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Stackhouse CI, Pierson KN, Labrecque CL, Mawson C, Berg J, Fuglestad B, Nucci NV. Characterization of 10MAG/LDAO reverse micelles: Understanding versatility for protein encapsulation. Biophys Chem 2024; 311:107269. [PMID: 38815545 PMCID: PMC11225088 DOI: 10.1016/j.bpc.2024.107269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024]
Abstract
Reverse micelles (RMs) are spontaneously organizing nanobubbles composed of an organic solvent, surfactants, and an aqueous phase that can encapsulate biological macromolecules for various biophysical studies. Unlike other RM systems, the 1-decanoyl-rac-glycerol (10MAG) and lauryldimethylamine-N-oxide (LDAO) surfactant system has proven to house proteins with higher stability than other RM mixtures with little sensitivity to the water loading (W0, defined by the ratio of water to surfactant). We investigated this unique property by encapsulating three model proteins - cytochrome c, myoglobin, and flavodoxin - in 10MAG/LDAO RMs and applying a variety of experimental methods to characterize this system's behavior. We found that this surfactant system differs greatly from the traditional, spherical, monodisperse RM population model. 10MAG/LDAO RMs were discovered to be oblate ellipsoids at all conditions, and as W0 was increased, surfactants redistributed to form a greater number of increasingly spherical ellipsoidal particles with pools of more bulk-like water. Proteins distinctively influence the thermodynamics of the mixture, encapsulating at their optimal RM size and driving protein-free RM sizes to scale accordingly. These findings inform the future development of similarly malleable encapsulation systems and build a foundation for application of 10MAG/LDAO RMs to analyze biological and chemical processes under nanoscale confinement.
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Affiliation(s)
- Crystal I Stackhouse
- Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States; Department of Biomedical and Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States.
| | - Kali N Pierson
- Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States; Department of Biomedical and Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States.
| | - Courtney L Labrecque
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States.
| | - Cara Mawson
- Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States; Department of Biomedical and Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States.
| | - Joshua Berg
- Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States; Department of Biomedical and Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States
| | - Brian Fuglestad
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States.
| | - Nathaniel V Nucci
- Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States; Department of Biomedical and Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States.
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2
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Yang L, Guo S, Liao C, Hou C, Jiang S, Li J, Ma X, Shi L, Ye L, He X. Spatial Layouts of Low-Entropy Hydration Shells Guide Protein Binding. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2300022. [PMID: 37483413 PMCID: PMC10362119 DOI: 10.1002/gch2.202300022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/29/2023] [Indexed: 07/25/2023]
Abstract
Protein-protein binding enables orderly biological self-organization and is therefore considered a miracle of nature. Protein‒protein binding is driven by electrostatic forces, hydrogen bonding, van der Waals force, and hydrophobic interactions. Among these physical forces, only hydrophobic interactions can be considered long-range intermolecular attractions between proteins due to the electrostatic shielding of surrounding water molecules. Low-entropy hydration shells around proteins drive hydrophobic attraction among them that essentially coordinate protein‒protein binding. Here, an innovative method is developed for identifying low-entropy regions of hydration shells of proteins by screening off pseudohydrophilic groups on protein surfaces and revealing that large low-entropy regions of the hydration shells typically cover the binding sites of individual proteins. According to an analysis of determined protein complex structures, shape matching between a large low-entropy hydration shell region of a protein and that of its partner at the binding sites is revealed as a universal law. Protein‒protein binding is thus found to be mainly guided by hydrophobic collapse between the shape-matched low-entropy hydration shells that is verified by bioinformatics analyses of hundreds of structures of protein complexes, which cover four test systems. A simple algorithm is proposed to accurately predict protein binding sites.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
- School of AerospaceMechanical and Mechatronic EngineeringThe University of SydneyNSW2006Australia
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Chenchen Liao
- School of Electronics and Information EngineeringHarbin Institute of TechnologyHarbin150080P. R. China
| | - Chengyu Hou
- School of Electronics and Information EngineeringHarbin Institute of TechnologyHarbin150080P. R. China
| | - Shenda Jiang
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Lin Ye
- School of System Design and Intelligent ManufacturingSouthern University of Science and TechnologyShenzhen518055P. R. China
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
- Shenzhen STRONG Advanced Materials Research Institute Co., LtdShenzhen518035P. R. China
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3
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Shi J, Cho JH, Hwang W. Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding. J Chem Theory Comput 2023; 19:1875-1887. [PMID: 36820489 PMCID: PMC10848206 DOI: 10.1021/acs.jctc.2c00776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Indexed: 02/24/2023]
Abstract
Atomistic-level understanding of surface hydration mediating protein-protein interactions and ligand binding has been a challenge due to the dynamic nature of water molecules near the surface. We develop a computational method to evaluate the solvation free energy based on the density map of the first hydration shell constructed from all-atom molecular dynamics simulation and use it to examine the binding of two intrinsically disordered ligands to their target protein domain. One ligand is from the human protein, and the other is from the 1918 Spanish flu virus. We find that the viral ligand incurs a 6.9 kcal/mol lower desolvation penalty upon binding to the target, which is consistent with its stronger binding affinity. The difference arises from the spatially fragmented and nonuniform water density profiles of the first hydration shell. In particular, residues that are distal from the ligand-binding site contribute to a varying extent to the desolvation penalty, among which the "entropy hotspot" residues contribute significantly. Thus, ligand binding alters hydration on remote sites in addition to affecting the binding interface. The nonlocal effect disappears when the conformational motion of the protein is suppressed. The present results elucidate the interplay between protein conformational dynamics and surface hydration. Our approach of measuring the solvation free energy based on the water density of the first hydration shell is tolerant of the conformational fluctuation of protein, and we expect it to be applicable to investigating a broad range of biomolecular interfaces.
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Affiliation(s)
- Jie Shi
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 777843, United States
| | - Jae-Hyun Cho
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas 77843, United States
| | - Wonmuk Hwang
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, United States
- Department
of Materials Science and Engineering, Texas
A&M University, College Station, Texas 77843, United States
- Department
of Physics and Astronomy, Texas A&M
University, College Station, Texas 77843, United States
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4
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Dubey A, Takeuchi K, Reibarkh M, Arthanari H. The role of NMR in leveraging dynamics and entropy in drug design. JOURNAL OF BIOMOLECULAR NMR 2020; 74:479-498. [PMID: 32720098 PMCID: PMC7686249 DOI: 10.1007/s10858-020-00335-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/11/2020] [Indexed: 05/03/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has contributed to structure-based drug development (SBDD) in a unique way compared to the other biophysical methods. The potency of a ligand binding to a protein is dictated by the binding free energy, which is an intricate interplay between entropy and enthalpy. In addition to providing the atomic resolution structural information, NMR can help to identify protein-ligand interactions that potentially contribute to the enthalpic component of the free energy. NMR can also illuminate dynamic aspects of the interaction, which correspond to the entropic term of the free energy. The ability of NMR to access both terms in the free energy equation stems from the suite of experiments developed to shed light on various aspects that contribute to both entropy and enthalpy, deepening our understanding of the biological function of macromolecules and assisting to target them in physiological conditions. Here we provide a brief account of the contribution of NMR to SBDD, highlighting hallmark examples and discussing the challenges that demand further method development. In the era of integrated biology, the unique ability of NMR to directly ascertain structural and dynamical aspects of macromolecule and monitor changes in these properties upon engaging a ligand can be combined with computational and other structural and biophysical methods to provide a more complete picture of the energetics of drug engagement with the target. Such efforts can be used to engineer better drugs.
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Affiliation(s)
- Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute & Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan.
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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5
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Marques BS, Stetz MA, Jorge C, Valentine KG, Wand AJ, Nucci NV. Protein conformational entropy is not slaved to water. Sci Rep 2020; 10:17587. [PMID: 33067552 PMCID: PMC7567893 DOI: 10.1038/s41598-020-74382-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
Conformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The "solvent slaving" model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side chain dynamics of several proteins are unaffected by changes to the hydration layer and bulk water. These observations indicate that the participation of conformational entropy in protein function is not dictated by the interaction of protein molecules and solvent water under the range of conditions normally encountered.
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Affiliation(s)
- Bryan S Marques
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew A Stetz
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Christine Jorge
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen G Valentine
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77845-2128, USA.
| | - Nathaniel V Nucci
- Department of Physics and Astronomy and Department of Molecular and Cellular Biosciences, Rowan University, 201 Mullica Hill Road, Glassboro, NJ, 08028, USA.
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O'Brien ES, Fuglestad B, Lessen HJ, Stetz MA, Lin DW, Marques BS, Gupta K, Fleming KG, Wand AJ. Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy. Angew Chem Int Ed Engl 2020; 59:11108-11114. [PMID: 32277554 PMCID: PMC7318686 DOI: 10.1002/anie.202003527] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Indexed: 12/31/2022]
Abstract
The internal motions of integral membrane proteins have largely eluded comprehensive experimental characterization. Here the fast side-chain dynamics of the α-helical sensory rhodopsin II and the β-barrel outer membrane protein W have been investigated in lipid bilayers and detergent micelles by solution NMR relaxation techniques. Despite their differing topologies, both proteins have a similar distribution of methyl-bearing side-chain motion that is largely independent of membrane mimetic. The methyl-bearing side chains of both proteins are, on average, more dynamic in the ps-ns timescale than any soluble protein characterized to date. Accordingly, both proteins retain an extraordinary residual conformational entropy in the folded state, which provides a counterbalance to the absence of the hydrophobic effect. Furthermore, the high conformational entropy could greatly influence the thermodynamics underlying membrane-protein functions, including ligand binding, allostery, and signaling.
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Affiliation(s)
- Evan S. O'Brien
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
| | - Brian Fuglestad
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
- Present address: Department of ChemistryVirginia Commonwealth UniversityRichmondVA23284USA
| | - Henry J. Lessen
- Department of BiophysicsJohns Hopkins UniversityBaltimoreMD21218USA
| | - Matthew A. Stetz
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
| | - Danny W. Lin
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
| | - Bryan S. Marques
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
| | - Kushol Gupta
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
| | - Karen G. Fleming
- Department of BiophysicsJohns Hopkins UniversityBaltimoreMD21218USA
| | - A. Joshua Wand
- Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTX77843USA
- Department of Biochemistry & BiophysicsUniversity of PennsylvaniaPerelman School of MedicinePhiladelphiaPA19104USA
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7
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O'Brien ES, Fuglestad B, Lessen HJ, Stetz MA, Lin DW, Marques BS, Gupta K, Fleming KG, Wand AJ. Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Evan S. O'Brien
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
| | - Brian Fuglestad
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
- Present address: Department of Chemistry Virginia Commonwealth University Richmond VA 23284 USA
| | - Henry J. Lessen
- Department of Biophysics Johns Hopkins University Baltimore MD 21218 USA
| | - Matthew A. Stetz
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
| | - Danny W. Lin
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
| | - Bryan S. Marques
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
| | - Kushol Gupta
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
| | - Karen G. Fleming
- Department of Biophysics Johns Hopkins University Baltimore MD 21218 USA
| | - A. Joshua Wand
- Department of Biochemistry & Biophysics Texas A&M University College Station TX 77843 USA
- Department of Biochemistry & Biophysics University of Pennsylvania Perelman School of Medicine Philadelphia PA 19104 USA
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8
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Liu X, Yu Q, Song A, Dong S, Hao J. Progress in nuclear magnetic resonance studies of surfactant systems. Curr Opin Colloid Interface Sci 2020. [DOI: 10.1016/j.cocis.2019.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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9
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Honegger P, Steinhauser O. The nuclear Overhauser Effect (NOE) as a tool to study macromolecular confinement: Elucidation and disentangling of crowding and encapsulation effects. J Chem Phys 2020; 152:024120. [PMID: 31941328 DOI: 10.1063/1.5135816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We propose a methodology to capture short-lived but biophysically important contacts of biomacromolecules using the biomolecule-water nuclear Overhauser effect as an indirect microscope. Thus, instead of probing the direct correlation with the foreign biomolecule, we detect its presence by the disturbance it causes in the surrounding water. In addition, this information obtained is spatially resolved and can thus be attributed to specific sites. We extend this approach to the influence of more than one change in chemical environment and show a methodological way of resolution. This is achieved by taking double differences of corresponding σNOE/σROE ratios of the systems studied and separating specific, unspecific, and intermediate influence. While applied to crowding and encapsulation in this study, this method is generally suitable for any combination of changes in chemical environment.
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Affiliation(s)
- Philipp Honegger
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
| | - Othmar Steinhauser
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstraße 17, A-1090 Vienna, Austria
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10
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Honegger P, Steinhauser O. The protein-water nuclear Overhauser effect (NOE) as an indirect microscope for molecular surface mapping of interaction patterns. Phys Chem Chem Phys 2019; 22:212-222. [PMID: 31799520 DOI: 10.1039/c9cp04752b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this computational study, the intermolecular solute-solvent Nuclear Overhauser Effect (NOE) of the model protein ubiquitin in different chemical environments (free, bound to a partner protein and encapsulated) is investigated. Short-ranged NOE observables such as the NOE/ROE ratio reveal hydration phenomena on absolute timescales such as fast hydration sites and slow water clefts. We demonstrate the ability of solute-solvent NOE differences measured of the same protein in different chemical environments to reveal hydration changes on the relative timescale. The resulting NOE/ROE-surface maps are shown to be a central key for analyzing biologically relevant chemical influences such as complexation and confinement: the presence of a complexing macromolecule or a confining surface wall modulates the water mobility in the vicinity of the probe protein, hence revealing which residues of said protein are proximate to the foreign interface and which are chemically unaffected. This way, hydration phenomena can serve to indirectly map the precise influence (position) of other molecules or interfaces onto the protein surface. This proposed one-protein many-solvents approach may offer experimental benefits over classical one-protein other-protein pseudo-intermolecular transient NOEs. Furthermore, combined influences such as complexation and confinement may exert non-additive influences on the protein compared to a reference state. We offer a mathematical method to disentangle the influence of these two different chemical environments.
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Affiliation(s)
- Philipp Honegger
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, A-1090 Vienna, Austria.
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11
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Dahanayake JN, Shahryari E, Roberts KM, Heikes ME, Kasireddy C, Mitchell-Koch KR. Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics. J Chem Inf Model 2019; 59:2407-2422. [PMID: 30865440 DOI: 10.1021/acs.jcim.9b00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate the pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer. The finding thus hinted at a handle for rapid evaluation of hydration dynamics at different regions on the protein surface in molecular dynamics simulations. Such an approach may move the analysis of hydration dynamics from a specialized venture to routine analysis, enabling an informatics approach to evaluate the role of hydration dynamics in biomolecular function. This paper first confirms that the correlation between regional diffusive dynamics and hydration layer structure (via water center of mass around protein side-chain atom RDF) is observed as a general relationship across a set of proteins. Second, it seeks to devise an approach for rapid analysis of hydration dynamics, determining the minimum amount of information and computational effort required to get a reliable value of hydration dynamics from structural data in MD simulations based on the protein-water RDF. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically equivalent apparent diffusion coefficients at the 95% confidence level for a set of 92 regions within five different proteins. In summary, RDF analysis of 10 ns of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is anticipated that a quick look at protein-water RDFs, comparing peak heights, will be useful to provide a qualitative ranking of regions of faster and slower hydration dynamics at the protein surface for rapid analysis when investigating the role of solvent dynamics in protein function.
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Affiliation(s)
- Jayangika N Dahanayake
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Elaheh Shahryari
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Kirsten M Roberts
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Micah E Heikes
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Chandana Kasireddy
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Katie R Mitchell-Koch
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
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