TY - CHAP
T1 - Molecular Dynamics Flexible Fitting
T2 - All You Want to Know About Resolution Exchange
AU - Vant, John W.
AU - Sarkar, Daipayan
AU - Gupta, Chitrak
AU - Shekhar, Mrinal S.
AU - Mittal, Sumit
AU - Singharoy, Abhishek
N1 - Publisher Copyright:
© 2020, Springer Science+Business Media, LLC, part of Springer Nature.
PY - 2020
Y1 - 2020
N2 - In recent years, owing to the advances in instrumentation, cryo-EM has emerged as the go-to tool for obtaining high-resolution structures of biomolecular systems. However, building three-dimensional atomic structures of biomolecules from these high-resolution maps remains a concern for the traditional map-guided structure-determination schemes. Recently, we developed a computational tool, Resolution Exchange Molecular Dynamics Flexible Fitting (ReMDFF) to address this problem by re-refining a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution (Wang et al., J Struct Biol 204(2):319–328, 2018). In this chapter, we present a step-by-step outline for preparing, executing, and analyzing ReMDFF refinements of simple proteins and multimeric complexes. The structure determination of carbon monoxide dehydrogenase and Mg2+-channel CorA are employed as case studies. All scripts are provided via GitHub (Vant, Resolution exchange molecular dynamics flexible fitting (ReMDFF) all you want to know about flexible fitting, 2019, https://github.com/jvant/ReMDFF_Singharoy_Group.git).
AB - In recent years, owing to the advances in instrumentation, cryo-EM has emerged as the go-to tool for obtaining high-resolution structures of biomolecular systems. However, building three-dimensional atomic structures of biomolecules from these high-resolution maps remains a concern for the traditional map-guided structure-determination schemes. Recently, we developed a computational tool, Resolution Exchange Molecular Dynamics Flexible Fitting (ReMDFF) to address this problem by re-refining a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution (Wang et al., J Struct Biol 204(2):319–328, 2018). In this chapter, we present a step-by-step outline for preparing, executing, and analyzing ReMDFF refinements of simple proteins and multimeric complexes. The structure determination of carbon monoxide dehydrogenase and Mg2+-channel CorA are employed as case studies. All scripts are provided via GitHub (Vant, Resolution exchange molecular dynamics flexible fitting (ReMDFF) all you want to know about flexible fitting, 2019, https://github.com/jvant/ReMDFF_Singharoy_Group.git).
KW - Hybrid structure determination
KW - Molecular dynamics flexible fitting
KW - NAMD
KW - Real-space refinement
KW - Resolution exchange
KW - VMD
UR - http://www.scopus.com/inward/record.url?scp=85087472707&partnerID=8YFLogxK
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U2 - 10.1007/978-1-0716-0708-4_18
DO - 10.1007/978-1-0716-0708-4_18
M3 - Chapter
C2 - 32621233
AN - SCOPUS:85087472707
T3 - Methods in Molecular Biology
SP - 301
EP - 315
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -