TY - JOUR
T1 - Deoxyadenosine sugar puckering pathway simulated by the stochastic difference equation algorithm
AU - Arora, Karunesh
AU - Schlick, Tamar
N1 - Funding Information:
We are grateful to Prof. Ron Elber, Dr. Alfredo Cárdenas, and Ileana Stoica for making us available the latest code of MOIL and for technical assistance with its implementation. We thank the Elber lab for hosting K. Arora at Cornell and allowing him to gain experience with the SDE code. We thank Dr. Ravi Radhakrishnan for many useful discussions regarding the free energy calculations. We thank the reviewer for pointing out recent accomplishments using QM/MM methodologies. This work was supported by NIH Grant R01 GM55164, NSF Grant ASC-9318159, and ACS-PRF 39115-AC4 Grant to T.S.
PY - 2003/8/29
Y1 - 2003/8/29
N2 - The conformational transition pathway of sugar puckering between the C2′-endo and C3′-endo conformations of deoxyadenosine (dA) is reported using the stochastic difference equation (SDE) algorithm, which approximates long-time pathways. The south pucker is favored over the north by 0.34±0.2 kcal/mol, and the free energy barrier is about 2.2±0.2 kcal/mol above the global minimum. The transition occurs through the east barrier, with significant decrease in puckering amplitude near the barrier. These results are consistent with prior studies on sugars in nucleic acids and indicate that the SDE has potential for large nucleic acid and nucleic acid/protein systems.
AB - The conformational transition pathway of sugar puckering between the C2′-endo and C3′-endo conformations of deoxyadenosine (dA) is reported using the stochastic difference equation (SDE) algorithm, which approximates long-time pathways. The south pucker is favored over the north by 0.34±0.2 kcal/mol, and the free energy barrier is about 2.2±0.2 kcal/mol above the global minimum. The transition occurs through the east barrier, with significant decrease in puckering amplitude near the barrier. These results are consistent with prior studies on sugars in nucleic acids and indicate that the SDE has potential for large nucleic acid and nucleic acid/protein systems.
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U2 - 10.1016/S0009-2614(03)01195-3
DO - 10.1016/S0009-2614(03)01195-3
M3 - Article
AN - SCOPUS:0141451738
VL - 378
SP - 1
EP - 8
JO - Chemical Physics Letters
JF - Chemical Physics Letters
SN - 0009-2614
IS - 1-2
ER -