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sticky:sticky [2018/03/01 13:58] – created richter | sticky:sticky [2018/03/01 14:56] – wade | ||
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+ | 01.03.2018 | ||
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+ | Discussion on simulations to probe the molecular factors contributing to the observations in Zotter et al, JBC, 2017[[http:// | ||
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+ | Present: RW, HXZ, NB, ANA, SKS, PF | ||
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+ | Questions to address with simulations: | ||
+ | - Is the rate of diffusion (trans, rot) of the substrate slower in a crowded environment (like the cell) due to non-specific sticky (hydrophobic) interactions? | ||
+ | - Can SDAMM-type simulations be compared directly to expts that could be done for in vitro systems by Gideon or by Hofmann at Weizmann? | ||
+ | - Is the bimolecular rate constant for diffusional association of the substrate to beta-lactamase slower in a crowded environment? | ||
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+ | Aim: Tackle the first set of questions and aim to have some progress that we can discuss with Gideon at BDBDB4. | ||
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+ | To do: | ||
+ | - Generate 3D structures and force field parameters of CFF2, beta-lactam without D and A fluorophores, | ||
+ | - Build SDA boxes of molecules with several substrate molecules (ca. 20?, negatively charged) and HEWL (+ve charge) or Myoglobin (small net charge) crowders at different (initially 2) protein concentrations (low and high (near cellular)). | ||
+ | - If we see trends in slower diffusion dependent on substrate and protein crowder type, do these relate to interaction strengths? | ||
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+ | other (just to bear in mind for now) : | ||
+ | Systems with enzyme and substrate and no crowder: | ||
+ | -Do NAM kon calculations for b-lac and different substrates and b-lac mutants: would give reference for uncrowded system | ||
+ | -Do periodic box kon/MFPT calculations for b-lac + substrate + varying crowder concs. Post analysis may miss satisfaction of reaction criteria. Would need to introduce correct monitoring of rxn criteria during simulations into sda(mm). | ||
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