1
|
Iorio A, Perin L, Gallo P. Structure and slow dynamics of protein hydration water with cryopreserving DMSO and trehalose upon cooling. J Chem Phys 2024; 160:244502. [PMID: 38912631 DOI: 10.1063/5.0205569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
We study, through molecular dynamics simulations, three aqueous solutions with one lysozyme protein and three different concentrations of trehalose and dimethyl sulfoxide (DMSO). We analyze the structural and dynamical properties of the protein hydration water upon cooling. We find that trehalose plays a major role in modifying the structure of the network of HBs between water molecules in the hydration layer of the protein. The dynamics of hydration water presents, in addition to the α-relaxation, typical of glass formers, a slower long-time relaxation process, which greatly slows down the dynamics of water, particularly in the systems with trehalose, where it becomes dominant at low temperatures. In all the solutions, we observe, from the behavior of the α-relaxation times, a shift of the Mode Coupling Theory crossover temperature and the fragile-to-strong crossover temperature toward higher values with respect to bulk water. We also observe a strong-to-strong crossover from the temperature behavior of the long-relaxation times. In the aqueous solution with only DMSO, the transition shifts to a lower temperature than in the case with only lysozyme reported in the literature. We observe that the addition of trehalose to the mixture has the opposite effect of restoring the original location of the strong-to-strong crossover. In all the solutions analyzed in this work, the observed temperature of the protein dynamical transition is slightly shifted at lower temperatures than that of the strong-to-strong crossover, but their relative order is the same, showing a correlation between the motion of the protein and that of the hydration water.
Collapse
Affiliation(s)
- Antonio Iorio
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
| | - Leonardo Perin
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
| | - Paola Gallo
- Dipartimento di Fisica, Università Roma Tre, Via della Vasca Navale 84, I-00146 Roma, Italy
| |
Collapse
|
2
|
Vugmeyster L, Ostrovsky D, Rodgers A, Gwin K, Smirnov SL, McKnight CJ, Fu R. Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR. Chemphyschem 2024; 25:e202300565. [PMID: 38175858 PMCID: PMC10922872 DOI: 10.1002/cphc.202300565] [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: 08/09/2023] [Revised: 12/01/2023] [Indexed: 01/06/2024]
Abstract
Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.
Collapse
Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO USA 80204
| | - Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Kirsten Gwin
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Serge L. Smirnov
- Department of Chemistry, Western Washington University, Bellingham, WA 98225
| | - C. James McKnight
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL USA 32310
| |
Collapse
|
3
|
Bock LV, Grubmüller H. Effects of cryo-EM cooling on structural ensembles. Nat Commun 2022; 13:1709. [PMID: 35361752 PMCID: PMC8971465 DOI: 10.1038/s41467-022-29332-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/10/2022] [Indexed: 01/01/2023] Open
Abstract
Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures. The rapid temperature drop during plunge-freezing affects the structural ensembles obtained by cryo-EM. To quantify the extent of perturbation, Bock and Grubmüller combined continuum calculations, MD simulations, and kinetic models.
Collapse
Affiliation(s)
- Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Bauer JA, Pavlović J, Bauerová-Hlinková V. Normal Mode Analysis as a Routine Part of a Structural Investigation. Molecules 2019; 24:molecules24183293. [PMID: 31510014 PMCID: PMC6767145 DOI: 10.3390/molecules24183293] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Normal mode analysis (NMA) is a technique that can be used to describe the flexible states accessible to a protein about an equilibrium position. These states have been shown repeatedly to have functional significance. NMA is probably the least computationally expensive method for studying the dynamics of macromolecules, and advances in computer technology and algorithms for calculating normal modes over the last 20 years have made it nearly trivial for all but the largest systems. Despite this, it is still uncommon for NMA to be used as a component of the analysis of a structural study. In this review, we will describe NMA, outline its advantages and limitations, explain what can and cannot be learned from it, and address some criticisms and concerns that have been voiced about it. We will then review the most commonly used techniques for reducing the computational cost of this method and identify the web services making use of these methods. We will illustrate several of their possible uses with recent examples from the literature. We conclude by recommending that NMA become one of the standard tools employed in any structural study.
Collapse
Affiliation(s)
- Jacob A Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia.
| | - Jelena Pavlović
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Vladena Bauerová-Hlinková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| |
Collapse
|
6
|
Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
Collapse
|
7
|
Lee Y, Kim S, Choi S, Hyeon C. Ultraslow Water-Mediated Transmembrane Interactions Regulate the Activation of A2A Adenosine Receptor. Biophys J 2017; 111:1180-1191. [PMID: 27653477 DOI: 10.1016/j.bpj.2016.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/09/2016] [Accepted: 08/02/2016] [Indexed: 01/04/2023] Open
Abstract
Water molecules inside a G-protein coupled receptor (GPCR) have recently been spotlighted in a series of crystal structures. To decipher the dynamics and functional roles of internal water molecules in GPCR activity, we studied the A2A adenosine receptor using microsecond molecular-dynamics simulations. Our study finds that the amount of water flux across the transmembrane (TM) domain varies depending on the receptor state, and that the water molecules of the TM channel in the active state flow three times more slowly than those in the inactive state. Depending on the location in solvent-protein interface as well as the receptor state, the average residence time of water in each residue varies from ∼O(10(2)) ps to ∼O(10(2)) ns. Especially, water molecules, exhibiting ultraslow relaxation (∼O(10(2)) ns) in the active state, are found around the microswitch residues that are considered activity hotspots for GPCR function. A continuous allosteric network spanning the TM domain, arising from water-mediated contacts, is unique in the active state, underscoring the importance of slow water molecules in the activation of GPCRs.
Collapse
Affiliation(s)
- Yoonji Lee
- National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea
| | - Songmi Kim
- Korea Institute for Advanced Study, Seoul, Korea
| | - Sun Choi
- National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea.
| | | |
Collapse
|
8
|
Benedetto A, Kearley GJ. Elastic Scattering Spectroscopy (ESS): an Instrument-Concept for Dynamics of Complex (Bio-) Systems From Elastic Neutron Scattering. Sci Rep 2016; 6:34266. [PMID: 27703184 PMCID: PMC5050422 DOI: 10.1038/srep34266] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/12/2016] [Indexed: 11/09/2022] Open
Abstract
A new type of neutron-scattering spectroscopy is presented that is designed specifically to measure dynamics in bio-systems that are difficult to obtain in any other way. The temporal information is largely model-free and is analogous to relaxation processes measured with dielectric spectroscopy, but provides additional spacial and geometric aspects of the underlying dynamics. Numerical simulations of the basic instrument design show the neutron beam can be highly focussed, giving efficiency gains that enable the use of small samples. Although we concentrate on continuous neutron sources, the extension to pulsed neutron sources is proposed, both requiring minimal data-treatment and being broadly analogous with dielectric spectroscopy, they will open the study of dynamics to new areas of biophysics.
Collapse
Affiliation(s)
- Antonio Benedetto
- School of Physics, University College Dublin, Dublin, Ireland
- Laboratory for Neutron Scattering, Paul Scherrer Institut, Villigen, Switzerland
| | - Gordon J. Kearley
- School of Materials Science and Engineering, UNSW Australia, Sydney, NSW 2052, Australia
| |
Collapse
|
9
|
Shukla N, Pomarico E, Chen L, Chergui M, Othon CM. Retardation of Bulk Water Dynamics by Disaccharide Osmolytes. J Phys Chem B 2016; 120:9477-83. [DOI: 10.1021/acs.jpcb.6b07751] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nimesh Shukla
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
| | - Enrico Pomarico
- Laboratoire
de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast
Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Lee Chen
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
| | - Majed Chergui
- Laboratoire
de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast
Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Christina M. Othon
- Department
of Physics, Wesleyan University, Middletown, Connecticut 06457, United States
- Molecular
Biophysics Program, Wesleyan University, Middletown, Connecticut 06457, United States
| |
Collapse
|
10
|
Pansare SK, Patel SM. Practical Considerations for Determination of Glass Transition Temperature of a Maximally Freeze Concentrated Solution. AAPS PharmSciTech 2016; 17:805-19. [PMID: 27193003 DOI: 10.1208/s12249-016-0551-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/09/2016] [Indexed: 12/31/2022] Open
Abstract
Glass transition temperature is a unique thermal characteristic of amorphous systems and is associated with changes in physical properties such as heat capacity, viscosity, electrical resistance, and molecular mobility. Glass transition temperature for amorphous solids is referred as (T g), whereas for maximally freeze concentrated solution, the notation is (T g'). This article is focused on the factors affecting determination of T g' for application to lyophilization process design and frozen storage stability. Also, this review provides a perspective on use of various types of solutes in protein formulation and their effect on T g'. Although various analytical techniques are used for determination of T g' based on the changes in physical properties associated with glass transition, the differential scanning calorimetry (DSC) is the most commonly used technique. In this article, an overview of DSC technique is provided along with brief discussion on the alternate analytical techniques for T g' determination. Additionally, challenges associated with T g' determination, using DSC for protein formulations, are discussed. The purpose of this review is to provide a practical industry perspective on determination of T g' for protein formulations as it relates to design and development of lyophilization process and/or for frozen storage; however, a comprehensive review of glass transition temperature (T g, T g'), in general, is outside the scope of this work.
Collapse
|
11
|
Mamontov E, O'Neill H. Microscopic relaxations in a protein sustained down to 160K in a non-glass forming organic solvent. Biochim Biophys Acta Gen Subj 2016; 1861:3513-3519. [PMID: 27154287 DOI: 10.1016/j.bbagen.2016.04.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/24/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND We have studied microscopic dynamics of a protein in carbon disulfide, a non-glass forming solvent, down to its freezing temperature of ca. 160K. METHODS We have utilized quasielastic neutron scattering. RESULTS A comparison of lysozyme hydrated with water and dissolved in carbon disulfide reveals a stark difference in the temperature dependence of the protein's microscopic relaxation dynamics induced by the solvent. In the case of hydration water, the common protein glass-forming solvent, the protein relaxation slows down in response to a large increase in the water viscosity on cooling down, exhibiting a well-known protein dynamical transition. The dynamical transition disappears in non-glass forming carbon disulfide, whose viscosity remains a weak function of temperature all the way down to freezing at just below 160K. The microscopic relaxation dynamics of lysozyme dissolved in carbon disulfide is sustained down to the freezing temperature of its solvent at a rate similar to that measured at ambient temperature. CONCLUSIONS Our results demonstrate that protein dynamical transition is not merely solvent-assisted, but rather solvent-induced, or, more precisely, is a reflection of the temperature dependence of the solvent's glass-forming dynamics. GENERAL SIGNIFICANCE We hypothesize that, if the long debated idea regarding the direct link between the microscopic relaxations and the biological activity in proteins is correct, then not only the microscopic relaxations, but also the activity, could be sustained in proteins all the way down to the freezing temperature of a non-glass forming solvent with a weak temperature dependence of its viscosity. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
Collapse
Affiliation(s)
- E Mamontov
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
| | - H O'Neill
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| |
Collapse
|
12
|
Frank AT, Zhang Q, Al-Hashimi HM, Andricioaei I. Slowdown of Interhelical Motions Induces a Glass Transition in RNA. Biophys J 2015; 108:2876-85. [PMID: 26083927 PMCID: PMC4472199 DOI: 10.1016/j.bpj.2015.04.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/21/2015] [Accepted: 04/21/2015] [Indexed: 12/29/2022] Open
Abstract
RNA function depends crucially on the details of its dynamics. The simplest RNA dynamical unit is a two-way interhelical junction. Here, for such a unit--the transactivation response RNA element--we present evidence from molecular dynamics simulations, supported by nuclear magnetic resonance relaxation experiments, for a dynamical transition near 230 K. This glass transition arises from the freezing out of collective interhelical motional modes. The motions, resolved with site-specificity, are dynamically heterogeneous and exhibit non-Arrhenius relaxation. The microscopic origin of the glass transition is a low-dimensional, slow manifold consisting largely of the Euler angles describing interhelical reorientation. Principal component analysis over a range of temperatures covering the glass transition shows that the abrupt slowdown of motion finds its explanation in a localization transition that traps probability density into several disconnected conformational pools over the low-dimensional energy landscape. Upon temperature increase, the probability density pools then flood a larger basin, akin to a lakes-to-sea transition. Simulations on transactivation response RNA are also used to backcalculate inelastic neutron scattering data that match previous inelastic neutron scattering measurements on larger and more complex RNA structures and which, upon normalization, give temperature-dependent fluctuation profiles that overlap onto a glass transition curve that is quasi-universal over a range of systems and techniques.
Collapse
Affiliation(s)
- Aaron T Frank
- Department of Chemistry, University of California at Irvine, Irvine, California
| | - Qi Zhang
- The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina
| | - Ioan Andricioaei
- Department of Chemistry, University of California at Irvine, Irvine, California.
| |
Collapse
|
13
|
Mallamace F, Corsaro C, Mallamace D, Vasi S, Vasi C, Stanley HE, Chen SH. Some thermodynamical aspects of protein hydration water. J Chem Phys 2015; 142:215103. [DOI: 10.1063/1.4921897] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Francesco Mallamace
- Dipartimento di Fisica e Scienze della Terra, Università di Messina and CNISM, I-98168 Messina, Italy
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
| | - Carmelo Corsaro
- Dipartimento di Fisica e Scienze della Terra, Università di Messina and CNISM, I-98168 Messina, Italy
- CNR-IPCF, Viale F. Stagno D’Alcontres 37, I-98158 Messina, Italy
| | | | - Sebastiano Vasi
- Dipartimento di Fisica e Scienze della Terra, Università di Messina and CNISM, I-98168 Messina, Italy
| | - Cirino Vasi
- CNR-IPCF, Viale F. Stagno D’Alcontres 37, I-98158 Messina, Italy
| | - H. Eugene Stanley
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
| | - Sow-Hsin Chen
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
14
|
Mallamace F, Corsaro C, Mallamace D, Vasi S, Vasi C, Stanley HE. Thermodynamic properties of bulk and confined water. J Chem Phys 2015; 141:18C504. [PMID: 25399169 DOI: 10.1063/1.4895548] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The thermodynamic response functions of water display anomalous behaviors. We study these anomalous behaviors in bulk and confined water. We use nuclear magnetic resonance (NMR) to examine the configurational specific heat and the transport parameters in both the thermal stable and the metastable supercooled phases. The data we obtain suggest that there is a behavior common to both phases: that the dynamics of water exhibit two singular temperatures belonging to the supercooled and the stable phase, respectively. One is the dynamic fragile-to-strong crossover temperature (T(L) ≃ 225 K). The second, T* ∼ 315 ± 5 K, is a special locus of the isothermal compressibility K(T)(T, P) and the thermal expansion coefficient α(P)(T, P) in the P-T plane. In the case of water confined inside a protein, we observe that these two temperatures mark, respectively, the onset of protein flexibility from its low temperature glass state (T(L)) and the onset of the unfolding process (T*).
Collapse
Affiliation(s)
- Francesco Mallamace
- Dipartimento di Fisica e Scienza della Terra Università di Messina and CNISM, I-98168 Messina, Italy
| | - Carmelo Corsaro
- Dipartimento di Fisica e Scienza della Terra Università di Messina and CNISM, I-98168 Messina, Italy
| | - Domenico Mallamace
- Dipartimento di Scienze dell'Ambiente, della Sicurezza, del Territorio, degli Alimenti e della Salute, Università di Messina, I-98166 Messina, Italy
| | | | | | - H Eugene Stanley
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
| |
Collapse
|
15
|
Enrichment of druggable conformations from apo protein structures using cosolvent-accelerated molecular dynamics. BIOLOGY 2015; 4:344-66. [PMID: 25906084 PMCID: PMC4498304 DOI: 10.3390/biology4020344] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 03/27/2015] [Accepted: 04/11/2015] [Indexed: 11/16/2022]
Abstract
Here we describe the development of an improved workflow for utilizing experimental and simulated protein conformations in the structure-based design of inhibitors for anti-apoptotic Bcl-2 family proteins. Traditional structure-based approaches on similar targets are often constrained by the sparsity of available structures and difficulties in finding lead compounds that dock against flat, flexible protein-protein interaction surfaces. By employing computational docking of known small molecule inhibitors, we have demonstrated that structural ensembles derived from either accelerated MD (aMD) or MD in the presence of an organic cosolvent generally give better scores than those assessed from analogous conventional MD. Furthermore, conformations obtained from combined cosolvent aMD simulations started with the apo-Bcl-xL structure yielded better average and minimum docking scores for known binders than an ensemble of 72 experimental apo- and ligand-bound Bcl-xL structures. A detailed analysis of the simulated conformations indicates that the aMD effectively enhanced conformational sampling of the flexible helices flanking the main Bcl-xL binding groove, permitting the cosolvent acting as small ligands to penetrate more deeply into the binding pocket and shape ligand-bound conformations not evident in conventional simulations. We believe this approach could be useful for identifying inhibitors against other protein-protein interaction systems involving highly flexible binding sites, particularly for targets with less accumulated structural data.
Collapse
|
16
|
Petridis L, O’Neill HM, Johnsen M, Fan B, Schulz R, Mamontov E, Maranas J, Langan P, Smith JC. Hydration Control of the Mechanical and Dynamical Properties of Cellulose. Biomacromolecules 2014; 15:4152-9. [DOI: 10.1021/bm5011849] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | | | | | - Bingxin Fan
- Department
of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Roland Schulz
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | | | - Janna Maranas
- Department
of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Paul Langan
- Department
of Chemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Jeremy C. Smith
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| |
Collapse
|
17
|
Dhindsa GK, Tyagi M, Chu XQ. Temperature-dependent dynamics of dry and hydrated β-casein studied by quasielastic neutron scattering. J Phys Chem B 2014; 118:10821-9. [PMID: 25144497 DOI: 10.1021/jp504548w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
β-Casein is a component of casein micelle with amphillic nature and is recognized as a "natively disordered" protein that lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of β-casein are explored by quasielastic neutron scattering (QENS). An upturn in the mean square displacement (MSD) of hydrated β-casein indicates an increase of protein flexibility at a temperature of ~225 K. Another increase in MSD at ~100 K, observed in both dry and hydrated β-casein, is ascribed to the methyl group rotations, which are not sensitive to hydration. QENS analysis in the energy domain reveals that the fraction of hydrogen atoms participating in motion in a sphere of diffusion is highly hydration dependent and increases with temperature. In the time domain analysis, a logarithmic-like decay is observed in the range of picosecond to nanosecond (β-relaxation time) in the dynamics of hydrated β-casein. This dynamical behavior has been observed in hydrated globular and oligomeric proteins. Our temperature-dependent QENS experiments provide evidence that lack of a secondary structure in β-casein results in higher flexibility in its dynamics and easier reversible thermal unfolding compared to other rigid biomolecules.
Collapse
Affiliation(s)
- Gurpreet K Dhindsa
- Department of Physics and Astronomy, Wayne State University , Detroit, Michigan 48201, United States
| | | | | |
Collapse
|
18
|
Hong L, Petridis L, Smith JC. Biomolecular Structure and Dynamics with Neutrons: The View from Simulation. Isr J Chem 2014. [DOI: 10.1002/ijch.201300137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
19
|
Yoon J, Lin JC, Hyeon C, Thirumalai D. Dynamical Transition and Heterogeneous Hydration Dynamics in RNA. J Phys Chem B 2014; 118:7910-9. [DOI: 10.1021/jp500643u] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jeseong Yoon
- Korea Institute for Advanced Study, 130-722 Seoul, Korea
| | - Jong-Chin Lin
- Department
of Chemistry and Biochemistry, and Biophysics
Program, Institute for Physical Sciences and Technology, University of Maryland, College
Park, Maryland 20742, United States
| | | | - D. Thirumalai
- Department
of Chemistry and Biochemistry, and Biophysics
Program, Institute for Physical Sciences and Technology, University of Maryland, College
Park, Maryland 20742, United States
| |
Collapse
|
20
|
Doster W, Nakagawa H, Appavou MS. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments. J Chem Phys 2014; 139:045105. [PMID: 23902030 DOI: 10.1063/1.4816513] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and∕or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at Td from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature Tg. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature Td.
Collapse
Affiliation(s)
- W Doster
- Physik-Department, Technische Universität München, D-85748 Garching, Germany.
| | | | | |
Collapse
|
21
|
Chakraborty K, Bandyopadhyay S. Correlated Dynamical Crossovers of the Hydration Layer of a Single-Stranded DNA Oligomer. J Phys Chem B 2014; 118:413-22. [DOI: 10.1021/jp408234k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kaushik Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| |
Collapse
|
22
|
Investigations of homologous disaccharides by elastic incoherent neutron scattering and wavelet multiresolution analysis. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
23
|
GhattyVenkataKrishna PK, Carri GA. The effect of complex solvents on the structure and dynamics of protein solutions: The case of Lysozyme in trehalose/water mixtures. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:14. [PMID: 23404569 DOI: 10.1140/epje/i2013-13014-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/15/2012] [Accepted: 01/17/2013] [Indexed: 06/01/2023]
Abstract
We present a Molecular Dynamics simulation study of the effect of trehalose concentration on the structure and dynamics of individual proteins immersed in trehalose/water mixtures. Hen egg-white Lysozyme is used in this study and trehalose concentrations of 0%, 10%, 20%, 30% and 100% by weight are explored. Surprisingly, we have found that changes in trehalose concentration do not change the global structural characteristics of the protein as measured by standard quantities like the mean square deviation, radius of gyration, solvent accessible surface area, inertia tensor and asphericity. Only in the limit of pure trehalose these metrics change significantly. Specifically, we found that the protein is compressed by 2% when immersed in pure trehalose. At the amino acid level there is noticeable rearrangement of the surface residues due to the change in polarity of the surrounding environment with the addition of trehalose. From a dynamic perspective, our computation of the Incoherent Intermediate Scattering Function shows that the protein slows down with increasing trehalose concentration; however, this slowdown is not monotonic. Finally, we also report in-depth results for the hydration layer around the protein including its structure, hydrogen-bonding characteristics and dynamic behavior at different length scales.
Collapse
|
24
|
Wood K, Gallat FX, Otten R, van Heel AJ, Lethier M, van Eijck L, Moulin M, Haertlein M, Weik M, Mulder FAA. Protein Surface and Core Dynamics Show Concerted Hydration-Dependent Activation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201205898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
25
|
Wood K, Gallat FX, Otten R, van Heel AJ, Lethier M, van Eijck L, Moulin M, Haertlein M, Weik M, Mulder FAA. Protein surface and core dynamics show concerted hydration-dependent activation. Angew Chem Int Ed Engl 2012; 52:665-8. [PMID: 23154872 DOI: 10.1002/anie.201205898] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/29/2012] [Indexed: 11/09/2022]
Abstract
By specifically labeling leucine/valine methyl groups and lysine side chains "inside" and "outside" dynamics of proteins on the nanosecond timescale are compared using neutron scattering. Surprisingly, both groups display similar dynamics as a function of temperature, and the buried hydrophobic core is sensitive to hydration and undergoes a dynamical transition.
Collapse
Affiliation(s)
- Kathleen Wood
- Australian Nuclear Science and Technology Organisation Bragg Institute, Menai NSW, Australia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Magazù S, Migliardo F, Caccamo MT. Innovative Wavelet Protocols in Analyzing Elastic Incoherent Neutron Scattering. J Phys Chem B 2012; 116:9417-23. [DOI: 10.1021/jp3060087] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. Magazù
- Dipartimento di Fisica dell’Università degli Studi di Messina, Viale S. D’Alcontres
31, 98166, Messina, Italy
| | - F. Migliardo
- Dipartimento di Fisica dell’Università degli Studi di Messina, Viale S. D’Alcontres
31, 98166, Messina, Italy
| | - M. T. Caccamo
- Dipartimento di Fisica dell’Università degli Studi di Messina, Viale S. D’Alcontres
31, 98166, Messina, Italy
| |
Collapse
|
27
|
|
28
|
Yang CY, Wang S. Hydrophobic Binding Hot Spots of Bcl-xL Protein-Protein Interfaces by Cosolvent Molecular Dynamics Simulation. ACS Med Chem Lett 2011; 2:280-4. [PMID: 24900309 PMCID: PMC4018050 DOI: 10.1021/ml100276b] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 01/05/2011] [Indexed: 12/31/2022] Open
Abstract
Identifying binding hot spots in protein-protein interfaces is important for understanding the binding specificity and for the design of nonpeptide, small molecule inhibitors. Molecular dynamics simulation in the isopropanol/water cosolvent environment and in water was employed to investigate Bcl-xL protein, which has a highly flexible, large, and primarily hydrophobic binding site. Simulations of either the apo- or holocrystal structures of the Bcl-xL in pure water fail to generate conformations found in the cocrystal structures of Bcl-xL in complex with its binding partners due to hydrophobic collapse. In contrast, simulations in cosolvent starting either from the apo- or holocrystal structure of the Bcl-xL yield binding-site conformations similar to that found in the cocrystal structures of Bcl-xL. Hydrophobic binding hot spots identified using the conformations from the cosolvent simulations are in excellent agreement with experimental structural data of known inhibitors. Importantly, cosolvent simulations revealed the highly dynamic nature of the hydrophobic binding pockets in Bcl-xL and yielded new structural insights for the design of novel Bcl-xL small-molecule inhibitors.
Collapse
Affiliation(s)
- Chao-Yie Yang
- Comprehensive Cancer Center, Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, Michigan 48109-0934, United States
| | - Shaomeng Wang
- Comprehensive Cancer Center, Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, Michigan 48109-0934, United States
| |
Collapse
|
29
|
Gur M, Erman B. Quasi-harmonic analysis of mode coupling in fluctuating native proteins. Phys Biol 2010; 7:046006. [DOI: 10.1088/1478-3975/7/4/046006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
30
|
Reátegui E, Aksan A. Effects of water on the structure and low/high temperature stability of confined proteins. Phys Chem Chem Phys 2010; 12:10161-72. [PMID: 20689888 DOI: 10.1039/c003517c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study well-characterized model proteins were confined in silica nanoporous matrices. Confinement of the proteins in silica matrices allowed us to explore the role of water hydrogen bonding on the structures of the proteins in a broad range of temperatures (-120 degrees C to 95 degrees C). At low temperatures confinement suppressed freezing of water, which remained in the liquid state. We obtained direct evidence that the changes in the hydrogen bonding of water induced changes in the structure of confined proteins. At high temperatures, a reduction of hydrogen bonding of water facilitated protein-silica interactions and the confined proteins underwent denaturation. However, the incorporation of the osmolyte, trehalose, reduced protein-silica interactions, and altered the hydrogen bonding of water. As a result, the high temperature thermal stability of the confined proteins was greatly improved.
Collapse
Affiliation(s)
- Eduardo Reátegui
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN, USA
| | | |
Collapse
|
31
|
Glass DC, Krishnan M, Nutt DR, Smith JC. Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models. J Chem Theory Comput 2010. [DOI: 10.1021/ct9006508] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dennis C. Glass
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Marimuthu Krishnan
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - David R. Nutt
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Jeremy C. Smith
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| |
Collapse
|
32
|
Zuo G, Wang J, Qin M, Xue B, Wang W. Effect of solvation-related interaction on the low-temperature dynamics of proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:031917. [PMID: 20365780 DOI: 10.1103/physreve.81.031917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 12/06/2009] [Indexed: 05/29/2023]
Abstract
The effect of solvation-related interaction on the low-temperature dynamics of proteins is studied by taking into account the desolvation barriers in the interactions of native contacts. It is found out that about the folding transition temperature, the protein folds in a cooperative manner, and the water molecules are expelled from the hydrophobic core at the final stage in the folding process. At low temperature, however, the protein would generally be trapped in many metastable conformations with some water molecules frozen inside the protein. The desolvation takes an important role in these processes. The number of frozen water molecules and that of frozen states of proteins are further analyzed with the methods based on principal component analysis (PCA) and the clustering of conformations. It is found out that both the numbers of frozen water molecules and the frozen states of the protein increase quickly below a certain temperature. Especially, the number of frozen states of the protein increases exponentially following the decrease in the temperature, which resembles the basic features of glassy dynamics. Interestingly, it is observed that the freezing of water molecules and that of protein conformations happen at almost the same temperature. This suggests that the solvation-related interaction performs an important role for the low-temperature dynamics of the model protein.
Collapse
Affiliation(s)
- Guanghong Zuo
- Nanjing National Laboratory of Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | | | | | | | | |
Collapse
|
33
|
Kealley C, Sokolova A, Kearley G, Kemner E, Russina M, Faraone A, Hamilton W, Gilbert E. Dynamical transition in a large globular protein: Macroscopic properties and glass transition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:34-40. [DOI: 10.1016/j.bbapap.2009.06.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 06/12/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
|
34
|
Nakagawa H, Kamikubo H, Kataoka M. Effect of conformational states on protein dynamical transition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:27-33. [DOI: 10.1016/j.bbapap.2009.06.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 06/10/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
|
35
|
Doster W. The protein-solvent glass transition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:3-14. [DOI: 10.1016/j.bbapap.2009.06.019] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 06/15/2009] [Accepted: 06/18/2009] [Indexed: 11/29/2022]
|
36
|
Crupi V, Majolino D, Paciaroni A, Stancanelli R, Venuti V. Influence of the "host-guest" interactions on the mobility of genistein/beta-cyclodextrin inclusion complex. J Phys Chem B 2009; 113:11032-8. [PMID: 19603804 DOI: 10.1021/jp810546h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inclusion complexes of cyclodextrins with nonpolar drugs are a topic of current interest in pharmaceutical science, because they increase the aqueous solubility, chemical stability and bioavailability of poorly water-soluble drugs. By means of elastic incoherent neutron scattering (EINS) technique on the backscattering spectrometer IN13, we measured, in the 150-340 K temperature range, the mean square displacements (MSD) of hydrogen atoms derived from elastic spectra of inclusion complex of beta-cyclodextrin (beta-CyD) with genistein (Gen), a phytoestrogen of great interest for its antioxidant, anticarcinogenic and antiosteoporotic activities. The mobility of the complex has been compared with the single components and the physical mixture. The elastic intensity has been interpreted in terms of the double-well model in the whole temperature range. In the case of Gen, a mainly vibrational dynamics is revealed, while for the other samples, the elastic intensity becomes non-Gaussian above a temperature T(d) congruent with 220-230 K. This dynamical activation, which is represented by an Arrhenius trend, seems to be promoted by the crystallization water molecules. The dynamics of the Gen/beta-CyD inclusion complex is restricted with respect to the physical mixture, due to the action of specific "host-guest" interactions upon complexation. Finally, the dynamical response of our systems to temperature is put in relationship with their thermal stability.
Collapse
Affiliation(s)
- Vincenza Crupi
- Department of Physics, University of Messina and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, C.da Papardo, S.ta Sperone 31, P.O. Box 55, 98166 S. Agata, Messina, Italy
| | | | | | | | | |
Collapse
|
37
|
Varga B, Migliardo F, Takacs E, Vertessy B, Magazù S, Telling MTF. Study of solvent-protein coupling effects by neutron scattering. J Biol Phys 2009; 36:207-20. [PMID: 19795216 DOI: 10.1007/s10867-009-9177-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Accepted: 09/09/2009] [Indexed: 11/30/2022] Open
Abstract
The present work aims to characterize the dynamical behavior of proteins immersed in bio-preserving liquids and glasses. For this purpose, the protein dUTPase was chosen, while the selected solvents were glycerol, a triol, and some homologous disaccharides, i.e., trehalose, maltose, and sucrose, which are known to be very effective bio-preserving agents. The results highlight that the disaccharides show a slowing down effect on the water dynamics, which is stronger for trehalose than in the case of the other disaccharides. Furthermore, a characterization of the medium which hosts the protein is performed by using an operative definition of fragility based on the mean square displacement extracted by elastic incoherent neutron scattering, which is directly connected to Angell's kinetic fragility based on the viscosity. Finally, a study of the dynamics of the protein sequestered within the solvents is performed. The result shows that the protein dynamics is coupled with that of the surrounding matrix.
Collapse
|
38
|
Reátegui E, Aksan A. Effects of the Low-Temperature Transitions of Confined Water on the Structures of Isolated and Cytoplasmic Proteins. J Phys Chem B 2009; 113:13048-60. [DOI: 10.1021/jp903294q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eduardo Reátegui
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Alptekin Aksan
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota
| |
Collapse
|
39
|
Aksan A, Hubel A, Bischof JC. Frontiers in biotransport: water transport and hydration. J Biomech Eng 2009; 131:074004. [PMID: 19640136 DOI: 10.1115/1.3173281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Biotransport, by its nature, is concerned with the motions of molecules in biological systems while water remains as the most important and the most commonly studied molecule across all disciplines. In this review, we focus on biopreservation and thermal therapies from the perspective of water, exploring how its molecular motions, properties, kinetic, and thermodynamic transitions govern biotransport phenomena and enable preservation or controlled destruction of biological systems.
Collapse
Affiliation(s)
- Alptekin Aksan
- Center for Biotransport, Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | |
Collapse
|
40
|
Abstract
Biotransport, by its nature, is concerned with the motions of molecules in biological systems while water remains as the most important and the most commonly studied molecule across all disciplines. In this review, we focus on biopreservation and thermal therapies from the perspective of water, exploring how its molecular motions, properties, kinetic, and thermodynamic transitions govern biotransport phenomena and enable preservation or controlled destruction of biological systems.
Collapse
Affiliation(s)
- Alptekin Aksan
- Center for Biotransport, Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN 55455; Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455
| | - Allison Hubel
- Center for Biotransport, Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN 55455; Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455
| | - John C. Bischof
- Center for Biotransport, Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN 55455; Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455
| |
Collapse
|
41
|
Frölich A, Gabel F, Jasnin M, Lehnert U, Oesterhelt D, Stadler AM, Tehei M, Weik M, Wood K, Zaccai G. From shell to cell: neutron scattering studies of biological water dynamics and coupling to activity. Faraday Discuss 2009; 141:117-30; dsicussion 175-207. [PMID: 19227354 DOI: 10.1039/b805506h] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An integrated picture of hydration shell dynamics and of its coupling to functional macromolecular motions is proposed from studies on a soluble protein, on a membrane protein in its natural lipid environment, and on the intracellular environment in bacteria and red blood cells. Water dynamics in multimolar salt solutions was also examined, in the context of the very slow water component previously discovered in the cytoplasm of extreme halophilic archaea. The data were obtained from neutron scattering by using deuterium labelling to focus on the dynamics of different parts of the complex systems examined.
Collapse
Affiliation(s)
- A Frölich
- Institut de Biologie Structurale, UMR 5075, CEA-CNRS-UJF, Grenoble, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Schulz R, Krishnan M, Daidone I, Smith JC. Instantaneous normal modes and the protein glass transition. Biophys J 2009; 96:476-84. [PMID: 19167298 DOI: 10.1016/j.bpj.2008.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 10/15/2008] [Indexed: 11/29/2022] Open
Abstract
In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at approximately 220 K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.
Collapse
Affiliation(s)
- Roland Schulz
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | | | | |
Collapse
|
43
|
Fontaine-Vive F, Merzel F, Johnson M, Kearley G. Collagen and component polypeptides: Low frequency and amide vibrations. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
44
|
Backus EHG, Nguyen PH, Botan V, Moretto A, Crisma M, Toniolo C, Zerbe O, Stock G, Hamm P. Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties. J Phys Chem B 2008; 112:15487-92. [DOI: 10.1021/jp806403p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ellen H. G. Backus
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Phuong H. Nguyen
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Virgiliu Botan
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Alessandro Moretto
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Marco Crisma
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Claudio Toniolo
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Oliver Zerbe
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Gerhard Stock
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Peter Hamm
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| |
Collapse
|
45
|
Fabiani E, Stadler AM, Madern D, Koza MM, Tehei M, Hirai M, Zaccai G. Dynamics of apomyoglobin in the α-to-β transition and of partially unfolded aggregated protein. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 38:237-44. [DOI: 10.1007/s00249-008-0375-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 09/17/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022]
|
46
|
Krasnenko V, Tkaczyk AH, Tkaczyk ER, Mauring K. Physicochemical properties of blue fluorescent protein determined via molecular dynamics simulation. Biopolymers 2008; 89:1136-43. [DOI: 10.1002/bip.21065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
47
|
Fujiwara S, Plazanet M, Matsumoto F, Oda T. Differences in internal dynamics of actin under different structural states detected by neutron scattering. Biophys J 2008; 94:4880-9. [PMID: 18326640 PMCID: PMC2397340 DOI: 10.1529/biophysj.107.125302] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 02/08/2008] [Indexed: 11/18/2022] Open
Abstract
F-actin, a helical polymer formed by polymerization of the monomers (G-actin), plays crucial roles in various aspects of cell motility. Flexibility of F-actin has been suggested to be important for such a variety of functions. Understanding the flexibility of F-actin requires characterization of a hierarchy of dynamical properties, from internal dynamics of the actin monomers through domain motions within the monomers and relative motions between the monomers within F-actin to large-scale motions of F-actin as a whole. As a first step toward this ultimate purpose, we carried out elastic incoherent neutron scattering experiments on powders of F-actin and G-actin hydrated with D(2)O and characterized the internal dynamics of F-actin and G-actin. Well established techniques and analysis enabled the extraction of mean-square displacements and their temperature dependence in F-actin and in G-actin. An effective force constant analysis with a model consisting of three energy states showed that two dynamical transitions occur at approximately 150 K and approximately 245 K, the former of which corresponds to the onset of anharmonic motions and the latter of which couples with the transition of hydration water. It is shown that behavior of the mean-square displacements is different between G-actin and F-actin, such that G-actin is "softer" than F-actin. The differences in the internal dynamics are detected for the first time between the different structural states (the monomeric state and the polymerized state). The different behavior observed is ascribed to the differences in dynamical heterogeneity between F-actin and G-actin. Based on structural data, the assignment of the differences observed in the two samples to dynamics of specific loop regions involved in the polymerization of G-actin into F-actin is proposed.
Collapse
Affiliation(s)
- Satoru Fujiwara
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan.
| | | | | | | |
Collapse
|
48
|
Molecular processes in biological thermosensation. JOURNAL OF BIOPHYSICS 2008; 2008:602870. [PMID: 20130806 PMCID: PMC2814129 DOI: 10.1155/2008/602870] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Accepted: 04/16/2008] [Indexed: 12/30/2022]
Abstract
Since thermal gradients are almost everywhere, thermosensation could represent one of the oldest sensory transduction processes that evolved in organisms. There are many examples of temperature changes affecting the physiology of living cells. Almost all classes of biological macromolecules in a cell (nucleic acids, lipids, proteins) can present a target of the temperature-related stimuli. This review discusses some features of different classes of temperature-sensing molecules as well as molecular and biological processes that involve thermosensation. Biochemical, structural, and thermodynamic approaches are applied in the paper to organize the existing knowledge on molecular mechanisms of thermosensation. Special attention is paid to the fact that thermosensitive function cannot be assigned to any particular functional group or spatial structure but is rather of universal nature. For instance, the complex of thermodynamic, structural, and functional features of hemoglobin family proteins suggests their possible accessory role as “molecular thermometers”.
Collapse
|
49
|
Krishnan M, Kurkal-Siebert V, Smith JC. Methyl Group Dynamics and the Onset of Anharmonicity in Myoglobin. J Phys Chem B 2008; 112:5522-33. [DOI: 10.1021/jp076641z] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Krishnan
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany, and Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee
| | - V. Kurkal-Siebert
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany, and Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee
| | - Jeremy C. Smith
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany, and Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee
| |
Collapse
|
50
|
Kurkal-Siebert V, Agarwal R, Smith JC. Hydration-dependent dynamical transition in protein: protein interactions at approximately 240 K. PHYSICAL REVIEW LETTERS 2008; 100:138102. [PMID: 18518001 DOI: 10.1103/physrevlett.100.138102] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Indexed: 05/26/2023]
Abstract
Interprotein motions in low and fully hydrated carboxymyoglobin crystals are investigated using molecular dynamics simulation. Below approximately 240 K, the calculated dynamic structure factor exhibits a peak arising from interprotein vibration. Above approximately 240 K, the intermolecular fluctuations of the fully hydrated crystal increase drastically, whereas the low-hydration model exhibits no transition. Autocorrelation function analysis shows the transition to be dominated by the activation of diffusive intermolecular motion. The potential of mean force for the interaction remains quasiharmonic. The results indicate useful experimental avenues on protein:protein interactions to be explored using next-generation neutron sources.
Collapse
Affiliation(s)
- Vandana Kurkal-Siebert
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany
| | | | | |
Collapse
|