Genomes and Genes
Summary: The scattering of NEUTRONS by matter, especially crystals, with accompanying variation in intensity due to interference effects. It is useful in CRYSTALLOGRAPHY and POWDER DIFFRACTION.
Publications260 found, 100 shown here
- Conformational changes in SP-B as a function of surface pressureWilfred K Fullagar
School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
Biophys J 85:2624-32. 2003....
- Neutron diffraction and simulation studies of the exocyclic hydroxymethyl conformation of glucosePhilip E Mason
Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, USA
J Chem Phys 125:224505. 2006The techniques of neutron diffraction with isotopic substitution (NDIS) and molecular dynamics (MD) simulations have been used to examine the rotational conformation of the exocyclic hydroxymethyl group of D-glucopyranose...
- Nanostructures of colloidal complexes formed in oppositely charged polyelectrolyte/surfactant dilute aqueous solutionsS Trabelsi
Laboratoire de Physique des Solides, Universite Paris Sud, Batiment 510, 91405 Orsay Cedex, France
Eur Phys J E Soft Matter 23:305-11. 2007..However, they possess a similar internal structure in both regimes. Carboxymethylcellulose/CTAB complexes are also large, soft and polydisperse but do not seem to exhibit well-defined internal structures...
- Crystal structure and hydrogen bonding system in cellulose I(alpha) from synchrotron X-ray and neutron fiber diffractionYoshiharu Nishiyama
Department of Biomaterial Sciences, Graduate School of Agriculture and Life Science, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113, Japan
J Am Chem Soc 125:14300-6. 2003..hydrogen-bonding system in cellulose I(alpha), has been determined using atomic-resolution synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from the cell wall ..
- Effects of macromolecular crowding on an intrinsically disordered protein characterized by small-angle neutron scattering with contrast matchingDaniel Johansen
Department of Biology, University of Utah, Salt Lake City, Utah, USA
Biophys J 100:1120-8. 2011..These results are reminiscent of the behavior of polymers in concentrated melts, suggesting that these synthetic mixtures may provide useful insights into the properties of unfolded proteins under crowding conditions...
- Protein-water displacement distributionsWolfgang Doster
Technische Universitat Munchen, Physik Department E 13, Garching, Germany
Biochim Biophys Acta 1749:173-86. 2005..The interaction with water induces further continuous protein motions on a small scale. Water acts as a plasticizer of displacements, which couple to functional processes such as open-closed transitions and ligand exchange...
- The active site protonation states of perdeuterated Toho-1 β-lactamase determined by neutron diffraction support a role for Glu166 as the general base in acylationStephen J Tomanicek
Oak Ridge National Laboratory, Neutron Scattering Science Division, Oak Ridge, TN 37831, USA
FEBS Lett 585:364-8. 2011Room temperature neutron diffraction data of the fully perdeuterated Toho-1 R274N/R276N double mutant β-lactamase in the apo form were used to visualize deuterium atoms within the active site of the enzyme...
- Structural and functional analysis of the symmetrical Type I restriction endonuclease R.EcoR124I(NT)James E Taylor
Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, United Kingdom
PLoS ONE 7:e35263. 2012..We show that the covalent linkage between the two target recognition domains of the specificity subunit is not required for subunit assembly or enzyme activity, and discuss the implications for the evolution of Type I enzymes...
- Compression of random coils due to macromolecular crowdingC Le Coeur
Laboratoire Leon Brillouin, CEA CNRS, CEA Saclay, 91191 Gif sur Yvette, France
Phys Rev E Stat Nonlin Soft Matter Phys 79:031910. 2009....
- On the hydration of the phosphocholine headgroup in aqueous solutionFabrizia Foglia
Department of Pharmaceutical Sciences, King s College London, London SE1 9NH, United Kingdom
J Chem Phys 133:145103. 2010..headgroup in 1,2-dipropionyl-sn-glycero-3-phosphocholine (C(3)-PC) in solution has been determined by using neutron diffraction enhanced with isotopic substitution in combination with computer simulation techniques...
- Constrained solution scattering modelling of human antibodies and complement proteins reveals novel biological insightsStephen J Perkins
Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
J R Soc Interface 6:S679-96. 2009..We conclude that constrained scattering modelling makes useful contributions to our understanding of antibody and complement structure and function...
- Structure and hydration of membranes embedded with voltage-sensing domainsDmitriy Krepkiy
Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
Nature 462:473-9. 2009..Here we use neutron diffraction, solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations to ..
- Hemoglobin dynamics in red blood cells: correlation to body temperatureA M Stadler
Institut Laue Langevin, Grenoble, France
Biophys J 95:5449-61. 2008..The results demonstrated that changes in molecular dynamics in the picosecond time range and angstrom length scale might well be connected to a macroscopic effect on whole RBCs that occurs at body temperature...
- Conformation of the HIV-1 Gag protein in solutionSiddhartha A K Datta
HIV Drug Resistance Program, National Cancer Institute Frederick, Frederick, MD 21702 1201, USA
J Mol Biol 365:812-24. 2007..Since Gag is a rod-shaped molecule in the assembled immature virion, these findings imply that Gag undergoes a major conformational change upon virus assembly...
- Structure of aqueous glucose solutions as determined by neutron diffraction with isotopic substitution experiments and molecular dynamics calculationsP E Mason
Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, USA
J Phys Chem B 109:13104-11. 2005b>Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to examine the structuring of solvent around d-glucose in aqueous solution...
- QUAFIT: a novel method for the quaternary structure determination from small-angle scattering dataFrancesco Spinozzi
Dipartimento di Scienze della Vita e dell Ambiente, Università Politecnica delle Marche and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, Ancona, Italy
Biophys J 103:511-21. 2012..Results are in very good agreement with the structural model derived from electron microscopy observations...
- Dynamics-stability relationships in apo- and holomyoglobin: a combined neutron scattering and molecular dynamics simulations studyAndreas Maximilian Stadler
Institute for Complex Systems ICS 5 Molecular Biophysics, Forschungszentrum Julich, Julich, Germany
Biophys J 102:351-9. 2012..It is of interest that in holo-Mb, higher MSD values are observed for the residues outside the heme pocket, indicating an entropic contribution to protein stabilization by heme binding, which is in agreement with experimental results...
- Deuterium labeling for neutron structure-function-dynamics analysisFlora Meilleur
Department of Molecular and Structural Biochemistry, North Carolina State University, Oak Ridge National Laboratory, Raleigh, Oak Ridge, NC, TN, USA
Methods Mol Biol 544:281-92. 2009..Once the target protein has been expressed, purification proceeds by the protocols developed for the hydrogenated protein. The deuteration levels of the final product are determined by mass spectrometry...
- Structure of liquid n-hexaneG Venturi
CNR INFM CRS SOFT c o Dipartimento di Fisica, Universita di Firenze, Via G Sansone 1, I 50019 Sesto Fiorentino, Italy
J Chem Phys 131:034508. 2009The structure of deuterated liquid n-hexane has been investigated at room temperature by neutron diffraction and molecular dynamics simulations...
- Neutron diffraction study of Pseudomonas aeruginosa lipopolysaccharide bilayersThomas Abraham
National Research Council, Canadian Neutron Beam Center, Chalk River, Ontario K0J 1J0, Canada
J Phys Chem B 111:2477-83. 2007..Here, we report on neutron diffraction studies performed on aligned, self-assembled bilayers of LPS isolated from Pseudomonas aeruginosa PAO1...
- Protein dynamics in solution and powder measured by incoherent elastic neutron scattering: the influence of Q-range and energy resolutionFrank Gabel
Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
Eur Biophys J 34:1-12. 2005..Finally, analogies between the Gaussian approximation in IENS and the Guinier approximation in small-angle scattering are discussed...
- Preference for isolated water molecules in a concentrated glycerol-water mixtureJ J Towey
School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, United Kingdom
J Phys Chem B 115:7799-807. 2011b>Neutron diffraction coupled with hydrogen/deuterium isotopic substitution has been used to investigate the structure of a concentrated glycerol water (4:1 mole fraction) solution...
- The hydration of the neurotransmitter acetylcholine in aqueous solutionE C Hulme
Division of Physical Biochemistry, MRC National Institute for Medical Research, London, United Kingdom
Biophys J 91:2371-80. 2006b>Neutron diffraction augmented with hydrogen isotope substitution has been used to examine the water structure around the acetylcholine molecular ion in aqueous solution...
- Structure of pi-pi interactions in aromatic liquidsThomas F Headen
London Centre for Nanotechnology, Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
J Am Chem Soc 132:5735-42. 2010High-resolution neutron diffraction has been used in conjunction with hydrogen/deuterium isotopic labeling to determine with unprecedented detail the structure of two archetypal aromatic liquids: benzene and toluene...
- Viewing the bilayer hydrocarbon core using neutron diffractionXue Han
Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
J Membr Biol 227:123-31. 2009..Here, we propose a simple approach to visualize the hydrocarbon core using neutron diffraction and deuterated lipids that are commercially available...
- Preliminary time-of-flight neutron diffraction study on diisopropyl fluorophosphatase (DFPase) from Loligo vulgarisMarc Michael Blum
Institute of Biophysical Chemistry, J W Goethe University Frankfurt, Max von Laue Strasse 9, D 60438 Frankfurt, Germany
Acta Crystallogr Sect F Struct Biol Cryst Commun 63:42-5. 2007..the protonation state of the active-site residues, large-sized crystals of DFPase have been prepared for neutron diffraction studies...
- Hydration of POPC bilayers studied by 1H-PFG-MAS-NOESY and neutron diffractionKlaus Gawrisch
Laboratory of Membrane Biochemistry and Biophysics, NIAAA, NIH, Bethesda, MD 20892, USA
Eur Biophys J 36:281-91. 2007..The distribution of water molecules over the lipid bilayer was measured at identical water content by neutron diffraction. Water molecules penetrate deep into the interfacial region of bilayers but water concentration in the ..
- Selective deuteration of tryptophan and methionine residues in maltose binding protein: a model system for neutron scatteringValerie Laux
ILL EMBL Deuteration Laboratory, Partnership for Structural Biology, Institut Laue Langevin, 38042, Grenoble Cedex 9, France
Eur Biophys J 37:815-22. 2008..analysis of small-angle neutron scattering (SANS) data, neutron reflection (NR) data, and high-resolution neutron diffraction data. The selective labelling was carried out in E...
- Dynamics of apomyoglobin in the alpha-to-beta transition and of partially unfolded aggregated proteinE Fabiani
Institut Laue Langevin, BP156, Grenoble, France
Eur Biophys J 38:237-44. 2009..A study in a wide temperature range between 20 and 360 K revealed that a dynamical transition at about 200 K for motions in the 50 ps time scale exists also for a hydrated powder of heat-denatured aggregated ApoMb...
- Solvent isotope effect on macromolecular dynamics in E. coliMarion Jasnin
Institut de Biologie Structurale, UMR 5075 CEA CNRS UJF, 41 rue Jules Horowitz, 38027 Grenoble, France
Eur Biophys J 37:613-7. 2008..The smaller [Symbol: see text]k'[Symbol: see text] value suggested a larger entropy content in the D2O case due to increased sampling of macromolecular conformational substates...
- Atomistic structure of a micelle in solution determined by wide Q-range neutron diffractionRowan Hargreaves
STFC ISIS Neutron Scattering Facility, Didcot, United Kingdom
J Am Chem Soc 133:16524-36. 2011..By using wide Q-range neutron diffraction measurements of H/D isotopically substituted solutions of decyltrimethylammonimum bromide (C(10)TAB) ..
- Sample preparation methods to analyze DNA-induced structural changes in replication protein AChris A Brosey
Department of Biochemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
Methods Mol Biol 922:101-22. 2012..Here we describe a basic protocol for characterizing and optimizing sample conditions for RPA/ssDNA complexes prior to study by SAXS and/or SANS...
- Neutron diffraction measurements of skeletal muscle using the contrast variation technique: analysis of the equatorial diffraction patternsSatoru Fujiwara
Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2 4 Shirakata Shirane, Tokai mura, Naka gun, Ibaraki 319 1195, Japan
J Struct Biol 167:25-35. 2009..in order to explore the possibilities of the contrast variation technique in neutron fiber diffraction, neutron diffraction measurements of skeletal muscles were performed...
- Puzzle of protein dynamical transitionSalvatore Magazù
Dipartimento di Fisica, Università di Messina, Viale Ferdinando Stagno D Alcontres n 31, P O Box 55, Vill S Agata 98166 Messina, Italy
J Phys Chem B 115:7736-43. 2011..and show that it is not due to finite instrumental energy resolution effects and it is not connected to numerical errors in the data analysis protocol, differently to what W. Doster et al. proposed [Phys. Rev. Lett.2010, 104, 098101]...
- The low-temperature inflection observed in neutron scattering measurements of proteins is due to methyl rotation: direct evidence using isotope labeling and molecular dynamics simulationsKathleen Wood
Institut Laue Langevin, Grenoble Cedex 9, France
J Am Chem Soc 132:4990-1. 2010..Methyl group correlation times measured by solid state NMR in the purple membrane, taken from previous work, support the interpretation...
- Neutron diffraction studies of fluid bilayers with transmembrane proteins: structural consequences of the achondroplasia mutationXue Han
Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
Biophys J 91:3736-47. 2006..Here we use neutron diffraction to determine the disposition of FGFR3 transmembrane domain in fluid lipid bilayers, and investigate whether ..
- Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteinsIan S Millett
Department of Applied Physics, Stanford University, Stanford, California 92343, USA
Adv Protein Chem 62:241-62. 2002
- Protein dynamics studied by neutron scatteringFrank Gabel
Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble, France
Q Rev Biophys 35:327-67. 2002..The biological relevance of the experimental results is discussed. The major conclusion of the last decade concerns the strong dependence of internal dynamics on the macromolecular environment...
- Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurementsShigeki Arai
Neutron Science Research Center, Japan Atomic Energy Research Institute 2 4 Shirakatashirane, Tokai, Ibaraki 319 1195, Japan
Nucleic Acids Res 33:3017-24. 2005..By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions ..
- The structure of polyunsaturated lipid bilayers important for rhodopsin function: a neutron diffraction studyMihaela Mihailescu
Biophys J 90:L04-6. 2006..bilayers with perdeuterated stearoyl- or docosahexaenoyl hydrocarbon chains was investigated by neutron diffraction. Experiments were conducted at two different relative humidities, 66 and 86%...
- Hydrogen and hydration in proteinsNobuo Niimura
Neutron Science Research Center, Japan Atomic Energy Research Institute, Shirane, Tokai mura, Naka gun, Ibaraki Ken, Japan
Cell Biochem Biophys 40:351-69. 2004b>Neutron diffraction provides an experimental method of directly locating hydrogen atoms in proteins...
- Analysis of X-ray and neutron scattering from biomacromolecular solutionsMaxim V Petoukhov
EMBL, Hamburg Outstation, Germany
Curr Opin Struct Biol 17:562-71. 2007....
- Controlling the protein dynamical transition with sugar-based bioprotectant matrices: a neutron scattering studyE Cornicchi
Dipartimento di Fisica dell Università di Perugia, CEMIN Centro di Eccellenza per i Materiali Innovativi Nanostrutturati and INFM CRS SOFT, 06123 Perugia, Italy
Biophys J 91:289-97. 2006..A possible connection between the protein dynamical response versus T and the thermal stability in glucose-water bioprotectant matrices is proposed...
- Neutron diffraction reveals sequence-specific membrane insertion of pre-fibrillar islet amyloid polypeptide and inhibition by rifampicinKia Balali-Mood
Veterinary Biomedical Sciences, R D SVS, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
FEBS Lett 579:1143-8. 2005..In the first structural study of membrane-associated hIAPP, lamellar neutron diffraction shows that oligomeric hIAPP inserts into phospholipid bilayers, and extends across the membrane...
- Bulk-solvent and hydration-shell fluctuations, similar to alpha- and beta-fluctuations in glasses, control protein motions and functionsP W Fenimore
Theory Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Proc Natl Acad Sci U S A 101:14408-13. 2004..The large number of conformational substates is essential; proteins cannot function without this reservoir of entropy, which resides mainly in the hydration shell...
- Relationship between structure, dynamics and function of hydrated purple membrane investigated by neutron scattering and dielectric spectroscopyAlexandra Buchsteiner
Hahn Meitner Institut Berlin, Glienicker Str 100, D 14109 Berlin, Germany
J Mol Biol 371:914-23. 2007..PM) with its protein bacteriorhodopsin (BR), a light-driven proton pump, complementary information from neutron diffraction, quasi-elastic neutron scattering (QENS) and dielectric spectroscopy will form a comprehensive picture of ..
- Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexateBrad Bennett
Department of Biochemistry, Cellular and Molecular Biology, M407 Walters Life Sciences, University of Tennessee, Knoxville, TN 37996, USA
Proc Natl Acad Sci U S A 103:18493-8. 2006..Several D(2)Os are observed at hydrophobic surfaces, including two pockets near the MTX-binding site. A previously unidentified D(2)O hydrogen bonds with the catalytic D27 in mon. B, stabilizing its negative charge...
- Localization of coenzyme Q10 in the center of a deuterated lipid membrane by neutron diffractionThomas Hauss
Hahn Meitner Institute, Berlin Neutron Scattering Centre, Glienicker Strasse 100, D 14109 Berlin, Germany Darmstadt University of Technology, Dept of Chemistry, Physical Biochemistry, Petersenstrasse 22, D 64287 Darmstadt, Germany
Biochim Biophys Acta 1710:57-62. 2005..Seeking unambiguous evidence for the localization of ubiquinone within lipid bilayers, we have employed neutron diffraction. CoQ10 was incorporated into stacked bilayers of perdeuterated dimyristoyl phosphatidyl choline doped with ..
- Influence of hydration on the dynamics of lysozymeJ H Roh
Department of Polymer Science, The University of Akron, Akron, Ohio 44325 3909, USA
Biophys J 91:2573-88. 2006....
- Shape and subunit organisation of the DNA methyltransferase M.AhdI by small-angle neutron scatteringP Callow
EPSAM and ISTM Research Institutes, Keele University, Staffordshire ST5 5BG, UK
J Mol Biol 369:177-85. 2007....
- Fatty acid interdigitation in stratum corneum model membranes: a neutron diffraction studyA Ruettinger
Institute of Pharmacy, Martin Luther University, Wolfgang Langenbeck Str 4, 06120, Halle Saale, Germany
Eur Biophys J 37:759-71. 2008..CER [AP]), cholesterol (Ch), FFA and cholesterol sulphate (ChS) was investigated by neutron diffraction. The internal nanostructure of the SC lipid membrane in addition to the water distribution function was ..
- Global rigid body modeling of macromolecular complexes against small-angle scattering dataMaxim V Petoukhov
European Molecular Biology Laboratory, Hamburg, Germany
Biophys J 89:1237-50. 2005..The methods described are implemented in publicly available computer programs running on major hardware platforms...
- Conditioning action of the environment on the protein dynamics studied through elastic neutron scatteringA Paciaroni
Dipartimento di Fisica dell Università di Perugia, CNR INFM CRS SOFT, Via A Pascoli, 06123, Perugia, Italy
Eur Biophys J 35:591-9. 2006..The dynamical response of the protein to temperature is put in relationship with its thermal stability...
- Protein folding in membranes: insights from neutron diffraction studies of a membrane beta-sheet oligomerXue Han
The Johns Hopkins University, Department of Materials Science and Engineering, Baltimore, Maryland 21218, USA
Biophys J 94:492-505. 2008..Yet, the exact structure of the oligomer in the lipid bilayer is unknown. Here we use neutron diffraction to study the disposition of the peptides in bilayers...
- Membrane insertion of a lipidated ras peptide studied by FTIR, solid-state NMR, and neutron diffraction spectroscopyDaniel Huster
Junior Research Group Solid State NMR Studies of Membrane Associated Proteins, University of Leipzig, Liebigstrasse 27, D 04103 Leipzig, Germany
J Am Chem Soc 125:4070-9. 2003..the C-terminus of the human N-ras protein was studied by Fourier transform infrared, solid-state NMR, and neutron diffraction spectroscopy...
- Cholesterol hydroxyl group is found to reside in the center of a polyunsaturated lipid membraneThad A Harroun
National Research Council, Canadian Neutron Beam Centre, Chalk River, Ontario K0J 1J0, Canada
Biochemistry 45:1227-33. 2006..We attribute the change in location to the high disorder of polyunsaturated fatty acids (PUFA) that is incompatible with close proximity to the steroid moiety in its usual "upright" orientation...
- Small-angle scattering and neutron contrast variation for studying bio-molecular complexesAndrew E Whitten
Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, N S W, Australia
Methods Mol Biol 544:307-23. 2009....
- Crystallization of a large single crystal of cubic insulin for neutron protein crystallographyM Maeda
Neutron Science Research Center, Japan Atomic Energy Research Institute, 2 4 Sirakata Shirane, Tokai mura, Naka gun, Ibaraki Ken, 319 1195, Japan
J Synchrotron Radiat 11:41-4. 2004..of cubic porcine insulin for characterization of hydrogen and hydration in cubic insulin crystals by neutron diffraction analysis is reported...
- Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromoleculesKazuo Kurihara
Neutron Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319 1195, Japan
Proc Natl Acad Sci U S A 101:11215-20. 2004..The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND3+ terminus that may contribute to the unusual thermostability of this molecule...
- Hydration structures in proteins and neutron diffraction experiment on dissimilatory sul te reductase D (DsrD)Toshiyuki Chatake
Neutron Structural Biology, Neutron Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319 1195, Japan
J Synchrotron Radiat 11:72-5. 2004..In addition, the neutron diffraction study of a DNA-binding protein, dissimilatory sulfite reductase D (DsrD) is briefly described, and some ..
- A new neutron single-crystal diffractometer dedicated for biological macromolecules (BIX-4)Kazuo Kurihara
Neutron Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319 1195, Japan
J Synchrotron Radiat 11:68-71. 2004..5 times larger than previous BIX-3. That higher performance increases the opportunities to apply neutron crystallography to biological macromolecules which give only weak reflections and/or small crystals...
- Hydration in proteins observed by high-resolution neutron crystallographyToshiyuki Chatake
Advanced Science Research Center, Japan Atomic Energy Research Institute, Tokai mura, Ibaraki Ken, Japan
Proteins 50:516-23. 2003..Our results further show that there are strong relationships between these shapes and the water environments...
- Insertion of externally administered amyloid beta peptide 25-35 and perturbation of lipid bilayersSilvia Dante
Physical Biochemistry, Darmstadt University of Technology, Petersenstrasse 22, D 64287 Darmstadt, Germany
Biochemistry 42:13667-72. 2003..Abeta(25-35) has been localized in the region of the lipid alkyl chain, and it has a severe disordering effect on the lamellar order of the lipid bilayer. Both of these results are of biomedical relevance...
- Neutron diffraction and simulation studies of CsNO3 and Cs2CO3 solutionsPhilip E Mason
Department of Food Science, Stocking Hall, Cornell University, Ithaca, New York 14853, USA
J Am Chem Soc 128:15136-44. 2006b>Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to study the structuring in aqueous solution of two cesium salts, cesium carbonate, and cesium nitrate...
- Dynamics of Water in NaxCoO2.yH2ONiina Jalarvo
Hahn Meitner Institut, Glienicker Strasse 100, 14109 Berlin, Germany
J Phys Chem B 112:703-9. 2008..Furthermore, our results indicate that, at room temperature, the sodium ions have no influence on the rotational dynamics of the "fast" water molecules...
- Dispersion relation of lipid membrane shape fluctuations by neutron spin-echo spectrometryMaikel C Rheinstädter
Institut Laue Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9, France
Phys Rev Lett 97:048103. 2006..The softening of a mode which can be associated with the formation of the ripple structure is observed close to the main phase transition...
- SANS/SAXS study of the BSA solvation properties in aqueous urea solutions via a global fit approachRaffaele Sinibaldi
Dipartimento di Scienze Applicate ai Sistemi Complessi, Universita Politecnica delle Marche, Via Brecce Bianche, 60019 Ancona, Italy
Eur Biophys J 37:673-81. 2008..Results confirm that urea preferentially sticks to the protein surface, inducing a noticeable change in both the repulsive and the attractive interaction potentials...
- X-ray and neutron scattering studies of the hydration structure of alkali ions in concentrated aqueous solutionsS Ansell
ISIS Division, Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
Biophys Chem 124:171-9. 2006..focus on the structural properties of ions in water and it will be shown how the 'difference' methods of neutron diffraction with isotopic substitution (NDIS) and anomalous X-ray diffraction (AXD) can be used to obtain direct ..
- Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering dataNorbert Kucerka
Canadian Neutron Beam Centre, National Research Council, Chalk River, Ontario K0J 1J0, Canada
Biophys J 95:2356-67. 2008....
- Effects of hydration water on protein methyl group dynamics in solutionDaniela Russo
CNR INFM and CRS Soft, c o Institut Laue Langevin, 6 rue J Horowitz, BP156, F 38042 Grenoble, France
Phys Rev E Stat Nonlin Soft Matter Phys 75:040902. 2007..They provide unique experimental evidence that the structural and dynamical properties of the interfacial water strongly influence the side-chain dynamics and the activation of diffusive motion...
- Hydration dependence of active core fluctuations in bacteriorhodopsinKathleen Wood
Institut Laue Langevin, BP 156, F 38042 Grenoble Cedex 9, France
Biophys J 95:194-202. 2008..The results suggest that the inhibition of high-amplitude motions by lowering hydration may play a key role in the slowing down of the photocycle and the proton pumping activity of BR...
- Water structure around dipeptides in aqueous solutionsSylvia E McLain
Neutron Scattering Sciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, TN 37831 6475, USA
Eur Biophys J 37:647-55. 2008..glycyl-L-proline and L:-alanyl-L-proline-has been determined by a combination of neutron diffraction with isotopic substitution and empirical potential structural refinement techniques...
- Short-range order and collective dynamics of DMPC bilayers: a comparison between molecular dynamics simulations, X-ray, and neutron scattering experimentsJochen S Hub
Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
Biophys J 93:3156-68. 2007..The conventional interpretation in terms of the three-effective-eigenmode model is found to be only partly suitable to describe the complex fluid dynamics of lipid chains...
- Conformation of poly(L-lysine)-graft-poly(ethylene glycol) molecular brushes in aqueous solution studied by small-angle neutron scatteringL Feuz
Laboratory for Surface Science and Technology, Department of Materials, ETH Zurich, Wolfgang Pauli Strasse 10, CH 8093 Zurich, Switzerland
Eur Phys J E Soft Matter 23:237-45. 2007..This finding is in agreement with earlier simulation and recent theoretical results...
- Clathrate formation and dissociation in vapor/water/ice/hydrate systems in SBA-15, sol-gel and CPG porous media, as probed by NMR relaxation, novel protocol NMR cryoporometry, neutron scattering and ab initio quantum-mechanical molecular dynamics simulatiJ Beau W Webber
Institute of Petroleum Engineering, Heriot Watt University, Edinburgh EH14 4AS, UK
Magn Reson Imaging 25:533-6. 2007..Ab initio quantum-mechanical molecular dynamics calculations are also being employed to probe the dynamics of liquids in pores at nanometric dimensions...
- High-pressure/low-temperature neutron scattering of gas inclusion compounds: progress and prospectsYusheng Zhao
Los Alamos Neutron Science Center, Earth and Environmental Sciences Division, and Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Proc Natl Acad Sci U S A 104:5727-31. 2007..We have developed high-pressure/low-temperature gas/fluid cells in conjunction with neutron diffraction and inelastic neutron scattering instruments allowing in situ and real-time examination of gas uptake/..
- Neutron protein crystallography: beyond the folding structure of biological macromoleculesNobuo Niimura
Institute of Applied Beam Science, Graduate School of Science and Engineering, Ibaraki University, 4 12 1 Naka Narusawa, Hitachi, Ibaraki 316 8511, Japan
Acta Crystallogr A 64:12-22. 2008b>Neutron diffraction provides an experimental method of directly locating H atoms in proteins, a technique complementary to ultra-high-resolution X-ray diffraction...
- Nanosecond molecular relaxations in lipid bilayers studied by high energy-resolution neutron scattering and in situ diffractionMaikel C Rheinstädter
Institut Laue Langevin, 6 rue Jules Horowitz, Boite Postale 156, 38042 Grenoble Cedex 9, France
Phys Rev E Stat Nonlin Soft Matter Phys 75:011907. 2007..From this analysis we quantify two relaxation processes. We associate the fast relaxation with translational diffusion of lipid and water molecules while the slow process likely stems from collective dynamics...
- Protein structure and hydration probed by SANS and osmotic stressChristopher Stanley
NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
Biophys J 94:2777-89. 2008..These results provide a framework for studying other biomolecular systems and assemblies using neutron scattering together with osmotic stress...
- Dynamics of C-phycocyanin in various deuterated trehalose/water environments measured by quasielastic and elastic neutron scatteringIngo Köper
Laboratoire Léon Brillouin UMR 12 CEA CNRS, CEA Saclay, 91191, Gif sur Yvette Cedex, France
Eur Biophys J 37:739-48. 2008..These results suggest that a role of trehalose would be to stabilize proteins by inhibiting some fluctuations at the origin of protein unfolding and denaturation...
- Temperature dependence of protein dynamics as affected by sugars: a neutron scattering studyS Magazu
Physics Department and INFM, Messina University, Messina, Italy
Eur Biophys J 36:685-91. 2007..Whereas the Q dependence of the elastic incoherent structure factor gives information about the geometry and the amplitudes of the motions...
- Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectraYasumasa Joti
Institute of Molecular and Cellular Biosciences, University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
Biophys J 94:4435-43. 2008..The fine structure of the dynamics structure factor is expected to be detected by the experiment if a high resolution instrument (< approximately 20 microeV) is developed in the near future...
- Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scatteringLars Meinhold
Heidelberg University, Interdisciplinary Center for Scientific Computing, Computational Molecular Biophysics, Heidelberg, Germany
Biophys J 94:4812-8. 2008..Therefore, these results imply that the thermophilic enzyme is the more flexible of the two...
- Structural studies on the hydration of L-glutamic acid in solutionSylvia E McLain
Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom
J Phys Chem B 110:21251-8. 2006A combination of neutron diffraction augmented with isotopic substitution and computer modeling using empirical potential structure refinement has been used to extract detailed structural information for L-glutamic acid dissolved in 2 M ..
- Ion solvation and water structure in potassium halide aqueous solutionsAlan K Soper
ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX, United Kingdom
Biophys Chem 124:180-91. 2006..8 ion pairs per 100 water molecules, using the combined techniques of neutron diffraction with hydrogen isotope substitution...
- Picosecond internal dynamics of lysozyme as affected by thermal unfolding in nonaqueous environmentA De Francesco
Istituto Nazionale per la Fisica della Materia, Dipartimento di Fisica dell Università di Perugia, Perugia 06121, Italy
Biophys J 86:480-7. 2004..Conversely the faster component might be ascribed to the local dynamics of hydrogen atoms caged by the nearest neighbors with characteristic time of approximately 0.3 ps...
- Refolding of a high molecular weight protein: salt effect on collapseD Lairez
Laboratoire Leon Brillouin, Gif sur Yvette, France
Biophys J 84:3904-16. 2003..This behavior is discussed with respect to the scaling theories for polymers and polyampholytes...
- Dynamic properties of an oriented lipid/DNA complex studied by neutron scatteringF Natali
INFM OGG, Grenoble, France
Biophys J 88:1081-90. 2005..Our results show that a substantial modification of the membrane dynamics is accompanied by the balancing of the total net charge inside the complex, together with the consequent displacement of interlayer water molecules...
- Detection of ligand- and solvent-induced shape alterations of cell-growth-regulatory human lectin galectin-1 in solution by small angle neutron and x-ray scatteringLizhong He
Institute for Coastal Research, Physical and Chemical Analysis, Geesthacht, Germany
Biophys J 85:511-24. 2003..We have hereby proven that ligand presence and an aprotic solvent significantly affect the shape of galectin-1 in solution...
- The 15-K neutron structure of saccharide-free concanavalin AM P Blakeley
European Molecular Biology Laboratory, 6 rue Jules Horowitz, B P 181, 38042 Grenoble 9, France
Proc Natl Acad Sci U S A 101:16405-10. 2004..Methodologically, this successful neutron cryo protein structure refinement opens up categories of neutron protein crystallography, including freeze-trapped structures and cryo to room temperature comparisons...
- An ordered low-temperature phase of barium nitroprusside trihydrate studied by neutron diffractionG Chevrier
Laboratoire Leon Brillouin, CEN Saclay, 91191 Gif sur Yvette, France
Acta Crystallogr C 59:i59-62. 2003..3H(2)O, have been studied by neutron diffraction in order to examine the structural behaviour of the compound in the 20-120 K temperature range and to ..
- Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solutionJennifer A Hayward
Interdisciplinary Centre for Computational Science JWR, University of Heidelberg, Heidelberg, Germany
Biophys J 85:679-85. 2003..The proportion that the external dynamics contributes to the protein mean-square displacement increases to approximately 30 and 60% at 300 K on the 10- and 100-ps timescales, respectively...
- Collective dynamics of lipid membranes studied by inelastic neutron scatteringM C Rheinstädter
Institut Laue Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9, France
Phys Rev Lett 93:108107. 2004..Finally, we can clearly identify an additional nondispersive (optical) mode predicted by molecular dynamics simulations [Phys. Rev. Lett. 87, 238101 (2001)]]...
- The structure of aqueous guanidinium chloride solutionsPhilip E Mason
Contribution from the Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA
J Am Chem Soc 126:11462-70. 2004The combination of neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations to characterize the structuring in an aqueous solution of the denaturant guanidinium chloride is described...
- Determination of bilayer thickness and lipid surface area in unilamellar dimyristoylphosphatidylcholine vesicles from small-angle neutron scattering curves: a comparison of evaluation methodsNorbert Kucerka
Department of Chemical Theory of Drugs, Faculty of Pharmacy, Comenius University, Kalinciakova 8, 832 32, Bratislava, Slovakia
Eur Biophys J 33:328-34. 2004..5 A(3), it was possible to obtain from the experimental data the DMPC surface area as 58.9+/-0.8 A(2), the bilayer thickness as 44.5+/-0.3 A and the number of water molecules as 6.8+/-0.2 per DMPC located in the bilayer polar region...
- Neutron diffraction studies on rubredoxin from Pyrococcus furiosusRobert Bau
Chemistry Department, University of Southern California, Los Angeles, CA 90007, USA
J Synchrotron Radiat 11:76-9. 2004Single-crystal neutron diffraction data up to a resolution of 1...
- Hydration dynamics near a model protein surfaceDaniela Russo
Department of Bioengineering, University of California at Berkeley, Berkeley, California 94720, USA
Biophys J 86:1852-62. 2004..We discuss the hydration dynamics results of this model protein system in the context of protein function and protein-protein recognition...
- X-ray and neutron diffraction studies and MD simulation of atomic configurations in polyamorphic Y2O3-Al2O3 systemsM C Wilding
Department of Geology and McClellan Nuclear Radiation Center, University of California at Davis, Davis, CA 95616, USA
Philos Transact A Math Phys Eng Sci 363:589-607. 2005..Calculated partial radial distribution functions indicate that the primary differences between HDA and LDA configurations occur among the Y-Y correlations...
- Structure and interaction in protein solutions as studied by small-angle neutron scatteringS Chodankar
Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
Phys Rev E Stat Nonlin Soft Matter Phys 72:041931. 2005..The time dependent data have been used to obtain the fraction of crystallization as a function of time...
- Adsorption structures of water in NaX studied by DRIFT spectroscopy and neutron powder diffractionJens Hunger
Institut fur Anorganische Chemie, Universitat Leipzig, Johannisallee 29, D 04103 Leipzig, Germany
J Phys Chem B 110:342-53. 2006..We find strong evidence for the formation of cyclic hexamers of water molecules localized in the 12-ring windows, which are further stabilized by hydrogen bonds to framework oxygen atoms...
- An assessment of the accuracy of methods for predicting hydrogen positions in protein structuresLucy R Forrest
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Proteins 61:296-309. 2005..9 A resolution), as well as of a number of relatively high-resolution neutron diffraction structures (< 1...
- Structural Basis for Bridged Bimetallic Enzyme CatalysisDagmar Ringe; Fiscal Year: 2007..mutagenesis, kinetic analysis, inhibitor design and synthesis, ultra-high resolution X-ray crystallography, neutron diffraction, and combined quantum mechanics/molecular mechanics simulations to probe the role of the second shell ..
- Structural Basis for Bridged Bimetallic Enzyme CatalysisDagmar Ringe; Fiscal Year: 2009..mutagenesis, kinetic analysis, inhibitor design and synthesis, ultra-high resolution X-ray crystallography, neutron diffraction, and combined quantum mechanics/molecular mechanics simulations to probe the role of the second shell ..
- CRYSTALLOGRAPHIC STUDIES ON RIBOSOMAL PARTICLESAda Yonath; Fiscal Year: 1993..The X-ray crystallographic studies are being supported by electron microscopy, image reconstruction, neutron diffraction, biochemistry and genetics manipulation...
- Neutron Diffraction and MD Studies of the Studies of the Structure of Aqueous SolJohn Brady; Fiscal Year: 2007..structure of aqueous solutions of complex biomolecular solutes using a combination of MD simulations and neutron diffraction with isotopic substitution (NDIS) experiments...
- Concerted membrane diffraction and simulation studiesStephen White; Fiscal Year: 2006..These new methods involve the concerted use of molecular dynamics simulations and x-ray & neutron diffraction measurements to obtain dynamic structural images of peptide-bilayer interactions in thermally disordered ..
- CATALYTIC MECHANISM OF CARBONIC ANHYDRASEDavid Silverman; Fiscal Year: 2009..Crystal structures of important mutants will be determined by X-ray and neutron diffraction, and we will attempt to observe hydrogen atoms in proton transfer pathways...
- CATALYTIC MECHANISM OF CARBONIC ANHYDRASEDavid Silverman; Fiscal Year: 2007..Crystal structures of important mutants will be determined by X-ray and neutron diffraction. We will determine specifically how distances, location, and environment in the active site influence the ..
- NEUTRON DETECTORS FOR MACROMOLECULAR CRYSTALLOGRAPHYKRISHNA MANDAL; Fiscal Year: 2004..b>Neutron diffraction provides a unique approach to investigate the structural biology by determining the position of hydrogen ..
- CRYSTALLOGRAPHIC STUDIES ON RIBOSOMAL PARTICLESAda Yonath; Fiscal Year: 1990..The crystallographic work will be supported by biochemistry, electron microscopy and neutron diffraction. Ribosomal particles to which functional probes (e.g. cDNA or tRNA) are attracted will also be studied...
- Cold Neutrons For Biology And TechnologyStephen White; Fiscal Year: 2005..At the same time, a high-performance computer system will be put in place to support the concerted use of neutron diffraction and molecular dynamics methods in order to deduce 3-D structural information from 1- or 2-D diffraction ..