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Abstract
X-ray scattering is uniquely suited to the study of disordered systems and thus has the potential to provide insight into dynamic processes where diffraction methods fail. In particular, while X-ray crystallography has been a staple of structural biology for more than half a century and will continue to remain so, a major limitation of this technique has been the lack of dynamic information. Solution X-ray scattering has become an invaluable tool in structural and mechanistic studies of biological macromolecules where large conformational changes are involved. Such systems include allosteric enzymes that play key roles in directing metabolic fluxes of biochemical pathways, as well as large, assembly-line type enzymes that synthesize secondary metabolites with pharmaceutical applications. Furthermore, crystallography has the potential to provide information on protein dynamics via the diffuse scattering patterns that are overlaid with Bragg diffraction. Historically, these patterns have been very difficult to interpret, but recent advances in X-ray detection have led to a renewed interest in diffuse scattering analysis as a way to probe correlated motions. Here, we will review X-ray scattering theory and highlight recent advances in scattering-based investigations of protein solutions and crystals, with a particular focus on complex enzymes.
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Affiliation(s)
- Steve P Meisburger
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - William C Thomas
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Nozomi Ando
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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2
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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.
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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
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3
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Horn M, Nienhaus K, Nienhaus GU. Fourier transform infrared spectroscopy study of ligand photodissociation and migration in inducible nitric oxide synthase. F1000Res 2014; 3:290. [PMID: 25653844 DOI: 10.12688/f1000research.5836.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2014] [Indexed: 03/23/2024] Open
Abstract
Inducible nitric oxide synthase (iNOS) is a homodimeric heme enzyme that catalyzes the formation of nitric oxide (NO) from dioxygen and L-arginine (L-Arg) in a two-step process. The produced NO can either diffuse out of the heme pocket into the surroundings or it can rebind to the heme iron and inhibit enzyme action. Here we have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy at cryogenic temperatures, using the carbon monoxide (CO) and NO stretching bands as local probes of the active site of iNOS. Characteristic changes were observed in the spectra of the heme-bound ligands upon binding of the cofactors. Unlike photolyzed CO, which becomes trapped in well-defined orientations, as indicated by sharp photoproduct bands, photoproduct bands of NO photodissociated from the ferric heme iron were not visible, indicating that NO does not reside in the protein interior in a well-defined location or orientation. This may be favorable for NO release from the enzyme during catalysis because it reduces self-inhibition. Moreover, we used temperature derivative spectroscopy (TDS) with FTIR monitoring to explore the dynamics of NO and carbon monoxide (CO) inside iNOS after photodissociation at cryogenic temperatures. Only a single kinetic photoproduct state was revealed, but no secondary docking sites as in hemoglobins. Interestingly, we observed that intense illumination of six-coordinate ferrous iNOS oxy-NO ruptures the bond between the heme iron and the proximal thiolate to yield five-coordinate ferric iNOS oxy-NO, demonstrating the strong trans effect of the heme-bound NO.
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Affiliation(s)
- Michael Horn
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany ; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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4
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Horn M, Nienhaus K, Nienhaus GU. Fourier transform infrared spectroscopy study of ligand photodissociation and migration in inducible nitric oxide synthase. F1000Res 2014; 3:290. [PMID: 25653844 PMCID: PMC4304226 DOI: 10.12688/f1000research.5836.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/11/2014] [Indexed: 11/20/2022] Open
Abstract
Inducible nitric oxide synthase (iNOS) is a homodimeric heme enzyme that catalyzes the formation of nitric oxide (NO) from dioxygen and L-arginine (L-Arg) in a two-step process. The produced NO can either diffuse out of the heme pocket into the surroundings or it can rebind to the heme iron and inhibit enzyme action. Here we have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy at cryogenic temperatures, using the carbon monoxide (CO) and NO stretching bands as local probes of the active site of iNOS. Characteristic changes were observed in the spectra of the heme-bound ligands upon binding of the cofactors. Unlike photolyzed CO, which becomes trapped in well-defined orientations, as indicated by sharp photoproduct bands, photoproduct bands of NO photodissociated from the ferric heme iron were not visible, indicating that NO does not reside in the protein interior in a well-defined location or orientation. This may be favorable for NO release from the enzyme during catalysis because it reduces self-inhibition. Moreover, we used temperature derivative spectroscopy (TDS) with FTIR monitoring to explore the dynamics of NO and carbon monoxide (CO) inside iNOS after photodissociation at cryogenic temperatures. Only a single kinetic photoproduct state was revealed, but no secondary docking sites as in hemoglobins. Interestingly, we observed that intense illumination of six-coordinate ferrous iNOS oxy-NO ruptures the bond between the heme iron and the proximal thiolate to yield five-coordinate ferric iNOS oxy-NO, demonstrating the strong trans effect of the heme-bound NO.
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Affiliation(s)
- Michael Horn
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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5
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Nienhaus K, Olson JS, Nienhaus GU. An engineered heme-copper center in myoglobin: CO migration and binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1824-31. [PMID: 23459127 DOI: 10.1016/j.bbapap.2013.02.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/19/2013] [Accepted: 02/20/2013] [Indexed: 11/19/2022]
Abstract
We have investigated CO migration and binding in CuBMb, a copper-binding myoglobin double mutant (L29H-F43H), by using Fourier transform infrared spectroscopy and flash photolysis over a wide temperature range. This mutant was originally engineered with the aim to mimic the catalytic site of heme-copper oxidases. Comparison of the wild-type protein Mb and CuBMb shows that the copper ion in the distal pocket gives rise to significant effects on ligand binding to the heme iron. In Mb and copper-free CuBMb, primary and secondary ligand docking sites are accessible upon photodissociation. In copper-bound CuBMb, ligands do not migrate to secondary docking sites but rather coordinate to the copper ion. Ligands entering the heme pocket from the outside normally would not be captured efficiently by the tight distal pocket housing the two additional large imidazole rings. Binding at the Cu ion, however, ensures efficient trapping in CuBMb. The Cu ion also restricts the motions of the His64 side chain, which is the entry/exit door for ligand movement into the active site, and this restriction results in enhanced geminate and slow bimolecular CO rebinding. These results support current mechanistic views of ligand binding in hemoglobins and the role of the CuB in the active of heme-copper oxidases. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany
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6
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Treuel L, Jiang X, Nienhaus GU. New views on cellular uptake and trafficking of manufactured nanoparticles. J R Soc Interface 2013; 10:20120939. [PMID: 23427093 DOI: 10.1098/rsif.2012.0939] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nanoparticles (NPs) are of similar size to typical cellular components and proteins, and can efficiently intrude living cells. A detailed understanding of the involved processes at the molecular level is important for developing NPs designed for selective uptake by specific cells, for example, for targeted drug delivery. In addition, this knowledge can greatly assist in the engineering of NPs that should not penetrate cells so as to avoid adverse health effects. In recent years, a wide variety of experiments have been performed to elucidate the mechanisms underlying cellular NP uptake. Here, we review some select recent studies, which are often based on fluorescence microscopy and sophisticated strategies for specific labelling of key cellular components. We address the role of the protein corona forming around NPs in biological environments, and describe recent work revealing active endocytosis mechanisms and pathways involved in their cellular uptake. Passive uptake is also discussed. The current state of knowledge is summarized, and we point to issues that still need to be addressed to further advance our understanding of cellular NP uptake.
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Affiliation(s)
- Lennart Treuel
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany
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7
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Nienhaus K, Lutz S, Meuwly M, Nienhaus GU. Reaction-pathway selection in the structural dynamics of a heme protein. Chemistry 2013; 19:3558-62. [PMID: 23401035 DOI: 10.1002/chem.201203558] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 12/28/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
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Nienhaus K, Zosel F, Nienhaus GU. Ligand binding to heme proteins: a comparison of cytochrome c variants with globins. J Phys Chem B 2012; 116:12180-8. [PMID: 22978708 DOI: 10.1021/jp306775n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We have studied the binding of carbon monoxide (CO) in mutants of Cyt c having its methionine at position 80 replaced by alanine, aspartate, and arginine, so that the sixth coordination is available for ligand binding. We have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy to examine interactions of the heme-bound and photolyzed CO (and also nitric oxide, NO) in the small heme pocket created by the mutations. By using FTIR temperature derivative spectroscopy (TDS) and nanosecond flash photolysis, the enthalpy barrier distributions for CO rebinding were determined. In flash photolysis experiments, the majority of ligands rebind to the heme iron on picosecond time scales so that only the high-barrier tail of the distributions is visible on the nanosecond scale. By continuous wave excitation prior to TDS characterization of the barriers, however, each Cyt c molecule is photoexcited multiple times and complete photodissociation can be achieved, which likely arises from a rotation of the CO within the heme pocket so that the oxygen faces the heme iron. Apparently, reorientation prior to rebinding constitutes an additional and significant contribution to the rebinding barrier. Our experiments reveal that the compact, rigid structure of Cyt c offers no alternative binding sites for photodissociated ligands in the protein matrix. A comparison of ligand binding in these Cyt c mutants and hemoglobins underscores the importance of internal ligand docking sites and ligand migration routes for conveying a ligand binding function to heme proteins.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, D-76131 Karlsruhe, Germany
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Achterhold K, Ostermann A, Moulin M, Haertlein M, Unruh T, Parak FG. Dynamical properties of the hydration shell of fully deuterated myoglobin. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:041930. [PMID: 22181198 DOI: 10.1103/physreve.84.041930] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 08/29/2011] [Indexed: 05/31/2023]
Abstract
Freeze-dried perdeuterated sperm whale myoglobin was kept in a water-saturated atmosphere in order to obtain a hydration degree of 335 H(2)O molecules per one myoglobin molecule. Incoherent neutron scattering was performed at the neutron spectrometer TOFTOF at the FRM II in an angular range of q from 0.6 to 1.8 Å(-1) and a temperature range from 4 to 297 K. We used neutrons with a wavelength of λ αE 6 Å and an energy resolution of about 65 μeV corresponding to motions faster than 10 ps. At temperatures above 225 K, broad lines appear in the spectra caused by quasielastic scattering. For an explanation of these lines, we assumed that there are only two types of protons, those that are part of the hydration water (72%) and those that belong to the protein (28%). The protons of the hydration water were analyzed with the diffusion model of Singwi and Sjölander [Phys. Rev. 119, 863 (1960)]. In this model, a water molecule stays for a time τ(0) in a bound state performing oscillatory motions. Thereafter, the molecule performs free diffusion for the time τ(1) in a nonbound state followed again by the oscillatory motions for τ(0) and so forth. We used the general formulation with no simplifications as τ(0)≫τ(1) or τ(1)≫τ(0). At room temperature, we obtained τ(0) αE 104 ps and τ(1) αE 37 ps. For the protein bound hydrogen, the dynamics is described by a Brownian oscillator where the protons perform overdamped motions in limited space.
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Affiliation(s)
- Klaus Achterhold
- Physik-Department E17, Technische Universität München, James-Franck-Strasse 1, D-85747 Garching, Germany
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Nienhaus K, Nickel E, Lu C, Yeh SR, Nienhaus GU. Ligand migration in human indoleamine-2,3 dioxygenase. IUBMB Life 2011; 63:153-9. [PMID: 21445845 DOI: 10.1002/iub.431] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Human indoleamine 2,3-dioxygenase (hIDO), a monomeric heme enzyme, catalyzes the oxidative degradation of L-tryptophan (L-Trp) and other indoleamine derivatives. Its activity follows typical Michaelis-Menten behavior only for L-Trp concentrations up to 50 μM; a further increase in the concentration of L-Trp causes a decrease in the activity. This substrate inhibition of hIDO is a result of the binding of a second L-Trp molecule in an inhibitory substrate binding site of the enzyme. The molecular details of the reaction and the inhibition are not yet known. In the following, we summarize the present knowledge about this heme enzyme.
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Affiliation(s)
- Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe, Germany.
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11
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Nienhaus K, Nienhaus GU. Ligand dynamics in heme proteins observed by Fourier transform infrared-temperature derivative spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1030-41. [PMID: 20656073 DOI: 10.1016/j.bbapap.2010.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/14/2010] [Accepted: 07/15/2010] [Indexed: 11/29/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a powerful tool for the investigation of protein-ligand interactions in heme proteins. Nitric oxide and carbon monoxide are attractive physiologically relevant ligands because their bond stretching vibrations give rise to strong mid-infrared absorption bands that can be measured with exquisite sensitivity and precision using photolysis difference spectroscopy at cryogenic temperatures. These stretching bands are fine-tuned by electrostatic interactions with the environment and, therefore, ligands can be utilized as local probes of structure and dynamics. Bound to the heme iron, the ligand stretching bands are susceptible to changes in the iron-ligand bond and the electric field at the active site. Upon photolysis, the vibrational bands display changes due to ligand relocation to docking sites within the protein, rotational motions of the ligand in these sites and protein conformational changes. Photolysis difference spectra taken over a wide temperature range (3-300K) using specific temperature protocols for sample photodissociation can provide detailed insights into both protein and ligand dynamics. Moreover, temperature-derivative spectroscopy (TDS) has proven to be a particularly powerful technique to study protein-ligand interactions. The FTIR-TDS technique has been extensively applied to studies of carbon monoxide binding to heme proteins, whereas measurements with nitric oxide are still scarce. Here we describe infrared cryo-spectroscopy and present a variety of applications to the study of protein-ligand interactions in heme proteins. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics and Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1, D-76131 Karlsruhe, Germany
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12
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13
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Nienhaus K, Lutz S, Meuwly M, Nienhaus GU. Structural Identification of Spectroscopic Substates in Neuroglobin. Chemphyschem 2010; 11:119-29. [DOI: 10.1002/cphc.200900637] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Lutz S, Nienhaus K, Nienhaus GU, Meuwly M. Ligand Migration between Internal Docking Sites in Photodissociated Carbonmonoxy Neuroglobin. J Phys Chem B 2009; 113:15334-43. [DOI: 10.1021/jp905673p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stephan Lutz
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland; Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany; and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - Karin Nienhaus
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland; Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany; and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - G. Ulrich Nienhaus
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland; Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany; and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland; Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany; and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801
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Nickel E, Nienhaus K, Lu C, Yeh SR, Nienhaus GU. Ligand and substrate migration in human indoleamine 2,3-dioxygenase. J Biol Chem 2009; 284:31548-54. [PMID: 19767648 DOI: 10.1074/jbc.m109.039859] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human indoleamine 2,3-dioxygenase (hIDO), a monomeric heme enzyme, catalyzes the oxidative degradation of L-Trp and other indoleamine derivatives. Using Fourier transform infrared and optical absorption spectroscopy, we have investigated the interplay between ferrous hIDO, the ligand analog CO, and the physiological substrate L-Trp. These data provide the long sought evidence for two distinct L-Trp binding sites. Upon photodissociation from the heme iron at T > 200 K, CO escapes into the solvent. Concomitantly, L-Trp exits the active site and, depending on the l-Trp concentration, migrates to a secondary binding site or into the solvent. Although L-Trp is spectroscopically silent at this site, it is still noticeable due to its pronounced effect on the CO association kinetics, which are significantly slower than those of L-Trp-free hIDO. L-Trp returns to its initial site only after CO has rebound to the heme iron.
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Affiliation(s)
- Elena Nickel
- Institute of Biophysics, University of Ulm, 89069 Ulm, Germany
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16
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Nienhaus K, Nickel E, Davis MF, Franzen S, Nienhaus GU. Determinants of Substrate Internalization in the Distal Pocket of Dehaloperoxidase Hemoglobin of Amphitrite ornata. Biochemistry 2008; 47:12985-94. [DOI: 10.1021/bi801564r] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karin Nienhaus
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - Elena Nickel
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - Michael F. Davis
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - Stefan Franzen
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - G. Ulrich Nienhaus
- Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, and Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801
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17
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A physical picture of protein dynamics and conformational changes. J Biol Phys 2008; 33:371-87. [PMID: 19669525 DOI: 10.1007/s10867-008-9102-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 06/25/2008] [Indexed: 10/21/2022] Open
Abstract
A physical model is reviewed which explains different aspects of protein dynamics consistently. At low temperatures, the molecules are frozen in conformational substates. Their average energy is 3/2RT. Solid-state vibrations occur on a time scale of femtoseconds to nanoseconds. Above a characteristic temperature, often called the dynamical transition temperature, slow modes of motions can be observed occurring on a time scale between about 140 and 1 ns. These motions are overdamped, quasidiffusive, and involve collective motions of segments of the size of an alpha-helix. Molecules performing these types of motion are in the "flexible state". This state is reached by thermal activation. It is shown that these motions are essential for conformational relaxation. Based on this picture, a new approach is proposed to understand conformational changes. It connects structural fluctuations and conformational transitions.
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18
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Influence of distal residue B10 on CO dynamics in myoglobin and neuroglobin. J Biol Phys 2008; 33:357-70. [PMID: 19669524 DOI: 10.1007/s10867-008-9059-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2007] [Accepted: 02/08/2008] [Indexed: 10/22/2022] Open
Abstract
For many years, myoglobin has served as a paradigm for structure-function studies in proteins. Ligand binding and migration within myoglobin has been studied in great detail by crystallography and spectroscopy, showing that gaseous ligands such as O(2), CO, and NO not only bind to the heme iron but may also reside transiently in three internal ligand docking sites, the primary docking site B and secondary sites C and D. These sites affect ligand association and dissociation in specific ways. Neuroglobin is another vertebrate heme protein that also binds small ligands. Ligand migration pathways in neuroglobin have not yet been elucidated. Here, we have used Fourier transform infrared temperature derivative spectroscopy at cryogenic temperatures to compare the influence of the side chain volume of amino acid residue B10 on ligand migration to and rebinding from docking sites in myoglobin and neuroglobin.
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Meinhold L, Merzel F, Smith JC. Lattice dynamics of a protein crystal. PHYSICAL REVIEW LETTERS 2007; 99:138101. [PMID: 17930640 DOI: 10.1103/physrevlett.99.138101] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Indexed: 05/25/2023]
Abstract
All-atom lattice-dynamical calculations are reported for a crystalline protein, ribonuclease A. The sound velocities, density of states, heat capacity (C(V)) and thermal diffuse scattering are all consistent with available experimental data. C(V) proportional, variant T(1.68) for T < 35 K, significantly deviating from a Debye solid. In Bragg peak vicinity, inelastic scattering of x rays by phonons is found to originate from acoustic mode scattering. The results suggest an approach to protein crystal physics combining all-atom lattice-dynamical calculations with experiments on next-generation neutron sources.
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Affiliation(s)
- Lars Meinhold
- Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany.
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Pichler A, Rüdisser S, Rauch C, Flader W, Wellenzohn B, Winger RH, Liedl KR, Hallbrucker A, Mayer E. Restructuring of Hydration Shells Rules the Low-Temperature Dynamics of B-DNA via Its Two Conformer Substates. J Phys Chem B 2002. [DOI: 10.1021/jp013121+] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Nienhaus K, Lamb DC, Deng P, Nienhaus GU. The effect of ligand dynamics on heme electronic transition band III in myoglobin. Biophys J 2002; 82:1059-67. [PMID: 11806945 PMCID: PMC1301912 DOI: 10.1016/s0006-3495(02)75465-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Band III is a near-infrared electronic transition at ~13,000 cm(-1) in heme proteins that has been studied extensively as a marker of protein conformational relaxation after photodissociation of the heme-bound ligand. To examine the influence of the heme pocket structure and ligand dynamics on band III, we have studied carbon monoxide recombination in a variety of myoglobin mutants after photolysis at 3 K using Fourier transform infrared temperature-derivative spectroscopy with monitoring in three spectral ranges, (1) band III, the mid-infrared region of (2) the heme-bound CO, and (3) the photodissociated CO. Here we present data on mutant myoglobins V68F and L29W, which both exhibit pronounced ligand movements at low temperature. From spectral and kinetic analyses in the mid-infrared, a small number of photoproduct populations can be distinguished, differing in their distal heme pocket conformations and/or CO locations. We have decomposed band III into its individual photoproduct contributions. Each photoproduct state exhibits a different "kinetic hole-burning" (KHB) effect, a coupling of the activation enthalpy for rebinding to the position of band III. The analysis reveals that the heme pocket structure and the photodissociated CO markedly affect the band III transition. A strong kinetic hole-burning effect results only when the CO ligand resides in the docking site on top of the heme group. Migration of CO away from the heme group leads to an overall blue shift of band III. Consequently, band III can be used as a sensitive tool to study ligand dynamics after photodissociation in heme proteins.
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Affiliation(s)
- Karin Nienhaus
- Department of Biophysics, University of Ulm, 89069 Ulm, Germany
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23
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Teeter MM, Yamano A, Stec B, Mohanty U. On the nature of a glassy state of matter in a hydrated protein: Relation to protein function. Proc Natl Acad Sci U S A 2001; 98:11242-7. [PMID: 11572978 PMCID: PMC58714 DOI: 10.1073/pnas.201404398] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2000] [Accepted: 08/01/2001] [Indexed: 11/18/2022] Open
Abstract
Diverse biochemical and biophysical experiments indicate that all proteins, regardless of size or origin, undergo a dynamic transition near 200 K. The cause of this shift in dynamic behavior, termed a "glass transition," and its relation to protein function are important open questions. One explanation postulated for the transition is solidification of correlated motions in proteins below the transition. We verified this conjecture by showing that crambin's radius of gyration (Rg) remains constant below approximately 180 K. We show that both atom position and dynamics of protein and solvent are physically coupled, leading to a novel cooperative state. This glassy state is identified by negative slopes of the Debye-Waller (B) factor vs. temperature. It is composed of multisubstate side chains and solvent. Based on generalization of Adam-Gibbs' notion of a cooperatively rearranging region and decrease of the total entropy with temperature, we calculate the slope of the Debye-Waller factor. The results are in accord with experiment.
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Affiliation(s)
- M M Teeter
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA.
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24
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Affiliation(s)
- J B Clarage
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA
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25
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McMahon BH, Stojković BP, Hay PJ, Martin RL, Garcı́a AE. Microscopic model of carbon monoxide binding to myoglobin. J Chem Phys 2000. [DOI: 10.1063/1.1309524] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Ostermann A, Waschipky R, Parak FG, Nienhaus GU. Ligand binding and conformational motions in myoglobin. Nature 2000; 404:205-8. [PMID: 10724176 DOI: 10.1038/35004622] [Citation(s) in RCA: 308] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Myoglobin, a small globular haem protein that binds gaseous ligands such as O2, CO and NO reversibly at the haem iron, serves as a model for studying structural and dynamic aspects of protein reactions. Time-resolved spectroscopic measurements after photodissociation of the ligand revealed a complex ligand-binding reaction with multiple kinetic intermediates, resulting from protein relaxation and movements of the ligand within the protein. To observe the structural changes induced by ligand dissociation, we have carried out X-ray crystallographic investigations of carbon monoxy-myoglobin (MbCO mutant L29W) crystals illuminated below and above 180 K, complemented by time-resolved infrared spectroscopy of CO rebinding. Here we show that below 180 K photodissociated ligands migrate to specific sites within an internal cavity--the distal haem pocket--of an essentially immobilized, frozen protein, from where they subsequently rebind by thermally activated barrier crossing. Upon photodissociation above 180 K, ligands escape from the distal pocket, aided by protein fluctuations that transiently open exit channels. We recover most of the ligands in a cavity on the opposite side of the haem group.
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Affiliation(s)
- A Ostermann
- Fakultät für Physik, Technische Universität München, Garching, Germany
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27
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Kurzyński M. A synthetic picture of intramolecular dynamics of proteins. Towards a contemporary statistical theory of biochemical processes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1998; 69:23-82. [PMID: 9670774 DOI: 10.1016/s0079-6107(97)00033-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
An increasing body of experimental evidence indicates the slow character of internal dynamics of native proteins. The important consequence of this is that theories of chemical reactions, used hitherto, appear inadequate for description of most biochemical reactions. Construction of a contemporary, truly advanced statistical theory of biochemical processes will need simple but realistic models of microscopic dynamics of biomolecules. In this review, intended to be a contribution towards this direction, three topics are considered. First, an intentionally simplified picture of dynamics of native proteins which emerges from recent investigations is presented. Fast vibrational modes of motion, of periods varying from 10(-14) to 10(-11) s, are contrasted with purely stochastic conformational transitions. Significant evidence is adduced that the relaxation time spectrum of the latter spreads in the whole range from 10(-11) to 10(5) s or longer, and up to 10(-7) s it is practically quasi-continuous. Next, the essential ideas of the theory of reaction rates based on stochastic models of intramolecular dynamics are outlined. Special attention is paid to reactions involving molecules in the initial conformational substrates confirmed to the transition state, which is realized in actual experimental situations. And finally, the two best experimentally justified classes of models of conformational transition dynamics, symbolically referred to as "protein glass" and "protein machine", are described and applied to the interpretation of a few simple biochemical processes, perhaps the most important result reported is the demonstration of the possibility of predominance of the short initial condition-dependent stage of protein involved reactions over the main stage described by the standard kinetics. This initial stage, and not the latter, is expected to be responsible for the coupling of component reactions in the complete enzymatic cycles as well as more complex processes of biological free energy transduction.
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Affiliation(s)
- M Kurzyński
- Institute of Physics, A. Mickiewicz University, Poznań, Poland
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28
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Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH. NMR evidence for slow collective motions in cyanometmyoglobin. NATURE STRUCTURAL BIOLOGY 1997; 4:292-7. [PMID: 9095197 DOI: 10.1038/nsb0497-292] [Citation(s) in RCA: 217] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Residual dipolar couplings observed in NMR spectra at very high magnetic fields have been measured to a high degree of accuracy for the paramagnetic protein cyanometmyoglobin. Deviations of these measurements from predictions based on available crystallographic and solution structures are largely systematic and well correlated within a given helix of this highly alpha-helical protein. These observations can be explained by invoking collective motion and small displacements of representative helices from their reported average positions in the solid state. Thus, the measurements appear to be capable of providing important insights into slower, collective protein motions, which are likely to be important for function, and which have been difficult to study using established experimental techniques.
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Affiliation(s)
- J R Tolman
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
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29
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Abstract
The understanding of flexibility and deformability in proteins is one of the current major challenges of structural molecular biology. The knowledge of the average atomic positions of three-dimensional folding of proteins, which is obtained either by X-ray diffraction or n.m.r. spectroscopy, is generally not sufficient to explain their functional mechanisms. Very often it is necessary to consider the existence of other concerted atomic motions as, for example, in the well-known case of the CO molecule fixation at the active site of myoglobin which requires the concerted displacement of a large number of atoms in order to open a channel down to this site. This opening, which depends on the physico-chemical conditions, plays the role of a regulator in the biochemical reactions (Janin & Wodak, 1983; Tainer et al. 1984; Westhof et al. 1984; Ormos et al. 1988).
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Affiliation(s)
- J P Benoit
- Laboratoire d'Utilisation du Rayonnement Electromagnétique, Université Paris-Sud, Orsay, France
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30
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Diffuse X-ray scattering from macromolecular crystals using synchrotron radiation. Radiat Phys Chem Oxf Engl 1993 1995. [DOI: 10.1016/0969-806x(94)00146-b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Thüne T, Badger J. Thermal diffuse X-ray scattering and its contribution to understanding protein dynamics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1995; 63:251-76. [PMID: 8599030 DOI: 10.1016/0079-6107(95)00006-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- T Thüne
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02254, USA
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32
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Gibrat JF, Garnier J, G? N. Normal mode analysis of oligomeric proteins: Reduction of the memory requirement by consideration of rigid geometry and molecular symmetry. J Comput Chem 1994. [DOI: 10.1002/jcc.540150804] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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33
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Abstract
Zwitterionic L-alanine forms crystals containing strong hydrogen-bonding and methylmethyl interactions. Well-defined low-frequency lattice vibrations exist in the crystals involving correlated intermolecular motions on the picosecond timescale. A characterization of these vibrations is expected to provide useful information on the nature of nonbonded interactions in peptides and proteins. We examine some of the vibrations using coherent inelastic neutron scattering and computer simulation techniques. The neutron scattering measurements are used to determine phonon dispersion relations for the acoustic and some low-frequency optic modes in the crystal. There is evidence for interaction between the two lowest frequency optical phonons and the longitudinal acoustic mode. The velocity of sound is anisotropic and can be correlated with the hydrogen-bonding arrangement in the crystal. Corresponding phonon dispersion relations are derived from normal mode analyses of the crystal using the program CHARMM. Although some calculated vibrational frequencies are somewhat too high, the form of the calculated dispersion relations are in good agreement with experiment.
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Affiliation(s)
- D Durand
- Laboratoire Léon Brillouin, Centre d'Etudes de Saclay, Gif-sur-Yvette, France
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34
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35
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Plachinda AS, Sedov VE, Khromov VI, Suzdalev IP, Goldanskii VI, Nienhaus GU, Parak F. Mössbauer studies of bound diffusion in a model polymer system. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 45:7716-7723. [PMID: 10000579 DOI: 10.1103/physrevb.45.7716] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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36
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37
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Clarage JB, Clarage MS, Phillips WC, Sweet RM, Caspar DL. Correlations of atomic movements in lysozyme crystals. Proteins 1992; 12:145-57. [PMID: 1603804 DOI: 10.1002/prot.340120208] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Diffuse scattering data have been collected on two crystal forms of lysozyme, tetragonal and triclinic, using synchrotron radiation. The observed diffraction patterns were simulated using an exact theory for simple model crystals which relates the diffuse scattering intensity distribution to the amplitudes and correlations of atomic movements. Although the mean square displacements in the tetragonal form are twice that in the triclinic crystal, the predominant component of atomic movement in both crystals is accounted for by short-range coupled motions where displacement correlations decay exponentially as a function of atomic separation, with a relaxation distance of approximately 6 A. Lattice coupled movements with a correlation distance approximately 50 A account for only about 5-10% of the total atomic mean square displacements in the protein crystals. The results contradict various presumptions that the disorder in protein crystals can be modeled predominantly by elastic vibrations or rigid body movements.
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Affiliation(s)
- J B Clarage
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254
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38
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39
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Young RD, Frauenfelder H, Johnson J, Lamb DC, Nienhaus G, Philipp R, Scholl R. Time- and temperature dependence of large-scale conformational transitions in myoglobin. Chem Phys 1991. [DOI: 10.1016/0301-0104(91)87075-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Smith JC. Protein dynamics: comparison of simulations with inelastic neutron scattering experiments. Q Rev Biophys 1991; 24:227-91. [PMID: 1749823 DOI: 10.1017/s0033583500003723] [Citation(s) in RCA: 302] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To deepen our understanding of the principles determining the folding and functioning of globular proteins the determination of their three-dimensional structures must be supplemented with the characterization of their internal motions. Although dynamical events in proteins occur on time-scale ranging from femtoseconds to at least seconds, the physical properties of globular proteins are such that picosecond (ps) time-scale motions make a particularly important contribution to the internal fluctuations of the atoms from their mean positions.
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Affiliation(s)
- J C Smith
- Département de Biologie Cellulaire et Moléculaire, CEN-Saclay, Gif-sur-Yvette, France
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41
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Kuriyan J, Osapay K, Burley SK, Brünger AT, Hendrickson WA, Karplus M. Exploration of disorder in protein structures by X-ray restrained molecular dynamics. Proteins 1991; 10:340-58. [PMID: 1946343 DOI: 10.1002/prot.340100407] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Conformational disorder in crystal structures of ribonuclease-A and crambin is studied by including two independent structures in least-squares optimizations against X-ray data. The optimizations are carried out by X-ray restrained molecular dynamics (simulated annealing refinement) and by conventional least-squares optimization. Starting from two identical structures, the optimizations against X-ray data lead to significant deviations between the two, with rms backbone displacements of 0.45 A for refinement of ribonuclease at 1.53 A resolution, and 0.31 A for crambin at 0.945 A. More than 15 independent X-ray restrained molecular dynamics runs have been carried out for ribonuclease, and the displacements between the resulting structures are highly reproducible for most atoms. These include residues with two or more conformations with significant dihedral angle differences and alternative hydrogen bonding, as well as groups of residues that undergo displacements that are suggestive of rigid-body librations. The crystallographic R-values obtained are approximately 13%, as compared to 15.3% for a comparable refinement with a single structure. Least-squares optimization without an intervening restrained molecular dynamics stage is sufficient to reproduce most of the observed displacements. Similar results are obtained for crambin, where the higher resolution of the X-ray data allows for refinement of unconstrained individual anisotropic temperature factors. These are shown to be correlated with the displacements in the two-structure refinements.
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Affiliation(s)
- J Kuriyan
- Howard Hughes Medical Institute, Rockefeller University, New York, New York 10021
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42
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Krupyanskii YF, Goldanskii VI, Nienhaus GU, Parak F. Dynamics of protein-water systems revealed by Rayleigh scattering of Mössbauer radiation (RSMR). ACTA ACUST UNITED AC 1990. [DOI: 10.1007/bf02101039] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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43
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