SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins
- Creators
- Curtis, Joseph E.
- Zhang, Hailiang
- Nanda, Hirsh
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
- Eprint ID
- 50448
- DOI
- 10.1016/j.cpc.2014.07.006
- Resolver ID
- CaltechAUTHORS:20141016-111934974
- R01-GM101647-02
- NIH
- EP/K039121/1
- Engineering and Physical Sciences Research Council (EPSRC)
- CHE-1265821
- NSF
- Created
-
2014-10-16Created from EPrint's datestamp field
- Updated
-
2021-11-10Created from EPrint's last_modified field