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Computational Design and Simulation of a Cyclized Dimeric Multipass Transmembrane Protein
Author(s) -
AldanaMendoza Jonathan Agust,
DeGrado William Agust
Publication year - 2018
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2018.32.1_supplement.798.23
Subject(s) - transmembrane protein , protein design , rational design , protein data bank (rcsb pdb) , computational biology , protein structure , structural biology , chemistry , circular dichroism , protein data bank , sequence (biology) , structural motif , transmembrane domain , biophysics , biochemistry , nanotechnology , biology , amino acid , materials science , receptor
Transmembrane (TM) proteins play critical roles in cell surface markers, receptors, and can serve as channels for molecular transport. Therefore characterizing this structural class of proteins is important for understanding a wide variety of cellular functions. With the influx of solved structures of alpha helical TM proteins, we are better equipped to address the unique structural characteristics of these proteins. We hypothesize that a de novo design and synthesis of a tm protein cold be carried out with accurate atomic level prediction of its tertiary structure. We based our design on the characterized GX6G motif of alpha‐helical proteins; to set parameters for searching naturally occurring alpha‐helices in the PDB. Then using these naturally occurring proteins to analyze any sequence preference given the alpha‐helical structure. We plan on validating our design and simulation through the synthesis of this peptide using solid phase Fmoc synthesis. Structure analysis will be performed on the product through circular dichroism, infrared/vibrational, and NMR spectroscopy. The synthesis and accurate prediction of this alpha‐helical tm protein, will demonstrate our capacity to predict structures of tm proteins that contain the sequence/structural motifs through in cooperation in a rational design. Enabling us to rationally design tm proteins, or small molecules that target tm proteins, and therefore have powerful therapeutic potential. Support or Funding Information NIH Grant # GM 49001, CSU‐LSAMP is supported by the National Science Foundation under Grant # HRD‐1302873 and the CSU Office of the Chancellor This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .