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Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme.
Open accessAbstract
A method is presented for finding particular normal modes for large molecules such as proteins and nucleic acids. The method is based on an iterative approach that extracts eigenvectors of interest from the full second-derivative matrix. Application of the method to the interdomain (hinge-bending) motion of lysozyme yields a frequency of 3.6 cm-1. This is similar to the value obtained from earlier adiabatic-energy-minimization studies. Analysis of the mode shows that the relaxation associated with the hinge bending is highly delocalized; that is, the dihedral angle and energy changes are distributed over many residues, including some (e.g., Trp-28) that are distant from the cleft and hinge region.
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Cited by
Putnam, C. D., Hammel, M., Hura, G. L., & Tainer, J. A. (2007) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583507004635 · Cited by 1,184
Protein elastic network models and the ranges of cooperativity
Yang, L., Song, G., & Jernigan, R. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902159106 · Cited by 260
Panjkovich, A., & Svergun, D. I. (2016) · Physical Chemistry Chemical Physics · doi:10.1039/c5cp04540a · Cited by 204
The Application of Terahertz Spectroscopy to Protein Detection: A Review
Xie, L., Yao, Y., & Ying, Y. (2014) · Applied Spectroscopy Reviews · doi:10.1080/05704928.2013.847845 · Cited by 137
Craddock, T. J. A., Kurian, P., Preto, J., Sahu, K., Hameroff, S. R., Klobukowski, M., & Tuszynski, J. A. (2017) · Scientific Reports · doi:10.1038/s41598-017-09992-7 · Cited by 109
Metadata
- Authors
- Brooks, B., & Karplus, M.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 1985-08
- Volume
- 82
- Issue
- 15
- Pages
- 4995-4999
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2068128475
- Cited by
- 342
- References
- 0
- FWCI
- 0.88
- Type
- journal article
- Language
- en
- Open access
- green
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- CoChat. (2026). Citation check: Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. https://app.cochat.ai/papers/10.1073/pnas.82.15.4995
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- Brooks, B., & Karplus, M. (1985). Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.82.15.4995
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
