Corrigendum to “Atomic stress tensor analysis of proteins” [Chem. Phys. Lett. 539 (2012) 144–150]

Ishikura, Takakazu; Hatano, Tatsuro; Yamato, Takahisa

doi:10.1016/j.cplett.2014.07.059

Cited by 1 publication

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“…Previously, we calculated irEF values based on the ad hoc partition of the multibody potential energy into individual atomic contributions . In this study, the interatomic forces were evaluated in a consistent manner based on pairwise separation of multibody force‐field functions . During the k th NVE simulation ( k = 1, 2,…, 100), the irEF is calculated at each time point, t , using the following equations:

J_{i \leftarrow j}^{k} (t) = \frac{1}{2} true(v_{i} \cdot F_{i j} - v_{j} \cdot F_{j i} true)

and

J_{A \leftarrow B}^{k} (t) = \sum_{i \in A}^{N_{A}} \sum_{j \in B}^{N_{B}} J_{i \leftarrow j}^{k} (t),

where N A and N B are the total number of atoms in residues A and B , respectively, and atoms i and j are taken from residues A and B , respectively; v i is the velocity of the i th atom, and F ij is the pairwise interatomic force from atom j to i .…”

Section: Methodsmentioning

confidence: 99%

“…The strength of residue–residue interactions was evaluated in terms of the inter‐residue energy conductivity (irEC) or the amount of energy transferred from one residue to another per unit time . The CURrent calculation for Proteins (CURP) ver. 1.0 computer program calculates the irEC based on molecular dynamics (MD) simulations and presents the overall pattern of intraprotein interactions represented by the energy exchange network (EEN) as a graphical output.…”

Section: Introductionmentioning

confidence: 99%

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Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A computational study

et al. 2015

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Protein function is regulated not only by the structure but also by physical dynamics and thermal fluctuations. We have developed the computer program, CURrent calculation for proteins (CURP), for the flow analysis of physical quantities within thermally fluctuating protein media. The CURP program was used to calculate the energy flow within the third PDZ domain of the neuronal protein PSD-95, and the results were used to illustrate the energy exchange network of inter-residue interactions based on atomistic molecular dynamics simulations. The removal of the α3 helix is known to decrease ligand affinity by 21-fold without changing the overall protein structure; nevertheless, we demonstrated that the helix constitutes an essential part of the network graph.

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