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A Anukanth

Publications and source records attributed to A Anukanth.

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Structure and function in rhodopsin. Requirements of a specific structure for the intradiscal domain.

We concluded previously from mutagenesis in the intradiscal domain of bovine rhodopsin that the formation of a tertiary structure comprising the N-terminal tail and the three polypeptide loops is essential to the in vivo assembly of the functional rhodopsin. We now report on more comprehensive mutagenic studies in the intradiscal domain to determine more precisely the requirement for the formation of the above-proposed tertiary structure. Three large deletions, two consisting of groups of 10 amino acids each, and the third of 34 amino acids, were carried out in the N-terminal loop. All the three mutant opsins only poorly formed the rhodopsin chromophore. In the BC loop, we carried out five 2 amino acid deletions, 2 single amino acid deletions, and three mutations in which short sequences in the loop were reversed. All the resulting mutant opsins had lost the ability to bind 11-cis-retinal. In the DE loop, where extensive mutagenesis had previously been carried out, we carried out 3 amino acid replacements (Asn, Thr, Tyr) at Cys187. None of these mutants bound 11-cis-retinal. In loop FG, we carried out four 2 amino acid deletions, 1 single amino acid deletion, 3 amino acid replacements, and one mutation in which the sequence of the 7 amino acids was reversed. All the mutants in FG loop partially formed the rhodopsin chromophore. All the mutants now described appeared to be retained in the endoplasmic reticulum: several that were examined in detail were complexed with non-opsin proteins, the chaperonins. Treatment with ATP-MgCl2 released the latter from the mutant rhodopsins. Our overall conclusion is that the formation of the specific structure in the intradiscal domain has highly stringent spatial requirements.

Amino Acid Sequence↗

Conformational characteristics of mixed sugar puckered deoxydinucleoside triphosphate units d-pCpGp and d-pGpCp from energy minimization studies.

The deoxydinucleoside triphosphate units d-pCpGp and d-pGpCp were subjected to a rigorous theoretical investigation with a view to describing their distinctive conformational characteristics. For each unit 216 probable three-dimensional forms defined by the backbone-base dihedral angles and sugar pucker modes were considered for conformational energy minimization process and scrutinized with reference to properties, such as base-stacking, hydrogen-bonding, internal flexibility and base sequence-phosphate influence. The P-O bond torsions and the phosphate groups were treated with special attention. The results reveal a number of preferred conformational states other than the known helical forms, such as, A-, B-, C-, Z-, and Watson-Crick conformation. Many interesting one-step (change in only one of the dihedral angles or sugar puckers) conformational transitions which involve just about a kcal/mol of energy came to light. The two base sequences CG and GC were noted to differ strikingly in many of their conformational characteristics.

DNA↗

Conformational characteristics of mixed sugar puckered deoxytetranucleoside triphosphate d-GpCpGpC from energy minimization studies.

As a continuation of our theoretical studies on nucleic acid subunit systems, in this article we consider the case of the tetranucleoside d-GpCpGpC, the minimally ideal representative unit for analyzing the relative stabilities of different forms of homo- and mixed helical conformation of polynucleotides. The four sugar rings are kept so as to generate B-genus, B+A genus and Z-genus conformations. Twenty five helical conformational states which resulted from judicious mixing of A-, B-, C-, W-, and Z-, states locally are subjected to energy minimization permitting the 19 dihedral angles to vary simultaneously. Conformational states corresponding to regular helical forms and mixed helical forms, when analyzed provide valuable information as to the local conformational flexibility and transitions available to polynucleotides.

DNA↗

Conformational characteristics of the dinucleoside triphosphate pCpGp from energy-minimization studies.

The influence of the 3'- and 5'- terminal phosphates on the conformational characteristics of the dinucleoside monophosphate CpG is described in this paper. The computed potential energy of the system is minimized with respect to the relevant 10 dihedral angles permitting the two sugar rings to adopt the alternative puckering states, 2E and 3E. Of the 84 conformations considered, 22 become energetically accessible. The familiar A-, B-, Z- and Watson-Crick-type backbone states of DNA subunits become low-energy forms for this RNA unit pCpGp also. The Watson-Crick-type backbone is invariably preferred in all the four sugar pucker sequences, indicating its importance in the dynamics of sugar pucker fluctuations and in the DNA-RNA association. The interphosphate geometries and the possible hydrogen-bonded states are discussed in relation to the varied folded/extended polynucleotide structures.

Calorimetry↗