A non-linear model for the synaptic basis of neuronal memory.

We propose a mathematical model for the synaptic basis of neuronal memory. The model incorporates non-linear effects in analogy with population growth problems of human beings, animals, biological species, crystal growth, etc., and provides a mechanism whereby the excitatory and inhibitory inputs produce alterations in a neurone which result in a long-lasting increase in transmitter release at a synapse.     

Dynamics of amino acid residues in globular proteins

The dynamic differential equation model developed and tested for bovine pancreatic trypsin inhibitor and tuna ferrocytochrome c in Ponnuswamy, P.K. & Bhaskaran, R. (Int. J. Peptide Protein Res. 24, 168-179, 1984) is extended for 17 more protein crystals in this work. Average displacements are computed for 20 amino acid residues observed in 19 proteins. Detailed information on the dynamic behaviour of the individual proteins and individual residues is presented. The effect of atomic packing on the fluctuations of the amino acid residues in alpha-chymotrypsin is illustrated. A number of general points on the dynamic characteristics of globular protein molecules are presented.     

Studies on the conformation of amino acids. X. Conformations of norvalyl, leucyl and aromatic side groups in a dipeptide unit

Backbone-side group conformations of amino acid residues including one or two δ-carbons in the side group have been investigated. Conformational energies of norvalyl, leucyl, phenylalanyl, tyrosyl, tryptophenyl, and histidinyl side groups in a dipeptide unit have been calculated by using classical energy expressions. The side group conformations about the C^α—C^β and C^β—C^γ bonds are restricted to specific values of the respective rotational angles. Thus, most favourable positions of γ- and δ-atoms of a linear side-chain (norvalyl) are restricted to (γ_I, δ_II) (γ_II, δ_I), (γ_II, δ_II), (γ_III, δ_II), and (γ_III, δ_III), whereas those of the side-chain branching at a sp³ γ-atom (leueyl) are further restricted. It is also shown that there is a definite correlation between the orientations of the two peptide planes and that of the planar group of the aromatic side chain of phenylalanyl type residues. The studies bring out an important fact that while the γ-atoms have definite and characteristic effects on the backbone rotational angles ? and ψ, the δ atoms and beyond have no effects on the preferred ? and ψ values. Thus, the preferred backbone conformations are independent of the preferred side group conformations beyond the γ-atom and vice versa. The observed ?, ψ, χ¹, and χ² values of amino acids, simple peptides, and of the three protein molecules lysozyme, myoglobin, and chymotrypsin have been compared with the theoretical predictions, and the agreement is found to be excellent.     

Structural analysis of NADPH depleted bovine liver catalase and its inhibitor complexes

To study the functional role of NADPH during mammalian catalase inhibition, the X-ray crystal structures of NADPH-depleted bovine liver catalase and its inhibitor complexes, cyanide and azide, determined at 2.8Å resolution. From the complex structures it is observed that subunits with and without an inhibitor/catalytic water molecule are linked by N-terminal domain swapping. Comparing mammalian- and fungal- catalases, we speculate that NADPH-depleted mammalian catalases may function as a domain-swapped dimer of dimers, especially during inactivation by inhibitors like cyanide and azide. We further speculate that in mammalian catalases the N-terminal hinge-loop region and α-helix is the structural element that senses NADPH binding. Although the above arguments are speculative and need further verification, as a whole our studies have opened up a new possibility, viz. that mammalian catalase acts as a domain-swapped dimer of dimers, especially during inhibitor binding. To generalize this concept to the formation of the inactive state in mammalian catalases in the absence of tightly bound NADPH molecules needs further exploration. The present study adds one more intriguing fact to the existing mysteries of mammalian catalases.