### Abstract

A geometric model is presented to interpret the anomalous T^{3+2m} temperature dependence of the Raman spin-lattice relaxation rates in heme and iron-sulfur proteins. Analysis of relaxation data is based on a modified Debye relationship between the spectral exponent m and the density of vibrational states ρ(v) ∝ v^{m-1}, where 0 ≤ v ≤ v_{max}. Magnetic relaxation measurements on cytochrome c-551 and putidaredoxin yield noninteger values of m that are influenced by changes in the ionic medium. The apparent physical significance of m is revealed, in part, by correlation to a protein's fractal geometry, which characterizes a repeating structural motif by a single parameter called the fractal dimension d̄. Estimates of d̄ for 70 proteins are computed by a method that identifies geometric and statistical self-similarities of α-carbon coordinates; values range within the limits (1 ≤ d̄ ≤ 2) of well-defined test structures and correlate principally with dominant elements of secondary structures. In six iron proteins, the highest values of m derived from relaxation data are approximated by the estimated values of d̄ calculated from the covalent structure. The interrelationship between the fractal models of protein structure and molecular dynamics, i.e., m = d̄, is also evident in the good agreement between the predicted ρ(v) ∝ v^{d̄-1} and the reported distribution of low-frequency normal modes (v ≤ 75 cm^{-1}) calculated for bovine pancreas trypsin inhibitor. The present findings indicate d̄ defines a fundamental parameter that is inherent to both the structural and dynamic properties of a protein.

Original language | English |
---|---|

Pages (from-to) | 5589-5594 |

Number of pages | 6 |

Journal | Journal of the American Chemical Society |

Volume | 107 |

Issue number | 20 |

Publication status | Published - 1985 |

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### ASJC Scopus subject areas

- Chemistry(all)

### Cite this

*Journal of the American Chemical Society*,

*107*(20), 5589-5594.

**Fractal models of protein structure, dynamics, and magnetic relaxation.** / Wagner, Gerald C.; Colvin, J. Trevor; Allen, James P.; Allen, James Paul.

Research output: Contribution to journal › Article

*Journal of the American Chemical Society*, vol. 107, no. 20, pp. 5589-5594.

}

TY - JOUR

T1 - Fractal models of protein structure, dynamics, and magnetic relaxation

AU - Wagner, Gerald C.

AU - Colvin, J. Trevor

AU - Allen, James P.

AU - Allen, James Paul

PY - 1985

Y1 - 1985

N2 - A geometric model is presented to interpret the anomalous T3+2m temperature dependence of the Raman spin-lattice relaxation rates in heme and iron-sulfur proteins. Analysis of relaxation data is based on a modified Debye relationship between the spectral exponent m and the density of vibrational states ρ(v) ∝ vm-1, where 0 ≤ v ≤ vmax. Magnetic relaxation measurements on cytochrome c-551 and putidaredoxin yield noninteger values of m that are influenced by changes in the ionic medium. The apparent physical significance of m is revealed, in part, by correlation to a protein's fractal geometry, which characterizes a repeating structural motif by a single parameter called the fractal dimension d̄. Estimates of d̄ for 70 proteins are computed by a method that identifies geometric and statistical self-similarities of α-carbon coordinates; values range within the limits (1 ≤ d̄ ≤ 2) of well-defined test structures and correlate principally with dominant elements of secondary structures. In six iron proteins, the highest values of m derived from relaxation data are approximated by the estimated values of d̄ calculated from the covalent structure. The interrelationship between the fractal models of protein structure and molecular dynamics, i.e., m = d̄, is also evident in the good agreement between the predicted ρ(v) ∝ vd̄-1 and the reported distribution of low-frequency normal modes (v ≤ 75 cm-1) calculated for bovine pancreas trypsin inhibitor. The present findings indicate d̄ defines a fundamental parameter that is inherent to both the structural and dynamic properties of a protein.

AB - A geometric model is presented to interpret the anomalous T3+2m temperature dependence of the Raman spin-lattice relaxation rates in heme and iron-sulfur proteins. Analysis of relaxation data is based on a modified Debye relationship between the spectral exponent m and the density of vibrational states ρ(v) ∝ vm-1, where 0 ≤ v ≤ vmax. Magnetic relaxation measurements on cytochrome c-551 and putidaredoxin yield noninteger values of m that are influenced by changes in the ionic medium. The apparent physical significance of m is revealed, in part, by correlation to a protein's fractal geometry, which characterizes a repeating structural motif by a single parameter called the fractal dimension d̄. Estimates of d̄ for 70 proteins are computed by a method that identifies geometric and statistical self-similarities of α-carbon coordinates; values range within the limits (1 ≤ d̄ ≤ 2) of well-defined test structures and correlate principally with dominant elements of secondary structures. In six iron proteins, the highest values of m derived from relaxation data are approximated by the estimated values of d̄ calculated from the covalent structure. The interrelationship between the fractal models of protein structure and molecular dynamics, i.e., m = d̄, is also evident in the good agreement between the predicted ρ(v) ∝ vd̄-1 and the reported distribution of low-frequency normal modes (v ≤ 75 cm-1) calculated for bovine pancreas trypsin inhibitor. The present findings indicate d̄ defines a fundamental parameter that is inherent to both the structural and dynamic properties of a protein.

UR - http://www.scopus.com/inward/record.url?scp=0000025304&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0000025304&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:0000025304

VL - 107

SP - 5589

EP - 5594

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 20

ER -