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CHARACTERIZING THE SPACE OF INTERATOMIC DISTANCE DISTRIBUTION FUNCTIONS CONSISTENT WITH SOLUTION SCATTERING DATA

PARITOSH A. KAVATHEKAR, BRUCE A. CRAIG, ALAN M. FRIEDMAN, CHRIS BAILEY-KELLOGG, DEVIN J. BALKCOM
2010 Journal of Bioinformatics and Computational Biology  
In this paper, we study one part of the problem of elucidating three-dimensional structure from solution scattering data, determining the distribution of interatomic distances, P(r).  ...  This problem is known to be ill-conditioned; for a single observed diffraction pattern, there may be many consistent distance distribution functions.  ...  METHODS Equation 1 describes the relationship between the scattering curve and the interatomic distance distribution function.  ... 
doi:10.1142/s0219720010004781 pmid:20401948 fatcat:d2xfkhrmgjbchdfysa34oaux5y

Characterization of Protein Fold by Wide-Angle X-ray Solution Scattering

Lee Makowski, Diane J. Rodi, Suneeta Mandava, Satish Devarapalli, Robert F. Fischetti
2008 Journal of Molecular Biology  
The distribution of proteins that are members of the four structure classes, α, β, α/β and α+β, are well separated in WAXS space when data extending to a spacing of 2.2 Å are used.  ...  Wide-angle X-ray solution scattering (WAXS) patterns contain substantial information about the three-dimensional structure of a protein.  ...  Supplementary Data Supplementary data associated with this article can be found, in the online version, at doi:10.1016/ j.jmb.2008.08.038  ... 
doi:10.1016/j.jmb.2008.08.038 pmid:18786543 fatcat:zznpov2mfjfrhbxn32lylzsdm4

X-ray solution scattering studies of the structural diversity intrinsic to protein ensembles

Lee Makowski, David Gore, Suneeta Mandava, David Minh, Sanghyun Park, Diane J. Rodi, Robert F. Fischetti
2011 Biopolymers  
The authors thank Celia Schiffer for the gift of HIV protease, both WT and T80N; and Tobin Sosnick for the ubiquitin WT and mutants.  ...  The two-dimensional (2D) scattering patterns were circularly averaged with Fit2D, 30, 31 and the resulting one-dimensional intensity distribution was plotted as a function of spacing 1/ d.  ...  WAXS patterns from WT exhibited statistically significant differences when inhibitor was added, whereas T80N did not (data not shown), consistent with its well characterized lack of functionality.  ... 
doi:10.1002/bip.21631 pmid:21462170 pmcid:PMC3103594 fatcat:pw5bhkm3mjgj7oyn4bl3rqirvu

Modulation of HIV protease flexibility by the T80N mutation

Hao Zhou, Shangyang Li, John Badger, Ellen Nalivaika, Yufeng Cai, Jennifer Foulkes-Murzycki, Celia Schiffer, Lee Makowski
2015 Proteins: Structure, Function, and Bioinformatics  
To investigate the potential influence of the T80N mutation on HIVp flexibility, wide-angle scattering (WAXS) data was measured for a series of HIV protease variants.  ...  Starting with a calculated WAXS pattern from a rigid atomic model, the modulations in the intensity distribution caused by structural fluctuations in the protein were predicted by simple analytic methods  ...  BioCAT is a National Institutes of Health-  ... 
doi:10.1002/prot.24737 pmid:25488402 pmcid:PMC4461556 fatcat:2njztzafi5c3fhybqiike5ompa

EXAFS studies of the local environment of lead and selenium atoms in PbTe1−x Sex solid solutions

A. I. Lebedev, I. A. Sluchinskaya, V. N. Demin, I. Munro
1999 Physics of the solid state  
Monte Carlo calculations show that these observations are related to the complicated structure of the distribution function for Pb-Pb distances.  ...  In addition to a bimodal distribution of the bond lengths in the firstcoordination sphere, an unusually large value of the Debye-Waller factors for the Pb-Pb interatomic distances ͑second-coordination  ...  FIG. 5 . 5 The Pb-Pb interatomic distance as a function of the composition x of PbTe 1Ϫx Se x solid solutions. The points are experimental data.  ... 
doi:10.1134/1.1130981 fatcat:vdjonyy4dbf27noxzq4baqlpl4

Molecular Crowding Inhibits Intramolecular Breathing Motions in Proteins

Lee Makowski, Diane J. Rodi, Suneeta Mandava, David D.L. Minh, David B. Gore, Robert F. Fischetti
2008 Journal of Molecular Biology  
Concentration-dependent changes in the observed scattering intensities are consistent with a model of structural fluctuations in which secondary structures undergo rigid-body motions relative to one another  ...  Here we use a combination of wide angle x-ray scattering (WAXS) and computational modeling to derive a quantitative measure of the spatial scale of conformational fluctuations in a protein solution.  ...  Acknowledgements This work and use of the Advanced Photon Source was supported by the U.S. Department of Energy under contract DE-AC-02-06CH11357.  ... 
doi:10.1016/j.jmb.2007.07.075 pmid:18031757 pmcid:PMC2219890 fatcat:4taaomtubjhkxg5l37dr2c46dq

Variable angle XAFS study of multilayer nanostructure: Determination of selective concentration profile and depth-dependent partial atomic distributions

Yuri Babanov, Yuri Salamatov, Enver Mukhamedzhanov
2009 Journal of Physics, Conference Series  
For determining the depth-dependent partial interatomic distances we use angle resolved EXAFS data.  ...  It is a Fredholm integral equation of the first kind, it belongs to the class of ill-posed problems and for solution it needs special methods. We use the regularization method.  ...  Acknowledgments The authors would like to thank Mikhail Milyaev for his preparation of the samples, Marina Andreeva and Evgeny Kravtsov for useful discussion.  ... 
doi:10.1088/1742-6596/190/1/012030 fatcat:xwcsv4isbvgftpuyya57cs6wza

Local structure studies using the pair distribution function

Pierre Bordet, M. Ceretti, W. Paulus, M.-H. Mathon, C. Ritter
2015 EPJ Web of Conferences  
It based on powder diffraction data fourier transformed to direct space. We will present here the main characteristics of the method, and its domain of application.  ...  This is an Open Access article distributed under the terms of the Creative Commons Attribution License 4.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original  ...  The author wants to express its gratitude to the following persons: M. Brunelli, I.E. Grey and I.  ... 
doi:10.1051/epjconf/20159901003 fatcat:dgirqpj43bhkrd6racv33k4u5i

Local structure studies using the pair distribution function

Pierre Bordet, M. Ceretti, W. Paulus, M.-H. Mathon, C. Ritter
2015 EPJ Web of Conferences  
It based on powder diffraction data fourier transformed to direct space. We will present here the main characteristics of the method, and its domain of application.  ...  This is an Open Access article distributed under the terms of the Creative Commons Attribution License 4.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original  ...  The author wants to express its gratitude to the following persons: M. Brunelli, I.E. Grey and I.  ... 
doi:10.1051/epjconf/201510401003 fatcat:4ugfsdrm3vf6tggwidawppsb44

On the Nanoscale Structure of KxFe2−yCh2 (Ch = S, Se): A Neutron Pair Distribution Function View

Panagiotis Mangelis, Hechang Lei, Marshall McDonnell, Mikhail Feygenson, Cedomir Petrovic, Emil Bozin, Alexandros Lappas
2018 Condensed Matter  
Comparative exploration of the nanometer-scale atomic structure of K x Fe 2−y Ch 2 (Ch = S, Se) was performed using neutron total scattering-based atomic pair distribution function (PDF) analysis of 5  ...  Comparison of structural parameters of the Fe-vacancy-disordered model indicates that the replacement of selenium (Se) by sulphur (S) results in an appreciable reduction in the Fe-Ch interatomic distances  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/condmat3030020 fatcat:mutxo3ra4jhqhddstuz53uulwu

Size-dependent characterization of embedded Ge nanocrystals: Structural and thermal properties

L. L. Araujo, R. Giulian, D. J. Sprouster, C. S. Schnohr, D. J. Llewellyn, P. Kluth, D. J. Cookson, G. J. Foran, M. C. Ridgway
2008 Physical Review B  
Specifically, increases in total disorder, interatomic distance, and the asymmetry in the distribution of distances were observed as the NC size decreased, demonstrating that finite-size effects govern  ...  Temperature-dependent EXAFS measurements in the range of 15-300 K were employed to probe the mean vibrational frequency and the variation of the interatomic distance distribution ͑mean value, variance,  ...  ͑third cumulant͒ of the first-shell interatomic distance distribution in the measured temperature range.  ... 
doi:10.1103/physrevb.78.094112 fatcat:76yomugfxfextgvnu3bnz2qj3e

X-Ray Absorption Spectroscopy of Strontium(II) Coordination

Peggy A. O'Day, Matthew Newville, Philip S. Neuhoff, Nita Sahai, Susan A. Carroll
2000 Journal of Colloid and Interface Science  
Empirical parameterization of Debye-Waller factor (σ 2 ) for strontium compounds as a function of backscatterer atomic number (Z), interatomic Sr-Z distance, and temperature of spectral data collection  ...  Analysis of anharmonic vibrational disorder (i.e., significant contribution from a third cumulant term (C 3 ) in the EXAFS phase-shift function) in compounds with low and high static disorder around strontium  ...  The consistent decrease in interatomic distance with increasing temperature may indicate a small anharmonic contribution to EXAFS scattering as noted above.  ... 
doi:10.1006/jcis.1999.6621 pmid:10662514 fatcat:yll4oneiuzgptg4eplkwipq7xm

Effects of Structural and Microstructural Features on the Total Scattering Pattern of Nanocrystalline Materials

Nicola Dengo, Norberto Masciocchi, Antonio Cervellino, Antonietta Guagliardi, Federica Bertolotti
2022 Nanomaterials  
modification of the histogram of interatomic distances derived therefrom is clearly discussed nor considered in the currently available protocols.  ...  Hereby, starting from atomistic models of a prototypical system (cadmium selenide), we simulate multiple effects on the atomic pair distribution function, obtained from reciprocal space patterns computed  ...  Acknowledgments: The technical staff of the MS-X04SA beamline of the SLS Synchrotron (PSI, Villigen, CH) is heartily acknowledged for the data collection of the silicon (reference @SLS); Maxwell W.  ... 
doi:10.3390/nano12081252 pmid:35457960 pmcid:PMC9030889 fatcat:x26rw4jxofbvnhpdc2l6bojdkq

Modelling of glass-like carbon structure and its experimental verification by neutron and X-ray diffraction

K. Jurkiewicz, S. Duber, H. E. Fischer, A. Burian
2017 Journal of Applied Crystallography  
The compatibility of the computer-generated models was verified by comparison of the simulations with the experimental diffraction data in both reciprocal and real spaces.  ...  This article reports on direct evidence of curved planes in glassy carbons using neutron and X-ray diffraction measurements and their analysis in real space using the atomic pair distribution function  ...  Acknowledgements KJ is grateful for the financial support of the National Centre of Science, grant No. 2015/19/N/ST3/01037.  ... 
doi:10.1107/s1600576716017660 fatcat:7q36m2lrdbfjhpzkwjc2fx7uvu

New methods for EXAFS analysis in structural genomics

Grant Bunker, Nicholas Dimakis, Gocha Khelashvili
2004 Journal of Synchrotron Radiation  
Data analysis is one of the remaining bottlenecks in high-throughput EXAFS for structural genomics.  ...  Here some recent developments in methodology are described that offer the potential for rapid and automated XAS analysis of metalloproteins.  ...  Reconstruction of the interatomic distance distribution amounts to solving a set of linear equations, which by virtue of their linearity have a single global minimum.  ... 
doi:10.1107/s090904950402881x pmid:15616365 fatcat:fvuno7fi2bf5jl3spi74jpz4rq
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