1
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Wang S, Wang M, Han L, Sun Y, Cai W, Shao X. Insight into the stability of protein in confined environment through analyzing the structure of water by temperature-dependent near-infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120581. [PMID: 34776375 DOI: 10.1016/j.saa.2021.120581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/13/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
To understand the stability of protein in confined environment, the near-infrared (NIR) spectra of aqueous solutions and reverse micelles (RMs) containing bovine serum albumin (BSA), human serum albumin (HSA) and ovalbumin (OVA) were measured at different temperature. With the resolution enhanced spectra calculated by continuous wavelet transform (CWT), the intensity change of the α-helix band at 4617 cm-1 with temperature shows a clear denaturation of the protein in aqueous solution but not in RMs. The effect of the confined environment on the stability of the proteins is indicated. More importantly, the intensity change of the spectral bands of water around 6956 and 6842 cm-1 provide an evidence for the denaturation, suggesting that water can be a probe exhibiting the structural change of proteins. Furthermore, comparing the spectral features of different water structures obtained by principal component analysis (PCA) from the spectra of RM with and without BSA, it is demonstrated that the bridging water connecting NH in protein and SO in the inner surface of RM may be the reason for the stabilization.
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Affiliation(s)
- Shiying Wang
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China
| | - Mian Wang
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China
| | - Li Han
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China
| | - Yan Sun
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China
| | - Wensheng Cai
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China
| | - Xueguang Shao
- Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, PR China.
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2
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Roy P, Sengupta N. Hydration of a small protein under carbon nanotube confinement: Adsorbed substates induce selective separation of the dynamical response. J Chem Phys 2021; 154:204702. [PMID: 34241160 DOI: 10.1063/5.0047078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The co-involvement of biological molecules and nanomaterials has increasingly come to the fore in modern-day applications. While the "bio-nano" (BN) interface presents physico-chemical characteristics that are manifestly different from those observed in isotropic bulk conditions, the underlying molecular reasons remain little understood; this is especially true of anomalies in interfacial hydration. In this paper, we leverage atomistic simulations to study differential adsorption characteristics of a small protein on the inner (concave) surface of a single-walled carbon nanotube whose diameter exceeds dimensions conducive to single-file water movement. Our findings indicate that the extent of adsorption is decided by the degree of foldedness of the protein conformational substate. Importantly, we find that partially folded substates, but not the natively folded one, induce reorganization of the protein hydration layer into an inner layer water closer to the nanotube axis and an outer layer water in the interstitial space near the nanotube walls. Further analyses reveal sharp dynamical differences between water molecules in the two layers as observed in the onset of increased heterogeneity in rotational relaxation and the enhanced deviation from Fickian behavior. The vibrational density of states reveals that the dynamical distinctions are correlated with differences in crucial bands in the power spectra. The current results set the stage for further systematic studies of various BN interfaces vis-à-vis control of hydration properties.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
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3
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Abel S, Marchi M. Deciphering the Structure of the Gramicidin A Channel in the Presence of AOT Reverse Micelles in Pentane Using Molecular Dynamics Simulations. J Phys Chem B 2020; 124:11802-11818. [PMID: 33346653 DOI: 10.1021/acs.jpcb.0c08902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural studies of proteins and, in particular, integral membrane proteins (IMPs) using solution NMR spectroscopy approaches are challenging due to not only their inherent structural complexities but also the fact that they need to be solubilized in biomimetic environments (such as micelles), which enhances the slow molecular reorientation. To deal with these difficulties and increase the effective rate of molecular reorientation, the encapsulation of IMPs in the aqueous core of the reverse micelle (RM) dissolved in a low-viscosity solvent has been proven to be a viable approach. However, the effect of the reverse micelle (RM) environment on the IMP structure and function is little known. To gain insight into these aspects, this article presents a series of atomistic unconstrained molecular dynamics (MD) of a model ion channel (gramicidin A, gA) with RMs formed with anionic surfactant diacyl chain bis(2-ethylhexyl) sodium succinate (AOT) in pentane at a water-to-surfactant molar ratio (W0) of 6. The simulations were carried out with different protocols and starting conditions for a total of 2.4 μs and were compared with other MDs used with the gA channel inserted in models of the SDS micelle or the DMPC membrane. We show here that in the presence of AOT RMs the gA dimer did not look like the "dumbbell-like" model anticipated by experiments, where the C-terminal parts of the gA are capped with two RMs and the rest of the dimer is protected from the oil solvent by the AOT acyl chains. In contrast, the MD simulations reveal that the AOT, Na+, and water formed two well-defined and elongated RMs attached to the C-terminal ends of the gA dimer, while the rest is in direct contact with the pentane. The initial β6.3 secondary structure of the gA is well conserved and filled with 6-9 waters, as in SDS micelles or the DMPC membrane. Finally, the water movement inside the gA is strongly affected by the presence of RMs at each extremity, and no passage of water molecules through the gA channel is observed even after a long simulation period, whereas the opposite was found for gA in SDS and DMPC.
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Affiliation(s)
- Stéphane Abel
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Massimo Marchi
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France
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4
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Ngo VA, Sarkar S, Neale C, Garcia AE. How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes. J Phys Chem B 2020; 124:5434-5453. [PMID: 32438809 DOI: 10.1021/acs.jpcb.0c02642] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RAS proteins are small membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the spatiotemporal properties of RAS through dimerization/clustering and signaling fidelity. To understand the effects of anionic lipids on key spatiotemporal properties of RAS, we dissected 1 ms of data from all-atom molecular dynamics simulations for KRAS4B on two model anionic lipid membranes that have 30% of POPS mixed with neutral POPC and 8% of PIP2 mixed with POPC. We unveiled the orientation space of KRAS4B, whose kinetics were slower and more distinguishable on the membrane containing PIP2 than the membrane containing POPS. Particularly, the PIP2-mixed membrane can differentiate a third kinetic orientation state from the other two known orientation states. We observed that each orientation state may yield different binding modes with an RAF kinase, which is required for activating the MAPK/ERK signaling pathway. However, an overall occluded probability, for which RAF kinases cannot bind KRAS4B, remains unchanged on the two different membranes. We identified rare fast diffusion modes of KRAS4B that appear coupled with orientations exposed to cytosolic RAF. Particularly, on the membrane having PIP2, we found nonlinear correlations between the orientation states and the conformations of the cationic farnesylated hypervariable region, which acts as an anchor in the membrane. Using diffusion coefficients estimated from the all-atom simulations, we quantified the effect of PIP2 and POPS on the KRAS4B dimerization via Green's function reaction dynamics simulations, in which the averaged dimerization rate is 12.5% slower on PIP2-mixed membranes.
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Affiliation(s)
- Van A Ngo
- Center for Nonlinear Studies (CNLS), Los Alamos National Lab, Los Alamos, New Mexico 87545, United States
| | - Sumantra Sarkar
- Center for Nonlinear Studies (CNLS), Los Alamos National Lab, Los Alamos, New Mexico 87545, United States
| | - Chris Neale
- Theoretical Biology and Biophysics Group, T-6, Los Alamos National Lab, Los Alamos, New Mexico 87545, United States
| | - Angel E Garcia
- Center for Nonlinear Studies (CNLS), Los Alamos National Lab, Los Alamos, New Mexico 87545, United States
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5
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Honegger P, Heid E, Schröder C, Steinhauser O. Dielectric spectroscopy and time dependent Stokes shift: two faces of the same coin? Phys Chem Chem Phys 2020; 22:18388-18399. [DOI: 10.1039/d0cp02840a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different types of spectroscopy capture different aspects of dynamics and different ranges of intermolecular contributions.
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- 1090 Vienna
- Austria
| | - Esther Heid
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- 1090 Vienna
- Austria
| | - Christian Schröder
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- 1090 Vienna
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- 1090 Vienna
- Austria
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6
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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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7
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Honegger P, Steinhauser O. Hydration dynamics of proteins in reverse micelles probed by 1H-NOESY/ 1H-ROESY NMR and 17O-nuclear quadrupole resonance (NQR). Phys Chem Chem Phys 2019; 21:14571-14582. [PMID: 31237595 DOI: 10.1039/c9cp02654a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study is based on extensive MD simulations of a protein in a reverse micelle to mimic the effect of confinement on biomolecules. This permits the calculation of measurable quantities appearing in NQR and Nuclear Overhauser-NMR despite the high computational effort. We address the long-standing debate about the intermolecular NOE showing that absolute quantities derived from NOESY and ROESY spectra do indeed contain considerable long-range contributions, while ratios thereof are effectively short-ranged due to almost perfect compensation effects. Based on NQR relaxation times, we predict strong rotational retardation of interstitial water between the protein and the surfactant surface. The computed NOE to ROE ratio correlates fairly with experimental results. The solvation dynamics mapped onto the protein surface reflects the spatial heterogeneity of a cell-like system with slow water dynamics in proximity to the cell wall and almost bulk-like behaviour in the water core.
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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.
| | - Othmar Steinhauser
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, A-1090 Vienna, Austria.
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8
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Honegger P, Steinhauser O. Towards capturing cellular complexity: combining encapsulation and macromolecular crowding in a reverse micelle. Phys Chem Chem Phys 2019; 21:8108-8120. [DOI: 10.1039/c9cp00053d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper studies the orientational structure and dynamics of multi-protein systems under confinement and discusses the implications on biological cells.
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
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9
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Heid E, Braun D. Fundamental limitations of the time-dependent Stokes shift for investigating protein hydration dynamics. Phys Chem Chem Phys 2019; 21:4435-4443. [DOI: 10.1039/c8cp07623e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the TDSS measured in protein systems, large protein contributions fully obscure hydration dynamics.
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Affiliation(s)
- Esther Heid
- Department of Computational Biological Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
| | - Daniel Braun
- Department of Computational Biological Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
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10
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Honegger P, Heid E, Schmode S, Schröder C, Steinhauser O. Changes in protein hydration dynamics by encapsulation or crowding of ubiquitin: strong correlation between time-dependent Stokes shift and intermolecular nuclear Overhauser effect. RSC Adv 2019; 9:36982-36993. [PMID: 35539058 PMCID: PMC9075347 DOI: 10.1039/c9ra08008b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022] Open
Abstract
The local changes in protein hydration dynamics upon encapsulation of the protein or macromolecular crowding are essential to understand protein function in cellular environments. We were able to obtain a spatially-resolved picture of the influence of confinement and crowding on the hydration dynamics of the protein ubiquitin by analyzing the time-dependent Stokes shift (TDSS), as well as the intermolecular Nuclear Overhauser Effect (NOE) at different sites of the protein by large-scale computer simulation of single and multiple proteins in water and confined in reverse micelles. Besides high advanced space resolved information on hydration dynamics we found a strong correlation of the change in NOE upon crowding or encapsulation and the change in the integral TDSS relaxation times in all investigated systems relative to the signals in a diluted protein solution. Changes in local protein hydration dynamics caused by encapsulation or crowding are reflected in the TDSS and the intermolecular NOE alike.![]()
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Esther Heid
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Stella Schmode
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Christian Schröder
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
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11
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Urano R, Pantelopulos GA, Song S, Straub JE. Characterization of dynamics and mechanism in the self-assembly of AOT reverse micelles. J Chem Phys 2018; 149:144901. [DOI: 10.1063/1.5042771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ryo Urano
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - George A. Pantelopulos
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - Shanshan Song
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - John E. Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
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12
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Honegger P, Schmollngruber M, Steinhauser O. Micellar confinement disrupts collective structure and accelerates collective dynamics of encapsulated water. Phys Chem Chem Phys 2018; 20:11454-11469. [DOI: 10.1039/c8cp01508b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Detailed numerical study of the dielectric spectrum of zwitterionic reverse micelles is combined with interpretation using a new semi-quantitative analytical model.
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Michael Schmollngruber
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
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13
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Honegger P, Steinhauser O. Revival of collective water structure and dynamics in reverse micelles brought about by protein encapsulation. Phys Chem Chem Phys 2018; 20:22932-22945. [DOI: 10.1039/c8cp03422b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel mechanism of depolarization in reverse micelles with zwitterionic surfactants and containing polar species but lacking ions is reported.
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Affiliation(s)
- Philipp Honegger
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - Othmar Steinhauser
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
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14
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Vierros S, Österberg M, Sammalkorpi M. Aggregation response of triglyceride hydrolysis products in cyclohexane and triolein. Phys Chem Chem Phys 2018; 20:27192-27204. [DOI: 10.1039/c8cp05104f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aggregation mechanism and the existence of cmc depend on apolar solvent quality and surfactant head group polarity.
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Affiliation(s)
- Sampsa Vierros
- Department of Chemistry and Materials Science
- Aalto University
- 00076 Aalto
- Finland
| | - Monika Österberg
- Department of Bioproducts and Biotechnology
- Aalto University
- 00076 Aalto
- Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science
- Aalto University
- 00076 Aalto
- Finland
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15
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Braun D, Schmollngruber M, Steinhauser O. Revival of the Intermolecular Nuclear Overhauser Effect for Mapping Local Protein Hydration Dynamics. J Phys Chem Lett 2017; 8:3421-3426. [PMID: 28686451 DOI: 10.1021/acs.jpclett.7b01013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The highly heterogeneous hydration dynamics of protein-water interfaces is considered important for protein stability and dynamics, protein folding, enzymatic activity, and even drug design. The nuclear Overhauser effect (NOE) between protein and water protons is the only experimental observable which, in principle, can provide a map of locally resolved hydration dynamics. However, its utility was questioned in various theoretical studies that emphasized the contributions of long-range NOE interactions. We show by a detailed analysis based on molecular dynamics simulations that, contrary to recent claims, the protein-water NOE is an excellent observable to map local hydration dynamics at the protein surface.
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Affiliation(s)
- Daniel Braun
- Department of Computational Biological Chemistry, University of Vienna , Währinger Straße 17, 1090 Vienna, Austria
| | - Michael Schmollngruber
- Department of Computational Biological Chemistry, University of Vienna , Währinger Straße 17, 1090 Vienna, Austria
| | - Othmar Steinhauser
- Department of Computational Biological Chemistry, University of Vienna , Währinger Straße 17, 1090 Vienna, Austria
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16
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Abstract
Previously published experimental studies have suggested that when the 40-residue amyloid beta peptide is encapsulated in a reverse micelle, it folds into a structure that may nucleate amyloid fibril formation (Yeung, P. S.-W.; Axelsen, P. H. J. Am. Chem. Soc. 2012, 134, 6061 ). The factors that induce the formation of this structure have now been identified in a multi-microsecond simulation of the same reverse micelle system that was studied experimentally. Key features of the polypeptide-micelle interaction include the anchoring of a hydrophobic residue cluster into gaps in the reverse micelle surface, the formation of a beta turn at the anchor point that brings N- and C-terminal segments of the polypeptide into proximity, high ionic strength that promotes intramolecular hydrogen bond formation, and deformation of the reverse micelle surface to facilitate interactions with the surface along the entire length of the polypeptide. Together, these features cause the simulation-derived vibrational spectrum to red shift in a manner that reproduces the red-shift previously reported experimentally. On the basis of these findings, a new mechanism is proposed whereby membranes nucleate fibril formation and facilitate the in-register alignment of polypeptide strands that is characteristic of amyloid fibrils.
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Affiliation(s)
- Gözde Eskici
- Department of Biochemistry & Biophysics, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
| | - Paul H Axelsen
- Departments of Pharmacology, Biochemistry and Biophysics, and Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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18
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Glycine molecules in ionic liquid based reverse micelles: Investigation of structure and dynamics using molecular dynamics simulations. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.01.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Schmollngruber M, Braun D, Steinhauser O. A computational component analysis of dielectric relaxation and THz spectra of water/AOT reverse micelles with different water loading. J Chem Phys 2016; 145:214702. [DOI: 10.1063/1.4971165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Daniel Braun
- Department of Computational Biological Chemistry, University of Vienna, Vienna, Austria
| | - Othmar Steinhauser
- Department of Computational Biological Chemistry, University of Vienna, Vienna, Austria
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20
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Abstract
Reverse micelles (RMs) made from water and sodium bis(2-ethylhexyl) sulfosuccinate (AOT) are commonly studied experimentally as models of aqueous microenvironments. They are small enough for individual RMs to also be studied by molecular dynamics (MD) simulation, which yields detailed insight into their structure and properties. Although RM size is determined by the water loading ratio (i.e., the molar ratio of water to AOT), experimental measurements of RM size are imprecise and inconsistent, which is problematic when seeking to understand the relationship between water loading ratio and RM size, and when designing models for study by MD simulation. Therefore, a systematic study of RM size was performed by MD simulation with the aims of determining the size of an RM for a given water loading ratio, and of reconciling the results with experimental measurements. Results for a water loading ratio of 7.5 indicate that the interaction energy between AOT anions and other system components is at a minimum when there are 62 AOT anions in each RM. The minimum is due to a combination of attractive and repulsive electrostatic interactions that vary with RM size and the dielectric effect of available water. Overall, the results agree with a detailed analysis of previously published experimental data over a wide range of water loading ratios, and help reconcile seemingly discrepant experimental results. In addition, water loss and gain from an RM is observed and the mechanism of water exchange is outlined. This kind of RM model, which faithfully reproduces experimental results, is essential for reliable insights into the properties of RM-encapsulated materials.
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Affiliation(s)
- Gözde Eskici
- Department of Biochemistry & Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia 19104, United States
| | - Paul H Axelsen
- Departments of Pharmacology, Biochemistry and Biophysics, and Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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21
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Schmollngruber M, Braun D, Oser D, Steinhauser O. Dielectric depolarisation and concerted collective dynamics in AOT reverse micelles with and without ubiquitin. Phys Chem Chem Phys 2016; 18:3606-17. [PMID: 26751837 DOI: 10.1039/c5cp07112g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this computational study we present molecular dynamics (MD) simulations of reverse micelles, i.e. nano-scale water pools encapsulated by sodium bis(2-ethylhexyl) sulfosuccinate (AOT) and dissolved in isooctane. Although consisting of highly polar components, such micro-emulsions exhibit surprisingly low dielectric permittivity, both static and frequency-dependent. This finding is well supported by experimental dielectric measurements. Furthermore, the computational dielectric spectra of reverse micelles with and without the polar protein ubiquitin are almost identical. A detailed component analysis of our simulated systems reveals the underlying mechanism of the observed dielectric depolarisation. While each component by itself would make a remarkable contribution to the static dielectric permittivity, mutual compensation leads to the observed marginal net result. This compensatory behavior is maintained for all but the highest frequencies. Dielectric model theory adapted to the peculiarities of reverse micelles provides an explanation: embedding a system in a cavity engulfed by a low dielectric medium automatically leads to depolarization. In this sense experiment, simulation and theory are in accordance.
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Affiliation(s)
| | - Daniel Braun
- Department of Computational Biological Chemistry, University of Vienna, Austria.
| | - Daniel Oser
- Department of Computational Biological Chemistry, University of Vienna, Austria.
| | - Othmar Steinhauser
- Department of Computational Biological Chemistry, University of Vienna, Austria.
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22
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Bellissent-Funel MC, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia AE. Water Determines the Structure and Dynamics of Proteins. Chem Rev 2016; 116:7673-97. [PMID: 27186992 DOI: 10.1021/acs.chemrev.5b00664] [Citation(s) in RCA: 528] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.
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Affiliation(s)
| | - Ali Hassanali
- International Center for Theoretical Physics, Condensed Matter and Statistical Physics 34151 Trieste, Italy
| | - Martina Havenith
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Richard Henchman
- Manchester Institute of Biotechnology The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Pohl
- Johannes Kepler University , Gruberstrasse, 40 4020 Linz, Austria
| | - Fabio Sterpone
- Institut de Biologie Physico-Chimique Laboratoire de Biochimie Théorique 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - David van der Spoel
- Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University , 751 24 Uppsala, Sweden
| | - Yao Xu
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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23
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Zhang Z, Ohl M, Diallo SO, Jalarvo NH, Hong K, Han Y, Smith GS, Do C. Dynamics of Water Associated with Lithium Ions Distributed in Polyethylene Oxide. PHYSICAL REVIEW LETTERS 2015; 115:198301. [PMID: 26588420 DOI: 10.1103/physrevlett.115.198301] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Indexed: 05/25/2023]
Abstract
The dynamics of water in polyethylene oxide (PEO)/LiCl solution has been studied with quasielastic neutron scattering experiments and molecular dynamics (MD) simulations. Two different time scales of water diffusion representing interfacial water and bulk water dynamics have been identified. The measured diffusion coefficient of interfacial water remained 5-10 times smaller than that of bulk water, but both were slowed by approximately 50% in the presence of Li(+). Detailed analysis of MD trajectories suggests that Li(+) is favorably found at the surface of the hydration layer, and the probability to find the caged Li(+) configuration formed by the PEO is lower than for the noncaged Li(+)-PEO configuration. In both configurations, however, the slowing down of water molecules is driven by reorienting water molecules and creating water-Li(+) hydration complexes. Performing the MD simulation with different ions (Na(+) and K(+)) revealed that smaller ionic radius of the ions is a key factor in disrupting the formation of PEO cages by allowing spaces for water molecules to come in between the ion and PEO.
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Affiliation(s)
- Zhe Zhang
- Biology and Soft-Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Forschungszentrum Jülich, Jülich Center for Neutron Science, Outstation at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Michael Ohl
- Forschungszentrum Jülich, Jülich Center for Neutron Science, Outstation at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Souleymane O Diallo
- Quantum Condensed Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Niina H Jalarvo
- Forschungszentrum Jülich, Jülich Center for Neutron Science, Outstation at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Kunlun Hong
- Center For Nanophase Materials Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Youngkyu Han
- Biology and Soft-Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Gregory S Smith
- Biology and Soft-Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Changwoo Do
- Biology and Soft-Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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24
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Chakraborty D, Taly A, Sterpone F. Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins. J Phys Chem B 2015; 119:12760-70. [PMID: 26335353 DOI: 10.1021/acs.jpcb.5b05791] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a systematic computational investigation of the internal hydration of a set of homologous proteins of different stability content and molecular complexities. The goal of the study is to verify whether structural water can be part of the molecular mechanisms ensuring enhanced stability in thermophilic enzymes. Our free-energy calculations show that internal hydration in the thermophilic variants is generally more favorable, and that the cumulated effect of wetting multiple sites results in a meaningful contribution to stability. Moreover, thanks to a more effective capability to retain internal water, some thermophilic proteins benefit by a systematic gain from internal wetting up to their optimal working temperature. Our work supports the idea that internal wetting can be viewed as an alternative molecular variable to be tuned for increasing protein stability.
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Affiliation(s)
- Debashree Chakraborty
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Antoine Taly
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité , 13 rue Pierre et Marie Curie, 75005 Paris, France
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25
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Duboué-Dijon E, Laage D. Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin. J Chem Phys 2015; 141:22D529. [PMID: 25494800 DOI: 10.1063/1.4902822] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hydration layer surrounding a protein plays an essential role in its biochemical function and consists of a heterogeneous ensemble of water molecules with different local environments and different dynamics. What determines the degree of dynamical heterogeneity within the hydration shell and how this changes with temperature remains unclear. Here, we combine molecular dynamics simulations and analytic modeling to study the hydration shell structure and dynamics of a typical globular protein, ubiquitin, and of the spruce budworm hyperactive antifreeze protein over the 230-300 K temperature range. Our results show that the average perturbation induced by both proteins on the reorientation dynamics of water remains moderate and changes weakly with temperature. The dynamical heterogeneity arises mostly from the distribution of protein surface topographies and is little affected by temperature. The ice-binding face of the antifreeze protein induces a short-ranged enhancement of water structure and a greater slowdown of water reorientation dynamics than the non-ice-binding faces whose effect is similar to that of ubiquitin. However, the hydration shell of the ice-binding face remains less tetrahedral than the bulk and is not "ice-like". We finally show that the hydrogen bonds between water and the ice-binding threonine residues are particularly strong due to a steric confinement effect, thereby contributing to the strong binding of the antifreeze protein on ice crystals.
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Affiliation(s)
- Elise Duboué-Dijon
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
| | - Damien Laage
- Département de Chimie, École Normale Supérieure-PSL Research University, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24, rue Lhomond, 75005 Paris, France
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26
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Martinez AV, Małolepsza E, Domínguez L, Lu Q, Straub JE. Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA2 in AOT Reverse Micelles. J Phys Chem B 2015; 119:9084-90. [PMID: 25337983 PMCID: PMC4516319 DOI: 10.1021/jp508813n] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/20/2014] [Indexed: 11/28/2022]
Abstract
The propensity of peptides to form α-helices has been intensely studied using theory, computation, and experiment. Important model peptides for the study of the coil-to-helix transition have been alanine-lysine (AKA) peptides in which the lysine residues are placed on opposite sides of the helix avoiding charge repulsion while enhancing solubility. In this study, the effects of capped versus zwitterionic peptide termini on the secondary structure of alanine-rich peptides in reverse micelles are explored. The reverse micelles are found to undergo substantial shape fluctuations, a property observed in previous studies of AOT reverse micelles in the absence of solvated peptide. The peptides are observed to interact with water, as well as the AOT surfactant, including interactions between the nonpolar residues and the aliphatic surfactant tails. Computation of IR spectra for the amide I band of the peptide allows for direct comparison with experimental spectra. The results demonstrate that capped AKA2 peptides form more stable α helices than zwitterionic AKA2 peptides in reverse micelles. The rotational anisotropy decay of water is found to be distinctly different in the presence or absence of peptide within the reverse micelle, suggesting that the introduction of peptide significantly alters the number of free waters within the reverse micelle nanopool. However, neither the nature of the peptide termini (capped or charged) nor the degree of peptide helicity is found to significantly alter the balance of interactions between the peptides and the environment. Observed changes in the degree of helicity in AKA2 peptides in bulk solution and in reverse micelle environments result from changes in peptide confinement and hydration as well as direct nonpolar and polar interactions with the water-surfactant interface.
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Affiliation(s)
- Anna Victoria Martinez
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Edyta Małolepsza
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Domínguez
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qing Lu
- Division
of Materials Science and Engineering, Boston
University, 15 Saint
Mary’s Street, Brookline, Massachusetts 02446, United States
| | - John E. Straub
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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27
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Parimal S, Garde S, Cramer SM. Interactions of Multimodal Ligands with Proteins: Insights into Selectivity Using Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:7512-7523. [PMID: 26030224 DOI: 10.1021/acs.langmuir.5b00236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Fundamental understanding of protein-ligand interactions is important to the development of efficient bioseparations in multimodal chromatography. Here we employ molecular dynamics (MD) simulations to investigate the interactions of three different proteins--ubiquitin, cytochrome C, and α-chymotrypsinogen A, sampling a range of charge from +1e to +9e--with two multimodal chromatographic ligands containing similar chemical moieties--aromatic, carboxyl, and amide--in different structural arrangements. We use a spherical harmonic expansion to analyze ligand and individual moiety density profiles around the proteins. We find that the Capto MMC ligand, which contains an additional aliphatic group, displays stronger interactions than Nuvia CPrime ligand with all three proteins. Studying the ligand densities at the moiety level suggests that hydrophobic interactions play a major role in determining the locations of high ligand densities. Finally, the greater structural flexibility of the Capto MMC ligand compared to that of the Nuvia cPrime ligand allows for stronger structural complementarity and enables stronger hydrophobic interactions. These subtle and not-so-subtle differences in binding affinities and modalities for multimodal ligands can result in significantly different binding behavior towards proteins with important implications for bioprocessing.
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Affiliation(s)
- Siddharth Parimal
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Shekhar Garde
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Steven M Cramer
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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28
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Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding. Sci Rep 2015; 5:10549. [PMID: 26023027 PMCID: PMC4448524 DOI: 10.1038/srep10549] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/17/2015] [Indexed: 01/09/2023] Open
Abstract
Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations.
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29
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Vierros S, Sammalkorpi M. Phosphatidylcholine reverse micelles on the wrong track in molecular dynamics simulations of phospholipids in an organic solvent. J Chem Phys 2015; 142:094902. [DOI: 10.1063/1.4914022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- S. Vierros
- Department of Chemistry, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - M. Sammalkorpi
- Department of Chemistry, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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30
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Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014; 43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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31
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Spiga E, Abriata LA, Piazza F, Dal Peraro M. Dissecting the effects of concentrated carbohydrate solutions on protein diffusion, hydration, and internal dynamics. J Phys Chem B 2014; 118:5310-21. [PMID: 24773474 DOI: 10.1021/jp4126705] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present herein a thorough description of the effects of high glucose concentrations on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive molecular dynamics simulations on several systems described at fully atomistic level. We observe that the protein acts as a seed that speeds up the natural propensity of glucose to cluster at high concentration; the sugar molecules thus aggregate around the protein trapping it inside a dynamic cage. This process extensively dehydrates the protein surface, restricts the motions of the remaining water molecules, and drags the large-scale, collective motions of protein atoms slowing down the rate of exploration of the conformational space despite only a slight dampening of fast, local dynamics. We discuss how these effects could be relevant to the function of sugars as preservation agents in biological materials, and how crowding by small sticky molecules could modulate proteins across different reaction coordinates inside the cellular cytosol.
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Affiliation(s)
- Enrico Spiga
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
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32
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Carlsson N, Gustafsson H, Thörn C, Olsson L, Holmberg K, Åkerman B. Enzymes immobilized in mesoporous silica: a physical-chemical perspective. Adv Colloid Interface Sci 2014; 205:339-60. [PMID: 24112562 DOI: 10.1016/j.cis.2013.08.010] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 01/13/2023]
Abstract
Mesoporous materials as support for immobilized enzymes have been explored extensively during the last two decades, primarily not only for biocatalysis applications, but also for biosensing, biofuels and enzyme-controlled drug delivery. The activity of the immobilized enzymes inside the pores is often different compared to that of the free enzymes, and an important challenge is to understand how the immobilization affects the enzymes in order to design immobilization conditions that lead to optimal enzyme activity. This review summarizes methods that can be used to understand how material properties can be linked to changes in enzyme activity. Real-time monitoring of the immobilization process and techniques that demonstrate that the enzymes are located inside the pores is discussed by contrasting them to the common practice of indirectly measuring the depletion of the protein concentration or enzyme activity in the surrounding bulk phase. We propose that pore filling (pore volume fraction occupied by proteins) is the best standard for comparing the amount of immobilized enzymes at the molecular level, and present equations to calculate pore filling from the more commonly reported immobilized mass. Methods to detect changes in enzyme structure upon immobilization and to study the microenvironment inside the pores are discussed in detail. Combining the knowledge generated from these methodologies should aid in rationally designing biocatalyst based on enzymes immobilized in mesoporous materials.
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Affiliation(s)
- Nils Carlsson
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Physical Chemistry, 412 96 Gothenburg, Sweden
| | - Hanna Gustafsson
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Applied Surface Chemistry, 412 96 Gothenburg, Sweden
| | - Christian Thörn
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Industrial Biotechnology, 412 96 Gothenburg, Sweden
| | - Lisbeth Olsson
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Industrial Biotechnology, 412 96 Gothenburg, Sweden
| | - Krister Holmberg
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Applied Surface Chemistry, 412 96 Gothenburg, Sweden.
| | - Björn Åkerman
- Chalmers University of Technology, Department of Chemical and Biological Engineering, Physical Chemistry, 412 96 Gothenburg, Sweden
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33
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Nguan H, Ahmadi S, Hashim R. Molecular dynamics simulations of the lyotropic reverse hexagonal (HII) of Guerbet branched-chain β-d-glucoside. Phys Chem Chem Phys 2014; 16:324-34. [DOI: 10.1039/c3cp52385c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Ganoth A, Tsfadia Y, Wiener R. Ubiquitin: Molecular modeling and simulations. J Mol Graph Model 2013; 46:29-40. [DOI: 10.1016/j.jmgm.2013.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/18/2023]
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35
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Feig M, Sugita Y. Reaching new levels of realism in modeling biological macromolecules in cellular environments. J Mol Graph Model 2013; 45:144-56. [PMID: 24036504 DOI: 10.1016/j.jmgm.2013.08.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/14/2013] [Accepted: 08/19/2013] [Indexed: 12/21/2022]
Abstract
An increasing number of studies are aimed at modeling cellular environments in a comprehensive and realistic fashion. A major challenge in these efforts is how to bridge spatial and temporal scales over many orders of magnitude. Furthermore, there are additional challenges in integrating different aspects ranging from questions about biomolecular stability in crowded environments to the description of reactive processes on cellular scales. In this review, recent studies with models of biomolecules in cellular environments at different levels of detail are discussed in terms of their strengths and weaknesses. In particular, atomistic models, implicit representations of cellular environments, coarse-grained and spheroidal models of biomolecules, as well as the inclusion of reactive processes via reaction-diffusion models are described. Furthermore, strategies for integrating the different models into a comprehensive description of cellular environments are discussed.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry & Molecular Biology and Department of Chemistry, Michigan State University, 603 Wilson Road, BCH 218, East Lansing, MI 48824, United States; RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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36
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Tian J, Sethi A, Swanson BI, Goldstein B, Gnanakaran S. Taste of sugar at the membrane: thermodynamics and kinetics of the interaction of a disaccharide with lipid bilayers. Biophys J 2013; 104:622-32. [PMID: 23442913 DOI: 10.1016/j.bpj.2012.12.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 12/03/2012] [Accepted: 12/05/2012] [Indexed: 11/29/2022] Open
Abstract
Sugar recognition at the membrane is critical in various physiological processes. Many aspects of sugar-membrane interaction are still unknown. We take an integrated approach by combining conventional molecular-dynamics simulations with enhanced sampling methods and analytical models to understand the thermodynamics and kinetics of a di-mannose molecule in a phospholipid bilayer system. We observe that di-mannose has a slight preference to localize at the water-phospholipid interface. Using umbrella sampling, we show the free energy bias for this preferred location to be just -0.42 kcal/mol, which explains the coexistence of attraction and exclusion mechanisms of sugar-membrane interaction. Accurate estimation of absolute entropy change of water molecules with a two-phase model indicates that the small energy bias is the result of a favorable entropy change of water molecules. Then, we incorporate results from molecular-dynamics simulation in two different ways to an analytical diffusion-reaction model to obtain association and dissociation constants for di-mannose interaction with membrane. Finally, we verify our approach by predicting concentration dependence of di-mannose recognition at the membrane that is consistent with experiment. In conclusion, we provide a combined approach for the thermodynamics and kinetics of a weak ligand-binding system, which has broad implications across many different fields.
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Affiliation(s)
- Jianhui Tian
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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37
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Abriata LA, Spiga E, Dal Peraro M. All-atom simulations of crowding effects on ubiquitin dynamics. Phys Biol 2013; 10:045006. [DOI: 10.1088/1478-3975/10/4/045006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Rosenman DJ, Connors CR, Chen W, Wang C, García AE. Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. J Mol Biol 2013; 425:3338-59. [PMID: 23811057 DOI: 10.1016/j.jmb.2013.06.021] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/15/2013] [Accepted: 06/12/2013] [Indexed: 12/24/2022]
Abstract
Amyloid β (Aβ) peptides are a primary component of fibrils and oligomers implicated in the etiology of Alzheimer's disease (AD). However, the intrinsic flexibility of these peptides has frustrated efforts to investigate the secondary and tertiary structure of Aβ monomers, whose conformational landscapes directly contribute to the kinetics and thermodynamics of Aβ aggregation. In this work, de novo replica exchange molecular dynamics (REMD) simulations on the microseconds-per-replica timescale are used to characterize the structural ensembles of Aβ42, Aβ40, and M35-oxidized Aβ42, three physiologically relevant isoforms with substantially different aggregation properties. J-coupling data calculated from the REMD trajectories were compared to corresponding NMR-derived values acquired through two different pulse sequences, revealing that all simulations converge on the order of hundreds of nanoseconds-per-replica toward ensembles that yield good agreement with experiment. Though all three Aβ species adopt highly heterogeneous ensembles, these are considerably more structured compared to simulations on shorter timescales. Prominent in the C-terminus are antiparallel β-hairpins between L17-A21, A30-L36, and V39-I41, similar to oligomer and fibril intrapeptide models that expose these hydrophobic side chains to solvent and may serve as hotspots for self-association. Compared to reduced Aβ42, the absence of a second β-hairpin in Aβ40 and the sampling of alternate β topologies by M35-oxidized Aβ42 may explain the reduced aggregation rates of these forms. A persistent V24-K28 bend motif, observed in all three species, is stabilized by buried backbone to side-chain hydrogen bonds with D23 and a cross-region salt bridge between E22 and K28, highlighting the role of the familial AD-linked E22 and D23 residues in Aβ monomer folding. These characterizations help illustrate the conformational landscapes of Aβ monomers at atomic resolution and provide insight into the early stages of Aβ aggregation pathways.
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Affiliation(s)
- David J Rosenman
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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39
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Martinez AV, Dominguez L, Małolepsza E, Moser A, Ziegler Z, Straub JE. Probing the structure and dynamics of confined water in AOT reverse micelles. J Phys Chem B 2013; 117:7345-51. [PMID: 23687916 DOI: 10.1021/jp402270e] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reverse micelles are attractive nanoscale systems used for the confinement of molecules in studies of structure and chemical reactions, including protein folding, and aggregation. The simulation of reverse micelles, in which a water "pool" is separated from a nonpolar bulk phase by a surfactant layer, poses significant challenges to empirical force fields due to the diversity of interactions between nonpolar, polar, and charged groups. We have explored the dependence of system density, reverse micelle structure, and water configurational relaxation times as a function of reverse micelle composition, including water:surfactant ratio, absolute number of water molecules, and force field using molecular dynamics simulations. The resulting structures and dynamics are found to depend more on the force field used than on varying interpretations of the water:surfactant ratio in terms of absolute size of the reverse micelle. Substantial deviations from spherical reverse micelle geometries are observed in all unrestrained simulations. Rotational anisotropy decay times and water residence times show a strong dependence on force field and water model used, but power-law relaxation in time is observed independent of the force field. Our results suggest the need for further experimental study of reverse micelles that can provide insight into the distribution and dynamics of shape fluctuations in these complex systems.
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40
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Roche J, Caro JA, Dellarole M, Guca E, Royer CA, García-Moreno BE, Garcia AE, Roumestand C. Structural, energetic, and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity-creating mutations. Proteins 2013; 81:1069-80. [PMID: 23239146 DOI: 10.1002/prot.24231] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/19/2012] [Accepted: 11/21/2012] [Indexed: 12/21/2022]
Abstract
The effects of cavity-creating mutations on the structural flexibility, local and global stability, and dynamics of the folded state of staphylococcal nuclease (SNase) were examined with NMR spectroscopy, MD simulations, H/D exchange, and pressure perturbation. Effects on global thermodynamic stability correlated well with the number of heavy atoms in the vicinity of the mutated residue. Variants with substitutions in the C-terminal domain and the interface between α and β subdomains showed large amide chemical shift variations relative to the parent protein, moderate, widespread, and compensatory perturbations of the H/D protection factors and increased local dynamics on a nanosecond time scale. The pressure sensitivity of the folded states of these variants was similar to that of the parent protein. Such observations point to the capacity of the folded proteins to adjust to packing defects in these regions. In contrast, cavity creation in the β-barrel subdomain led to minimal perturbation of the structure of the folded state, However, significant pressure dependence of the native state amide resonances, along with strong effects on native state H/D exchange are consistent with increased probability of population of excited state(s) for these variants. Such contrasted responses to the creation of cavities could not be anticipated from global thermodynamic stability or crystal structures; they depend on the local structural and energetic context of the substitutions.
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Affiliation(s)
- Julien Roche
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Universités de Montpellier, France
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41
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Rao JS, Cruz L. Effects of confinement on the structure and dynamics of an intrinsically disordered peptide: a molecular-dynamics study. J Phys Chem B 2013; 117:3707-19. [PMID: 23484883 DOI: 10.1021/jp310623x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In vivo, proteins and peptides are exposed to radically different environments than those in bulk. Because of the abundance of other cellular components, proteins perform their function in crowded and confined spaces. Confinement has been shown to alter the structure, dynamics, and folding of proteins that possess a native fold. Little is known, however, of the effects of confinement on biologically important intrinsically disordered proteins or peptides (IDP). Here, we use extensive molecular dynamics simulations to investigate the effects of confinement in an IDP, the Aβ21-30, a central folding nucleus of the full length amyloid β-protein. In this study, we report results derived from 107 μs of molecular dynamics simulations that subjected the Aβ21-30 to two types of confinement: hydrophilic and hydrophobic pores. Results show that turn structures are enhanced as a function of decreasing pore size (increasing confinement) over other structures, including coils, β-hairpins, and bridges. However, the percentage occurrence of the dominant hydrogen bond between amino acids Asp23 and Ser26 shown to stabilize the turn in bulk simulations does not increase as a function of confinement signifying a disconnect between structure and internal hydrogen bonding. Differences in structure and dynamics of the decapeptide due to hydrophilic and hydrophobic confinement are more apparent at the extreme confinement conditions, where a reduction of the available phase space in hydrophilic confinement is explained in terms of interactions between the decapeptide and a layer of water at the interface between the decapeptide and the surface of the pore, and a smaller size of the decapeptide in the hydrophobic pores is rationalized in terms of peptide-surface interactions.
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Affiliation(s)
- J Srinivasa Rao
- Department of Physics, 3141 Chestnut Street, Drexel University, Philadelphia, Pennsylvania 19104, USA
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42
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Luan B, Shan B, Baiz C, Tokmakoff A, Raleigh DP. Cooperative Cold Denaturation: The Case of the C-Terminal Domain of Ribosomal Protein L9. Biochemistry 2013; 52:2402-9. [DOI: 10.1021/bi3016789] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bowu Luan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400,
United States
| | - Bing Shan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400,
United States
| | - Carlos Baiz
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Andrei Tokmakoff
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Daniel P. Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400,
United States
- Graduate
Program in Biochemistry
and Structural Biology and Graduate Program in Biophysics, Stony Brook University, Stony Brook, New York 11794-3400,
United States
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43
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Saha R, Rakshit S, Verma PK, Mitra RK, Pal SK. Protein-cofactor binding and ultrafast electron transfer in riboflavin binding protein under the spatial confinement of nanoscopic reverse micelles. J Mol Recognit 2013; 26:59-66. [DOI: 10.1002/jmr.2246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/09/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Ranajay Saha
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Surajit Rakshit
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Pramod Kumar Verma
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
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44
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Sun T, Chan KK, Su H, Zhang D. Dissimilar stability of proteins in graphene bilayer: a molecular dynamics study. Mol Phys 2012. [DOI: 10.1080/00268976.2012.737034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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45
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Malik A, Kundu J, Mukherjee SK, Chowdhury PK. Myoglobin unfolding in crowding and confinement. J Phys Chem B 2012; 116:12895-904. [PMID: 23025527 DOI: 10.1021/jp306873v] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crowding and confinement have often been used synonymously with regard to their effect on the structure and dynamics of proteins. In this work, we have investigated the unfolding of the protein myoglobin (Mb) entrapped in the confinement of the water pool of AOT reverse micelles and in the presence of some commonly used macromolecular crowding agents (Ficoll 70, Dextran 70, and Dextran 40). Our results reveal that confinement effects can be quite destabilizing in nature for Mb with the extent of distortion depending on a host of factors apart from the size of the confining cage. Effects of the crowding agents on myoglobin also show a deviation from the general notion that synthetic macromolecular crowding agents are always stabilizing in nature. Ficoll 70 was observed to be particularly destabilizing in its influence on Mb unfolding. Moreover, tryptophan lifetime studies point to the fact that the Trp-heme distance in Mb might not always be a reliable probe of the secondary structural dissolution of the protein.
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Affiliation(s)
- Ashima Malik
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
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46
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Johnson E. Separability between overall and internal motion: a protein folding problem. Proteins 2012; 80:2645-51. [PMID: 22945391 DOI: 10.1002/prot.24175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/23/2012] [Accepted: 08/26/2012] [Indexed: 12/29/2022]
Abstract
The separability between overall and internal motions is evaluated over multiple folding trajectories of the villin headpiece subdomain. The analysis, which relies on the Prompers-Brüschweiler separability index, offers a potentially useful perspective on protein folding. The protein is considered folded in this study, not when it reaches some static target, but rather when it tumbles as a dynamically constrained object. The analysis also demonstrates how the separability index, when applied to protein folding simulations, can facilitate the analysis of NMR relaxation data.
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Affiliation(s)
- Eric Johnson
- Department of Chemistry and Physical Sciences, College of Mount St. Joseph, Cincinnati, OH 45233, USA.
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47
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Tian J, Sethi A, Anunciado D, Vu DM, Gnanakaran S. Characterization of a disordered protein during micellation: interactions of α-synuclein with sodium dodecyl sulfate. J Phys Chem B 2012; 116:4417-24. [PMID: 22439820 PMCID: PMC3357070 DOI: 10.1021/jp210339f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
To better understand the interaction of α-synuclein (αSyn) with lipid membranes, we carried out self-assembly molecular dynamics simulations of αSyn with monomeric and micellar sodium dodecyl sulfate (SDS), a widely used membrane mimic. We find that both electrostatic and hydrophobic forces contribute to the interactions of αSyn with SDS. In the presence of αSyn, our simulations suggest that SDS aggregates along the protein chain and forms small-size micelles at very early times. Aggregation is followed by formation of a collapsed protein-SDS micelle complex, which is consistent with experimental results. Finally, interaction of αSyn with preformed micelles induces alterations in the shape of the micelle, and the N-terminal helix (residues 3 through 37) tends to associate with micelles. Overall, our simulations provide an atomistic description of the early time scale αSyn-SDS interaction during the self-assembly of SDS into micelles.
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Affiliation(s)
- Jianhui Tian
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos 87545
| | - Anurag Sethi
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos 87545
| | - Divina Anunciado
- Physical Chemistry & Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos 87545
| | - Dung M. Vu
- Physical Chemistry & Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos 87545
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos 87545
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48
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Sterpone F, Stirnemann G, Laage D. Magnitude and Molecular Origin of Water Slowdown Next to a Protein. J Am Chem Soc 2012; 134:4116-9. [DOI: 10.1021/ja3007897] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabio Sterpone
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond,
75005 Paris, France
| | - Guillaume Stirnemann
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond,
75005 Paris, France
| | - Damien Laage
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond,
75005 Paris, France
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