Navnit K. Misra

Phonon dispersion in poly(l-arginine)

Poly(l-arginine) is a basic polypeptide, which undergoes dramatic conformational changes as a consequence of variation in its water content. Complete normal mode calculations and their dispersion are reported for the β-sheet conformation of this biopolymer using the Urey–Bradley force field and the Higgs method for infinite systems. The results indicate that the modes below 1350 cm−1 show appreciable dispersion. A study of its normal modes and their dispersive behavior shows repulsion with character exchange. Amide modes, side-chain modes, and mixed modes are reported. The heat capacity calculated from the dispersion curves via density-of-states using Debyes relation is compared with the experimental data in the temperature range 220–390K.

Phonon dispersion and heat capacity of poly(L-aspartic acid)

Abstract Normal modes and their dispersion are reported for the α-helical form of poly( l -aspartic acid) which is an important polypeptide used in the sustained release of drugs. Characteristic features of dispersion curves such as bunching and repulsion are discussed. Heat capacity is derived from the dispersion curves via density-of-states and compared with the available experimental data on sodium salt of the polymer.

Phonon dispersion and heat capacity in cross-β form of poly(O-acetyl, l-serine)

Abstract Poly( O -acetyl, l -serine), which is a precursor of poly( l -serine) in synthesic sequence, is found to exist in cross-β conformation. Normal mode analyses including phonon dispersion have been performed, to understand completely the FTIR spectra of this polypeptide, using Wilsons GF matrix method and Urey–Bradley force field. The characteristic features of dispersion curves like repulsion, exchange of character and bunching have been observed and discussed. In addition to the above the heat capacity is calculated as a function of temperature via density-of-states derived from dispersion curves.

Normal modes and their dispersion in poly(α-isobutyl, β-l-aspartate): II. 13/4 Helix

Abstract Poly(α-isobutyl-β- l- aspartate) is a stereoregular derivative of polyamides and exist in 4/1 and 13/4 helices. Normal mode analysis and their dispersion of the 4/1 form have been carried out using Urey–Bradley force constants. Apart from detailed assignment of modes, characteristic features of dispersion curves such as repulsion and cross-over have been explained as arising due to internal symmetry in the energy momentum space. Predictive values of heat capacity contribution from various types of modes are also reported.

Phonons and their dispersion in poly(S‐benzyl‐L‐cysteine)

Poly(S-benzyl-L-cysteine) (PBLC) is a S-benzyl derivative of the natural amino acid poly(L-cysteine). Its normal modes and their dispersion in antiparallel β-sheet conformation have been obtained within the first Brillouin zone using Wilsons G.F. matrix method, as modified by Higgs for an infinite polymeric chain. The zone center frequencies and the Urey Bradley force field have been obtained by best fitting the observed Fourier transform IR (FTIR) absorption bands. The characteristic features of dispersion curves such as crossing, repulsion, and exchange of character are discussed. Predictive values of heat capacity in the temperature range of 50-500 K are reported.

Phonon Dispersion in 1,4-cis-Poly-(2-Methyl-1,3-Pentadiene)

Polymers of 2-methyl-1,3-pentadiene are capable of existing in both isotactic, as well as syndiotactic, configuration. The isotactic 1,4-cis polymer also exists in two stable forms that have different melting points. A complete study of normal modes and their dispersion was carried out using Higgs modification of Wilsons dynamical GF matrix method and the Urey Bradley force field. The force constants have been best fitted to the Fourier transform infrared (FTIR) frequencies. Characteristic features of dispersion curves, like bunching, repulsion, and exchange of character between various pairs of modes, were observed and are discussed here. In addition, the frequency distribution function derived from dispersion curves was used to calculate the heat capacity in the temperature range 50–450 K.

Multistep transitions in collagens

Abstract It is well known that collagens exist in triple-helical form, and, on average, the individual chains have glycine at every third place. Collagens from different sources vary in distributions of other amino acids. They could also be different in the distribution of defects, which are generally nonhelical regions of low stability. Varying lengths of individual chains in the triple-helical system can also contribute to this variability. All these variations manifest themselves in the creation of a transition profile with undulations that are indicative of a multiphasic nature. In the present communication, we try to understand this variability by using essentially the Zimm and Bragg approach and suitably amending it for a triple-helical system. Factors that contribute to the multiphasic nature are incorporated into the transition model and discussed. Results obtained for collagen types I, II, III, Vx, Vy, and XI are in agreement with the experimental measurements. Transitions in the first three type...

A spectroscopic study of various conformational states of poly(β-benzyI, L-aspartate)

Poly(β-benzyl, L-aspartate) [PBLA] is an unusual synthetic homopolypeptide, which under varying conditions of preparation is capable of adopting four different conformations namely left-handed a helix, right-handed a helix, co helix and β pleated sheet [1–6]. The conformational versality of PBLA has made it a model of great interest from the view point of molecular dynamics of polypeptides and proteins, especially the reversal of the helix sense that occurs when different ester groups are substituted on the polyaspartate backbone. For example poly(β-methyl, L-aspartate) and PBLA adopt a left handed conformation upon replacement of the methyl group by a larger aliphatic one in the former or substitution of a nitro, chloro, cyno group in the para position of the benzyl group in the latter, thereby resulting in the reversal of the helix sense [3]. The degree of crystallisation and confromational features that undergo change from α to ω and further from ω to β form upon heat treatment have been successfully correlated with the disposition of side chains, particularly the packing of the benzene rings and its effect on the flexibility of the side chain.