Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis

Miyashita, Osamu; Gorba, Christian; Tama, Florence

doi:10.1016/j.jsb.2010.09.008

Cited by 17 publications

(14 citation statements)

References 88 publications

(109 reference statements)

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“…Using EM approaches can also aid SAXS, where interestingly, EM studies have revealed that normal modes could well describe conformational states of macromolecular machines [53], and as such have been used in the fitting of EM density maps [54–57]. These low-frequency normal modes that represent global motions of a macromolecule have also been applied to SAXS [58], where normal modes have been used to find a model best fitting the SAXS electron pair distribution [59]. Another potential EM-like approach is to fit a flexible macromolecule/complex into an ab initio SAXS envelope, using SITUS to convert a SAXS envelope into a synthetic EM envelope, for fitting with the use the NORMA software [60].…”

Section: 3 Resultsmentioning

confidence: 99%

Developing advanced X-ray scattering methods combined with crystallography and computation

Perry

Tainer

2013

Methods

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The extensive use of small angle x-ray scattering (SAXS) over the last few years is rapidly providing new insights into protein interactions, complex formation and conformational states in solution. This SAXS methodology allows for detailed biophysical quantification of samples of interest. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations include ab initio approaches from SAXS data alone, and when combined with previously determined crystal/NMR, atomistic modeling can further enhance structural solutions and assess validity. This combination can provide definitions of architectures, spatial organizations of protein domains within a complex, including those not determined by crystallography or NMR, as well as defining key conformational states of a protein interaction. SAXS is not generally constrained by macromolecule size, and the rapid collection of data in a 96-well plate format provides methods to screen sample conditions. This includes screening for co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. Such analyses may be useful for screening constructs and conditions to determine those most likely to promote crystal growth of a complex under study. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. This is in addition to potentially providing architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered as being part of one’s repertoire of biophysical analyses, when conducting characterizations of protein and other macromolecular interactions.

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Section: 3 Resultsmentioning

confidence: 99%

Developing advanced X-ray scattering methods combined with crystallography and computation

Perry

Tainer

2013

Methods

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“…Currently, small-angle X-ray scattering (SAXS) has become a central tool in structural biology for characterizing proteins in solution. Models using flexible regions and studied with normal mode analysis [13], molecular dynamics (MD) [14][15][16] or Monte Carlo simulations [17] have provided not only successful data validation but also accurate fitting of the scattering profile because of the potential to explore the protein conformation in space. Motivated by low computational costs, high control of the energetic parameters and good agreement with experiments, the models based on the energy landscape theory [18] have been extensively employed in several molecular systems, including protein folding, conformational changes and dynamic molecular machines [18][19][20][21][22][23][24].…”

Section: Introductionmentioning

confidence: 99%

Assembling a xylanase–lichenase chimera through all-atom molecular dynamics simulations

Cota

Oliveira

Damásio

et al. 2013

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (kcat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes.

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“…15 We briefly note that NMFF-based strategies have also been applied to small-angle X-ray scattering (SAXS) data. 120,121 …”

Section: Normal Mode Analysismentioning

confidence: 99%

Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling

Vashisth

Skiniotis²,

Brooks³

2014

Chem. Rev.

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Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis

Cited by 17 publications

References 88 publications

Developing advanced X-ray scattering methods combined with crystallography and computation

Developing advanced X-ray scattering methods combined with crystallography and computation

Assembling a xylanase–lichenase chimera through all-atom molecular dynamics simulations

Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling

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