (QCISD (T)), and density functional theory PBE1 (DFT-PBE1) methods in coupling with the ECP80MWB_AVQZ + 2f basis set for uranium and 6 − 311 + G∗ for carbon, hydrogen, and nitrogen. The dissociation energies of UC, UN, and UH are 5.7960, 4.5077, and 2.6999 eV at the QCISD (T) levels, respectively. The calculated energy was fitted to the potential functions of Morse, Lennard-Jones, and Rydberg by using the least square method. The anharmonicity constant of UC is 0.0047160. The anharmonic frequency of UC is 780.27 cm−1 which was obtained based on the PBE1 results. For UN, the anharmonicity constant is 0.0049827. The anharmonic frequency is 812.65 cm−1 which was obtained through the PBE1 results. For UH, the anharmonicity constant is 0.017300. The anharmonic frequency obtained via the QCISD (T) results is 1449.8 cm−1. The heat capacity and entropy in different temperatures were calculated using anharmonic frequencies. These properties are in good accordance with the direct DFT-UPBE1 results (for UC and UN) and QCISD (T) results (for UH). The relationship of entropy with temperature was established.

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Mechanism of Solvent Control of Protein Dynamics

Cited by 46 publications

References 64 publications

Water follows polar and nonpolar protein surface domains

Water follows polar and nonpolar protein surface domains

Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

Potential Functions and Thermodynamic Properties of UC, UN, and UH

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