MULCh: modules for the analysis of small-angle neutron contrast variation data from biomolecular assemblies

Abstract

Small-angle neutron scattering with contrast variation can fill important gaps in our understanding of biomolecular assemblies, providing constraints that can aid in the construction of molecular models and in subsequent model refinements. This paper describes the implementation of simple tools for analysing neutron contrast variation data, accessible via a user-friendly web-based interface (http:// www.mmb.usyd.edu.au/NCVWeb/). There are three modules accessible from the website to analyse neutron contrast variation data from bimolecular complexes. The first module, Contrast, computes neutron contrasts of each component of the complex required by the other two modules; the second module, R g , analyses the contrast dependence of the radii of gyration to yield information relating to the size and disposition of each component in the complex; and the third, Compost, decomposes the contrast variation series into composite scattering functions, which contain information regarding the shape of each component of the complex, and their orientation with respect to each other. computer programs J. Appl. Cryst. (2008). 41, 222-226 Andrew E. Whitten et al. MULCh 225 Figure 3Comparison between actual (solid line) and composite P(r) (dotted line) profiles for: Sda (top); KinA (middle); cross-term (bottom).

Structural Basis for Partial Redundancy in a Class of Transcription Factors, the LIM Homeodomain Proteins, in Neural Cell Type Specification

“…B, with the addition of Isl1 (white), the ternary complex is preferentially formed (12). Note that the self-association domain of Ldb1 forms trimers in vitro (21) gram MULCh (31). Guinier analysis of the desmeared data was performed using PRIMUS (32).…”

Hfq binding changes the structure ofEscherichia colismall noncoding RNAs OxyS and RprA, which are involved in the riboregulation ofrpoS

“…Theoretical volumes based on the amino acid or nucleic acid sequence and R g values determined from Guinier analysis were used as further constraints during the modeling process. The contrast was calculated using the program MULCh (Whitten et al 2008).…”

“…2 , where Δρ is the contrast or difference in scattering density between the solvent and the scattering particle, and υ is its partial specific volume (cm 3 /g). The program MULCh (ModULes for the analysis of contrast variation data) (Whitten et al 2008), was used to calculate the theoretical value of the scattering length density and scattering length difference, based on the amino acid sequence for the protein and/or nucleotide sequence for the sRNA substrates and buffer composition.…”

The Roles of the RIIβ Linker and N-terminal Cyclic Nucleotide-binding Domain in Determining the Unique Structures of the Type IIβ Protein Kinase A

“…The MULCh web server (37) was used to analyze the R g of the components from the contrast variation series data and to extract the basic scattering functions of each of the deuterated and hydrogenated components from the contrast series. GNOM (33) was used for the P(r) curves from the basic scattering functions.…”