Bonding in Proteins and Other Macromolecules

Mathematical Chemistry Research Unit, Department of Chemistry and Department of Mathematics and Statistics University of Saskatchewan, 

The interactions between various segments of a protein which are separated by several amino acids along the polypeptide chain but which fall within a short geometrical distance from one another due to the actual folding pattern, are expected to contribute to the stability of the protein conformation to a significant degree. 

The AFDF family of methods and the quantum chemical treatment of functional groups have been reviewed recently [11]. Here only a brief introduction of the notations and a summary of the basic results will be given. 

At each point r, the electronic density p(r,K) of a molecule of nuclear conformation K can be computed by the Hartree-Fock-Roothaan-Hall SCF LCAO ab initio method. Using a basis set cp(K) of atomic orbitals (pj(r,K) 

Electron density decreases exponentially with distance that suggests that an Additive Fuzzy Density Fragmentation (AFDF) approach can be used for both a fuzzy decomposition and construction of molecular electron densities. The simplest AFDF technique is the Mulliken-Mezey density matrix fragmentation [12,13], that is the basis of both the Molecular Electron Density Loge Assembler (MEDLA) [14-17] and the Adjustable Density Matrix Assembler (ADMA) [18-21] macromolecular quantum chemistry methods. 

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Mezey, P.G. (1998) Chemical bonding in proteins and other macromolecules. In Pauling s Legacy Modern Modelling of Chemical Bonding, Maksic, Z. and Orville-Thomas, J. (Eds.), Elsevier Science Publ., Amsterdam, The Netherlands. 

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