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NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials

Journal Article · · Journal of Chemical Information and Modeling
 [1];  [1];  [1]
  1. Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
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Noncanonical Amino Acids (NCAAs) provide numerous avenues for introduction of novel functionality to peptides and proteins. NCAAs can be incorporated through solid phase synthesis or genetic code expansion in conjugation with heterologous expression of the encoded protein modification. Due to the difficulty of synthesis, wide chemical space and lack of empirically resolved structures modeling the effects of NCAA mutation is critical for rational protein design. To evaluate the structural and functional perturbations NCAAs introduce we utilize molecular potentials that describe the forces in protein structure. Most potentials such as CHARMM are designed to model canonical residues but can be parameterized in include novel NCAAs. Here, in this work, we introduce NCAP a software package to generate CHARMM compatible parameters from quantum chemical calculation. Unlike currently available tools NCAP is designed to recognize NCAA structure and automatically bridge the gap between DFT calculations and potential parameters. For our software we discuss workflow, validation against canonical parameter sets and comparison to published NCAA-protein structures.
Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
Defense Threat Reduction Agency (DTRA); USDOE
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
2483836
Report Number(s):
PNNL-SA--197394
Journal Information:
Journal of Chemical Information and Modeling, Journal Name: Journal of Chemical Information and Modeling Journal Issue: 24 Vol. 64; ISSN 1549-9596
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English

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