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Published November 2014 | public
Journal Article

SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins

Abstract

SLDMOL is a program for modeling the 1-D scattering length density (SLD) profile of proteins at the lipid membrane–solution interface or adsorbed to other surfaces. The program reads experimental SLD data from neutron or XX-ray reflectivity measurements and compares the results to a trajectory of protein structures, finding the conformation and orientation that best fits the experimental data. SLDMOL is a freely distributed open source program written in python that can be run independently using command lines or a GUI. SLDMOL has also been integrated into the larger SASSIE package extending molecular modeling capabilities. Sample environment conditions can be replicated including H_2O/D_2O solvent contrasts, specific amino acid deuteration and complex molecular assemblies. Ensembles of protein conformations can be generated independently (e.g. molecular dynamics simulations) or with SASSIE. For each individual structure a best-fit SLD profile is outputted along with a goodness of fit parameter, protein depth penetration and surface coverage. In addition to individual comparisons SLD profiles can be calculated over ensemble averages of protein structures. As a result, SLDMOL provides a detailed molecular interpretation of reflectivity data or conversely can be used to predict experimental outcomes for different protein conformation and specific deuteration schemes prior to measurements.

Additional Information

© 2014 Elsevier B.V. Received 4 February 2014; Received in revised form; 27 June 2014 Accepted 3 July 2014; Available online 14 July 2014. This work is supported by NIH R01-GM101647-02 to H.N. This work benefited from CCP-SAS software developed through a joint EPSRC (EP/K039121/1) and NSF (CHE-1265821) grant.

Additional details

Created:
August 22, 2023
Modified:
October 17, 2023