Modeling of real 20‐component protein chains: Determination of the electronic density of states of aperiodic seven‐component polypeptide chains containing strongly different amino acid residues

Bakhshi, A.K.; Otto, P.; Liegener, C.‐M.; Rehm, E.; Ladik, J.

doi:10.1002/qua.560380407

Cited by 17 publications

(3 citation statements)

References 18 publications

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“…From Figure 3(a)-(c), one can learn that the DOS (in number of states/eV * 2 spin) of insulin is similar to those of random aperiodic seven-component polypeptide chains [35]. The differences are that the distribution of the states is more even in insulin than in the model protein, and the energy gap of insulin (1 1.6 eV) is in an amount smaller than that of the model protein (1 1.7 eV).…”

Section: Density Of Statesmentioning

confidence: 89%

Theory of hopping conductivity of proteins

Ladik

1994

Int J of Quantum Chemistry

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Quantum chemical calculations for two different kinds of native proteins (pig insulin and hen egg white lysozyme) were done by the extended negative factor counting method in which the matrix elements have been calculated at the ab initio level with the help of a minimal basis and the simulation of the aqueous solution environment. The hopping conductivities were worked out by the formulas of the random walk theory of Lax and co-workers. The electronic density of states of these native proteins confirmed the conclusions obtained previously from aperiodic model peptides chains. The results show that the ac conductivity vs. frequency curve of these native proteins lies in the range of some typical good inorganic amorphous conductors and thus confirm that proteins, if doped, are amorphous conductors. The behavior of the ac conductivities of the proteins in different ranges of frequencies are discussed. 0 1994 John Wiley & Sons, Inc.

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Section: Density Of Statesmentioning

confidence: 89%

Theory of hopping conductivity of proteins

Ladik

1994

Int J of Quantum Chemistry

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“…In this section, the full electronic structure of P173L was calculated using the software mainly based on the ODA and ENFC methods developed by Ladik and colleagues [11][12][13]. We further straightened out and revised some parts in this software.…”

Section: Full Electronic Structure Calculationmentioning

confidence: 99%

Full electronic structure calculation of the biological activity in P173L enzyme

Zhang

Guo

et al. 2006

Int J of Quantum Chemistry

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ABSTRACT:The biological activity variation along with the temperature in the heatsensitive mutant P173L with 26316 electrons has been studied by full electronic structure calculation and parallel molecular dynamics from temperature 302-318 K. The change of the energy gap between the frontier orbital energy level occupied by each of the four residues and the lowest unoccupied molecular orbital energy level was worked out as an index to quantify the biological activity variation. We reproduced the experimental results suggested by Fomenkov et al.: Residues GLU77, ASP94, GLU111, and GLU113 were essential to the enzyme catalytic function and the enzyme cleavage activity is decreased in turn at temperatures 303, 310, and 315 K. Moreover, our calculations revealed more elaborate information that was not found by the experiment: There is a range of temperature (ϳ307-313 K) between the experimental temperatures 303-315 K in which the enzyme cleavage activity increases.

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“…In the recent past there has been considerable interest in the quantum chemical treatment of model tripeptides, − specifically in N -acetyl- l -alanyl- l -alanine- N ‘-methyl amide − and N -formyl- l -alanyl- l -alanine amide (ALA-ALA, henceforth; Figure ). ,− The results for such compounds are often considered as paradigms for larger systems, such as oligopeptides and proteins − which are not yet readily accessible to advanced computational methods.…”

Section: Introductionmentioning

confidence: 99%

Local Geometry Trends and Torsional Sensitivity in N-Formyl-l-alanyl-l-alanine Amide and the Limitations of the Dipeptide Approximation

Schäfer

Ramek

1999

J. Phys. Chem. A

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Based on a database of 11 664 RHF/4-21G ab initio gradient-optimized structures of N-formyl-l-alanyl-l-alanine amide (ALA-ALA), the local geometries and torsional sensitivity of this compound were analyzed to test the dipeptide approximation frequently used in peptide conformational analyses. This database was generated by optimizing the geometries of this compound at grid points in its four-dimensional (φ1,ψ1,φ2,ψ2) conformational space defined by 40° increments along the outer torsions φ1 and ψ2, and by 30° increments along the inner torsions ψ1 and φ2. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces of the structural parameters of ALA-ALA, and of their gradients, in (φ1,ψ1,φ2,ψ2) space. Analysis of the structural surfaces shows not only that the structure of a given residue in a peptide chain depends acutely on the conformational state of a neighboring residue but also that the interresidue effects differ, depending on whether they are transmitted from right to left or from left to right in the peptide chain. Structural gradients are a qualitative measure of the torsional sensitivity, and therefore of the density of states and contributions to vibrational entropy. Analyses of the gradient surfaces show that the density of states in a residue is significantly affected by the dynamics of a neighboring residue. This opens the possibility of dynamic entropic conformational steering in extended peptide chains, i.e., the generation of free energy contributions from dynamic effects of one part of a molecule on another, possibly stabilizing a conformational region of a PES whose static energy profile is less favorable compared to other regions. The gradient trends illustrate how the overall stability of a complex molecule is not only a function of how the static energy minima of its isolated subunits combine but also of how the dynamics of the subunits interact with one other. These interactions between individual residues represent a hidden cooperative effect that is not apparent at all in the dynamics of isolated dipeptide units.

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Modeling of real 20‐component protein chains: Determination of the electronic density of states of aperiodic seven‐component polypeptide chains containing strongly different amino acid residues

Cited by 17 publications

References 18 publications

Theory of hopping conductivity of proteins

Theory of hopping conductivity of proteins

Full electronic structure calculation of the biological activity in P173L enzyme

Local Geometry Trends and Torsional Sensitivity in N-Formyl-l-alanyl-l-alanine Amide and the Limitations of the Dipeptide Approximation

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