SIRAH 2.0 GROMACS

SIRAH 2.0 for GROMACS and SIRAH Tools

SIRAH 2.0 AMBER

SIRAH 2.0 for AMBER and SIRAH Tools

What's been added?

New parameters are available for:

• ATP*, ADP
• GDP**, GTP**
• cAMP***
• cGMP****
• protonated Histidine sidechain***** (following AMBER rules, it is necessary to rename HIS to HIP in the input PDB)
• Glycans (******).

(*) Understanding the role of mTOR-mLst8 binding through coarse-grained simulation approaches. Kist, R, Timmers, L F S M, Caceres, R A. Mol. Simul. 2021; 47(14):1198–1207. doi: 10.1080/08927022.2021.1962525.

(**) In silico induced effect of N-ε-lysine acetylation on microtubule stability and subsequent interaction of microtubule-associated proteins. Rayevsky A, Bulgakov E, Sharifi M, Samofalova D, Ozheredov D, Karpov P, Pantano S, Blume Y. Cell Biol Int. 2023 Sep;47(9):1547-1557. doi: 10.1002/cbin.12052.

(***) FRET biosensor uncovers cAMP nano-domains at β-adrenergic targets that dictate precise tuning of cardiac contractility. Surdo NC, Berrera M, Koschinski A, Brescia M, Machado MR, Carr C, Wright P, Gorelik J, Morotti S, Grandi E, Bers DM, Pantano S, Zaccolo M. Nat Commun. 2017 Apr 20;8:15031. doi: 10.1038/ncomms15031.

(****) CUTie2: The Attack of the Cyclic Nucleotide Sensor Clones. Klein F, Sardi F, Machado MR, Ortega C, Comini MA, Pantano S. Front Mol Biosci. 2021 Mar 11;8:629773. doi: 10.3389/fmolb.2021.629773.

(*****) Investigation of the pH-dependent aggregation mechanisms of GCSF using low resolution protein characterization techniques and advanced molecular dynamics simulations. Suk Kyu Ko, Carolin Berner , Alina Kulakova, Markus Schneider, Iris Antes, Gerhard Winter, Pernille Harris, Günther H J Peters. Struct Biotechnol J. 2022 Mar 17:20:1439-1455. doi: 10.1016/j.csbj.2022.03.012.

(******) SIRAH Late Harvest: Coarse-Grained Models for Protein Glycosylation. Garay P. G., Machado M. R. , Verli H., Pantano S. J. Chem. Theory Comput 2024, 20, 2, 963–976. doi: 10.1021/acs.jctc.3c00783