Molecular dynamical approach to the conformational transition in peptide nanorings and nanotubes

Journal of Physical Chemistry B

Volumn 113, Issue 5, 2009, Pages 1473-1484

  Teranishi, Masato ^a   Okamoto, Hajime ^a   Takeda, Kyozaburo ^a   Nomura, Ken Ichi ^b   Nakano, Aiichiro ^b   Kalia, Rajiv K ^b   Vashishta, Priya ^b   Shimojo, Fuyuki ^c  

^a WASEDA UNIVERSITY   (Japan)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^c KUMAMOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; AMINO ACIDS; DYNAMICS; MOLECULAR DYNAMICS; NANORINGS; NANOSTRUCTURED MATERIALS; NANOTUBES; ORGANIC ACIDS;

AB INITIO ENERGY CALCULATIONS; AMINO ACID RESIDUES; CONFORMATIONAL CHANGES; CONFORMATIONAL TRANSITIONS; DIHEDRAL ANGLES; DYNAMICAL APPROACHES; DYNAMICAL STATE; PEPTIDE NANORINGS; SOUND VELOCITIES; STATIC STATE; TIME DEPENDENTS; TOTAL ENERGY CALCULATIONS; TRANSITION PROCESS;

ACTIVATION ENERGY;

EID: 61949195404     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp8067975     Document Type: Article

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20. **) even when the DFT calculation is achieved. Thus, it can be said that Eeq is energetically more unstable than Bax, and the corresponding energy difference is almost several kcal/mol or at least less than 10 kcal/mol.
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23. We also assume that these tubes are parallelly placed with the intertube length of 60 Å in order to represent the isolated single tube having a finite volume.
24. The sole difference is that the AMBER potential estimates the E-tube being energetically more stable than the B-tube by 1.18 kcal/mol per ring. This relation is completely opposite to that obtained by the firstprinciples calculation.