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Biomedical subjects

Lou Massa

Publications and source records attributed to Lou Massa.

9 recordsLinked to original sources
PubMed2006

The transition state for formation of the peptide bond in the ribosome.

Using quantum mechanics and exploiting known crystallographic coordinates of tRNA substrate located in the ribosome peptidyl transferase center around the 2-fold axis, we have investigated the mechanism for peptide-bond formation. The calculation is based on a choice of 50 atoms assumed to be important in the mechanism. We used density functional theory to optimize the geometry and energy of the transition state (TS) for peptide-bond formation. The TS is formed simultaneously with the rotatory motion enabling the translocation of the A-site tRNA 3' end into the P site, and we estimated the magnitude of rotation angle between the A-site starting position and the place at which the TS occurs. The calculated TS activation energy, E(a), is 35.5 kcal (1 kcal = 4.18 kJ)/mol, and the increase in hydrogen bonding between the rotating A-site tRNA and ribosome nucleotides as the TS forms appears to stabilize it to a value qualitatively estimated to be approximately 18 kcal/mol. The optimized geometry corresponds to a structure in which the peptide bond is being formed as other bonds are being broken, in such a manner as to release the P-site tRNA so that it may exit as a free molecule and be replaced by the translocating A-site tRNA. At TS formation the 2' OH group of the P-site tRNA A76 forms a hydrogen bond with the oxygen atom of the carboxyl group of the amino acid attached to the A-site tRNA, which may be indicative of its catalytic role, consistent with recent biochemical experiments.

Crystallography, X-Ray↗
PubMed2006

Fundamental importance of the Coulomb hole sum rule to the understanding of the Colle-Salvetti wave function functional.

In this paper we consider the general form of the correlated-determinantal wave function functional of Colle and Salvetti (CS) for the He atom. The specific form employed by CS is the basis for the widely used CS correlation energy formula and the Lee-Yang-Parr correlation energy density functional of Kohn-Sham density functional theory. We show the following: (i) The key assumption of CS for the determination of this wave function functional, viz., that the resulting single-particle density matrix and the Hartree-Fock theory Dirac density matrix are the same, is equivalent to the satisfaction of the Coulomb hole sum rule for each electron position. The specific wave function functional derived by CS does not satisfy this sum rule for any electron position. (ii) Application of the theorem on the one-to-one correspondence between the Coulomb hole sum rule for each electron position and the constraint of normalization for approximate wave functions then proves that the wave function derived by CS violates charge conservation. (iii) Finally, employing the general form of the CS wave function functional, the exact satisfaction of the Coulomb hole sum rule at each electron position then leads to a wave function that is normalized. The structure of the resulting approximate Coulomb holes is reasonably accurate, reproducing both the short- and the long-range behavior of the hole for this atom. Thus, the satisfaction of the Coulomb hole sum rule by an approximate wave function is a necessary condition for constructing wave functions in which electron-electron repulsion is represented reasonably accurately.

Models, Theoretical↗
PubMed2006

The Kernel Energy Method: application to a tRNA.

The Kernel Energy Method (KEM) may be used to calculate quantum mechanical molecular energy by the use of several model chemistries. Simplification is obtained by mathematically breaking a large molecule into smaller parts, called kernels. The full molecule is reassembled from calculations carried out on the kernels. KEM is as yet untested for RNA, and such a test is the purpose here. The basic kernel for RNA is a nucleotide that in general may differ from those of DNA. RNA is a single strand rather than the double helix of DNA. KEM energy has been calculated for a tRNA, whose crystal structure is known, and which contains 2,565 atoms. The energy is calculated to be E = -108,995.1668 (a.u.), in the Hartree-Fock approximation, using a limited basis. Interaction energies are found to be consistent with the hydrogen-bonding scheme previously found. In this paper, the range of biochemical molecules, susceptible of quantum studies by means of the KEM, have been broadened to include RNA.

Base Sequence↗
PubMed2005

Kernel energy method: application to DNA.

The kernel energy method (KEM) has been used in three recent papers (1-3) to calculate the quantum mechanical ab inito molecular energy of peptides and the protein insulin. It was found to have good accuracy. The computational difficulty of representing a molecule increases only modestly with the number of atoms. The calculations are simplified by adopting the approximation that a full biological molecule can be represented by smaller "kernels" of atoms. In this paper, the accuracy of the KEM is tested in the application to DNA, whose basic kernels, chemical bonding, and overall molecular structure are quite different from peptides and proteins. The basic kernel in the case of peptides and proteins is an amino acid. The basic kernel in the case of DNA is a nucleotide consisting of a phosphate-sugar-base. The molecular energy is calculated for all three basic types of DNA, i.e., B, A, and Z configurations of DNA. The results give an accuracy that is comparable to that achieved with peptides and proteins. Thus, the KEM is found to be applicable to major types of biological molecules.

Base Sequence↗
PubMed2005

Kernel energy method: application to insulin.

In two recent articles a method has been described for calculating the total energy of large molecules. The method is called the kernel energy method (KEM) and requires knowledge of the crystal structure of interest. Calculations are simplified by adopting the approximation that a full molecule could be represented by smaller kernels of atoms. The KEM was illustrated with peptides ranging in size from 4 to 19 amino acid residues, and was found to deliver accurate results. The use of the KEM does not depend upon a particular choice of basis functions and is applicable across quantum computational methods of differing levels of accuracy. These earlier investigations suggested that the KEM could be used to calculate the ab initio quantum mechanical energy of proteins. An application has been made with the protein insulin, composed of 51 aa. Accurate KEM Hartree-Fock energies are obtained for the separate A and B chains of insulin and for their composite structure in the full insulin molecule. A limited basis is used to make possible calculation of the full insulin molecule, which can be used as a standard of accuracy for the KEM calculation. The KEM result obtained is E(KEM) = -21104.7656 a.u. It differs from a full molecule Hartree-Fock result by only 0.000002%. The solvent molecules can be treated effectively as a separate kernel. The KEM result for the fully solvated insulin molecule is E(KEM) = -26275.4127 a.u., differing from the full molecule Hartree-Fock result by as little as 0.000023%.

Amino Acid Sequence↗
PubMed2004

Determination of a wave function functional.

We propose expanding the space of variations in traditional variational calculations for the energy by considering the wave function psi to be a functional of a set of functions chi:psi=psi[chi], rather than a function. A constrained search in a subspace over all functions chi such that the functional psi[chi] satisfies a sum rule or leads to a physical observable is then performed. An upper bound to the energy is subsequently obtained by variational minimization. The rigorous construction of such a constrained-search-variational wave function functional is demonstrated.

Quantum Theory↗
PubMed2002

Form factors for core electrons useful for the application of quantum crystallography (QCr) to organic molecules.

Form factors are calculated for the core electrons of the first-row atoms B, C, N, O and F. The form factors are presented in an analytical form, as appears in International Tables for X-ray Crystallography [Ibers & Hamilton (1974), Vol. IV, pp. 103-145. Birmingham: Kynoch Press; present distributor Kluwer Academic Publishers, Dordrecht]. Having such form factors for the core electrons reduces the number of parameters to be determined by the methods of quantum crystallography (QCr). It is shown that the form factors obtained are quite accurate. Thus, when they are used in QCr, they are expected to be consistent with accurate charge densities.

Crystallography, X-Ray↗