SViMULATE: a Computer Program Facilitating Interactive, Multi-mode Simulation of Analytical Ultracentrifugation Data

Overview

Journal Eur Biophys J

Specialty Biophysics

Date 2023 Mar 8

PMID 36890221

Authors

Chad A Brautigam

Affiliations

Soon will be listed here.

Abstract

The ability to simulate sedimentation velocity (SV) analytical ultracentrifugation (AUC) experiments has proved to be a valuable tool for research planning, hypothesis testing, and pedagogy. Several options for SV data simulation exist, but they often lack interactivity and require up-front calculations on the part of the user. This work introduces SViMULATE, a program designed to make AUC experimental simulation quick, straightforward, and interactive. SViMULATE takes user-provided parameters and outputs simulated AUC data in a format suitable for subsequent analyses, if desired. The user is not burdened by the necessity to calculate hydrodynamic parameters for simulated macromolecules, as the program can compute these properties on the fly. It also frees the user of decisions regarding simulation stop time. SViMULATE features a graphical view of the species that are under simulation, and there is no limit on their number. Additionally, the program emulates data from different experimental modalities and data-acquisition systems, including the realistic simulation of noise for the absorbance optical system. The executable is available for immediate download.

Citing Articles

Assembly landscape of the complete B-repeat superdomain from Staphylococcus epidermidis strain 1457.

Yarawsky A, Herr A Biophys J. 2024; 124(2):363-378.

PMID: 39668565 PMC: 11788477. DOI: 10.1016/j.bpj.2024.12.011.

Application of artificial neural network for the mechano-bactericidal effect of bioinspired nanopatterned surfaces.

Uzun Yaylaci E Eur Biophys J. 2024; 53(7-8):415-427.

PMID: 39373773 DOI: 10.1007/s00249-024-01723-x.

BASIS: BioAnalysis SEDFIT integrated software for cGMP analysis of SV-AUC data.

Yarawsky A, Gough E, Zai-Rose V, Figueroa N, Cunningham H, Burgner 2nd J Eur Biophys J. 2024; 53(3):111-121.

PMID: 38329496 DOI: 10.1007/s00249-024-01700-4.

Proceedings of the 25th Analytical Ultracentrifugation Workshops and Symposium.

Demeler B, Gilbert R, Patel T Eur Biophys J. 2023; 52(4-5):195-201.

PMID: 37526680 PMC: 10870507. DOI: 10.1007/s00249-023-01674-9.

AAV analysis by sedimentation velocity analytical ultracentrifugation: beyond empty and full capsids.

Yarawsky A, Zai-Rose V, Cunningham H, Burgner 2nd J, DeLion M, Paul L Eur Biophys J. 2023; 52(4-5):353-366.

PMID: 37037926 DOI: 10.1007/s00249-023-01646-z.

References

Behlke J, Ristau O . A new approximate whole boundary solution of the Lamm differential equation for the analysis of sedimentation velocity experiments. Biophys Chem. 2002; 95(1):59-68. DOI: 10.1016/s0301-4622(01)00248-4. View

Brautigam C, Deka R, Liu W, Norgard M . Crystal stuctures of MglB-2 (TP0684), a topologically variant d-glucose-binding protein from Treponema pallidum, reveal a ligand-induced conformational change. Protein Sci. 2018; 27(4):880-885. PMC: 5866939. DOI: 10.1002/pro.3373. View

Brautigam C, Tso S, Deka R, Liu W, Norgard M . Using modern approaches to sedimentation velocity to detect conformational changes in proteins. Eur Biophys J. 2020; 49(8):729-743. PMC: 7704540. DOI: 10.1007/s00249-020-01453-w. View

Brown P, Schuck P . A new adaptive grid-size algorithm for the simulation of sedimentation velocity profiles in analytical ultracentrifugation. Comput Phys Commun. 2008; 178(2):105-120. PMC: 2267755. DOI: 10.1016/j.cpc.2007.08.012. View

Burnham B, Nass S, Kong E, Mattingly M, Woodcock D, Song A . Analytical Ultracentrifugation as an Approach to Characterize Recombinant Adeno-Associated Viral Vectors. Hum Gene Ther Methods. 2015; 26(6):228-42. DOI: 10.1089/hgtb.2015.048. View

Cao W, Demeler B . Modeling analytical ultracentrifugation experiments with an adaptive space-time finite element solution for multicomponent reacting systems. Biophys J. 2008; 95(1):54-65. PMC: 2426643. DOI: 10.1529/biophysj.107.123950. View

Claverie J, Dreux H, Cohen R . Sedimentation of generalized systems of interacting particles. I. Solution of systems of complete Lamm equations. Biopolymers. 1975; 14(8):1685-1700. DOI: 10.1002/bip.1975.360140811. View

Dam J, Velikovsky C, Mariuzza R, Urbanke C, Schuck P . Sedimentation velocity analysis of heterogeneous protein-protein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s). Biophys J. 2005; 89(1):619-34. PMC: 1366561. DOI: 10.1529/biophysj.105.059568. View

Fleming P, Fleming K . HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties. Biophys J. 2018; 114(4):856-869. PMC: 5984988. DOI: 10.1016/j.bpj.2018.01.002. View

10.

Harris C, Millman K, van der Walt S, Gommers R, Virtanen P, Cournapeau D . Array programming with NumPy. Nature. 2020; 585(7825):357-362. PMC: 7759461. DOI: 10.1038/s41586-020-2649-2. View

11.

Kar S, Kingsbury J, Lewis M, Laue T, Schuck P . Analysis of transport experiments using pseudo-absorbance data. Anal Biochem. 2000; 285(1):135-42. DOI: 10.1006/abio.2000.4748. View

12.

Kirschner M, SCHACHMAN H . Conformational changes in proteins as measured by difference sedimentation studies. II. Effect of stereospecific ligands on the catalytic subunit of aspartate transcarbamylase. Biochemistry. 1971; 10(10):1919-26. DOI: 10.1021/bi00786a028. View

13.

Kirschner M, SCHACHMAN H . Conformational changes in proteins as measured by difference sedimentation studies. I. A technique for measuring small changes in sedimentation coefficient. Biochemistry. 1971; 10(10):1900-19. DOI: 10.1021/bi00786a027. View

14.

Ma J, Zhao H, Schuck P . A histogram approach to the quality of fit in sedimentation velocity analyses. Anal Biochem. 2015; 483:1-3. PMC: 4461538. DOI: 10.1016/j.ab.2015.04.029. View

15.

Maruno T, Usami K, Ishii K, Torisu T, Uchiyama S . Comprehensive Size Distribution and Composition Analysis of Adeno-Associated Virus Vector by Multiwavelength Sedimentation Velocity Analytical Ultracentrifugation. J Pharm Sci. 2021; 110(10):3375-3384. DOI: 10.1016/j.xphs.2021.06.031. View

16.

Nass S, Mattingly M, Woodcock D, Burnham B, Ardinger J, Osmond S . Universal Method for the Purification of Recombinant AAV Vectors of Differing Serotypes. Mol Ther Methods Clin Dev. 2018; 9:33-46. PMC: 5767896. DOI: 10.1016/j.omtm.2017.12.004. View

17.

Schuck P . Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation. Biophys J. 1998; 75(3):1503-12. PMC: 1299825. DOI: 10.1016/S0006-3495(98)74069-X. View

18.

Schuck P, Demeler B . Direct sedimentation analysis of interference optical data in analytical ultracentrifugation. Biophys J. 1999; 76(4):2288-96. PMC: 1300201. DOI: 10.1016/S0006-3495(99)77384-4. View

19.

Schuck P, MacPhee C, Howlett G . Determination of sedimentation coefficients for small peptides. Biophys J. 1998; 74(1):466-74. PMC: 1299399. DOI: 10.1016/S0006-3495(98)77804-X. View

20.

Stafford 3rd W . Boundary analysis in sedimentation transport experiments: a procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile. Anal Biochem. 1992; 203(2):295-301. DOI: 10.1016/0003-2697(92)90316-y. View