Limits...
Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.

Fenley AT, Muddana HS, Gilson MK - PLoS ONE (2014)

Bottom Line: However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context.The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms.Here, we review relevant theory and present illustrative applications.

View Article: PubMed Central - PubMed

Affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, 92093, United States of America.

ABSTRACT
Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications.

Show MeSH

Related in: MedlinePlus

Residue-averaged differences in stress between clusters 1 and 2 (cluster 1 minus cluster 2).The left color spectrum applies to the total stress, and the right color spectrum applies to all of the stress components.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4263534&req=5

pone-0113119-g001: Residue-averaged differences in stress between clusters 1 and 2 (cluster 1 minus cluster 2).The left color spectrum applies to the total stress, and the right color spectrum applies to all of the stress components.

Mentions: We focus in particular on differences in the atomic virial stresses averaged over all atoms within an amino acid residue between the two most thermodynamically distinct conformational clusters (1 and 2) identified in a 1 ms BPTI molecular dynamics simulation [57]–[59]. We compute the residue-averaged stress for residue per snapshot as, where is the instantaneous stress of atom within residue , and is the number of atoms per residue type. While such averaging results in stresses that in principle cannot be summed in a way to determine the virial of the whole system without properly shifting into the Lagrangian frame of reference of the residue, it can provide a clearer picture of the stress differences within distinct structural features, e.g. disulfide bridges, than the atomistic values. This residue-averaging approach provides an intuitive method of highlighting potentially mechanistically interesting regions within the structure. The differences in the total stress (Fig. 1, left) highlight a greater degree of tensile stress (purple), for cluster 1 relative to cluster 2, in the loop disulfide at the top of the protein (Cys14-Cys38), as well as in a segment of strand near the front, while other localized regions are under greater compressive stress (orange). Note that the loop disulfide has different preferred conformers in the two clusters. It is interesting to speculate that large stress differences may highlight residues that play key structural roles in stabilizing the two conformational states. In addition, differences in disulfide stress have been related to differences in chemical reactivity [63].


Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.

Fenley AT, Muddana HS, Gilson MK - PLoS ONE (2014)

Residue-averaged differences in stress between clusters 1 and 2 (cluster 1 minus cluster 2).The left color spectrum applies to the total stress, and the right color spectrum applies to all of the stress components.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263534&req=5

pone-0113119-g001: Residue-averaged differences in stress between clusters 1 and 2 (cluster 1 minus cluster 2).The left color spectrum applies to the total stress, and the right color spectrum applies to all of the stress components.
Mentions: We focus in particular on differences in the atomic virial stresses averaged over all atoms within an amino acid residue between the two most thermodynamically distinct conformational clusters (1 and 2) identified in a 1 ms BPTI molecular dynamics simulation [57]–[59]. We compute the residue-averaged stress for residue per snapshot as, where is the instantaneous stress of atom within residue , and is the number of atoms per residue type. While such averaging results in stresses that in principle cannot be summed in a way to determine the virial of the whole system without properly shifting into the Lagrangian frame of reference of the residue, it can provide a clearer picture of the stress differences within distinct structural features, e.g. disulfide bridges, than the atomistic values. This residue-averaging approach provides an intuitive method of highlighting potentially mechanistically interesting regions within the structure. The differences in the total stress (Fig. 1, left) highlight a greater degree of tensile stress (purple), for cluster 1 relative to cluster 2, in the loop disulfide at the top of the protein (Cys14-Cys38), as well as in a segment of strand near the front, while other localized regions are under greater compressive stress (orange). Note that the loop disulfide has different preferred conformers in the two clusters. It is interesting to speculate that large stress differences may highlight residues that play key structural roles in stabilizing the two conformational states. In addition, differences in disulfide stress have been related to differences in chemical reactivity [63].

Bottom Line: However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context.The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms.Here, we review relevant theory and present illustrative applications.

View Article: PubMed Central - PubMed

Affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, 92093, United States of America.

ABSTRACT
Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications.

Show MeSH
Related in: MedlinePlus