Physico-chemical and theoretical studies on polypeptide conformations

Abstract

One of the important secondary structures in globular and fibrous proteins is the ?-structure, originally proposed by Linus Pauling in the early fifties. The understanding of the ?-structure is, however, hampered by complications arising mainly from the presence of more than one form of the ?-structure. The three well-known forms are the parallel, the antiparallel, and the cross-? forms.

All three forms are characterized by the helical parameter n=2, where n represents the number of residues per turn of the polypeptide chain. Recent structural data on globular proteins from X-ray diffraction studies reveal the presence of yet another form, namely, the twisted ?-sheet, wherein n?2, in contrast to the above "regular" ?-structures.

The experimental characterization of the various ?-forms is made difficult not only by the lack of suitable criteria to distinguish them but also by problems arising from solubility, optical transparency, and related issues. Aim of the Studies

The aim of the studies reported in this thesis is twofold:

To determine the experimental parameters that characterize a given form of the ?-structure and use these to study its stability under experimental conditions.

To arrive, from theoretical considerations, at the energetically favourable manner in which a pair of antiparallel polypeptide chains can be brought together to form the ?-structure.

The scope and objectives of the present work are described in the introductory section of the thesis. Structure of the Thesis

The subject matter of the thesis is divided into two parts:

Part I: Experimental studies

Part II: Theoretical calculations on the ?-structure

Part I – Experimental Studies

General features of the different forms of the regular ?-structure are described.

A critical survey of available experimental studies on the ?-structure is presented, with discrepancies and their origins discussed.

Problems associated with studies in non-aqueous solvent systems are delineated.

Experimental Details: Polypeptides of O-substituted serine and S-substituted cysteine were chosen:

Poly-O-acetyl-L-serine (POAS)

Poly-O-carbobenzoxy-L-serine (POCBS)

Poly-S-benzyl-L-cysteine (PSBC)

Poly-S-carbobenzoxy-L-cysteine (PSCBC)

A mixed organic solvent system containing 1,2-dichloroethane (DCE) and trifluoroacetic acid (TFA) or dichloroacetic acid (DCA) was used. Spectroscopic techniques employed include IR, UV, circular dichroism (CD), optical rotatory dispersion (ORD), and nuclear magnetic resonance (NMR). Key Experimental Findings

Backbone Conformation: The ?-structure in films was identified by characteristic IR bands and ORD/CD spectra. In DCE-rich solutions, polypeptides exhibited positive ORD across the visible and UV ranges, with characteristic CD troughs in the peptide chromophore region. This behaviour is attributed to the cross-? form.

Side-Chain Orientation: Polypeptides with aromatic chromophores (POCBS, PSBC, PSCBC) showed aromatic CD bands, indicating asymmetric placement of phenyl rings. NMR confirmed stacking of phenyl rings, supported by molecular modelling.

? ? Coil Transition: Addition of TFA disrupted both backbone conformation and side-chain orientation, showing a cooperative transition. Thermal studies revealed an "inverted" transition, where the random coil was more stable at lower temperatures.

Relative Stability Order: POCBS > POAS > PSCBC > PSBC Thus, O-substituted serine derivatives are more stable ?-formers than S-substituted cysteine derivatives. Part II – Theoretical Studies

Earlier conformational energy calculations mainly considered intrachain interactions. In this work, both intrachain and interchain interactions were analysed for antiparallel ?-chains.

A methodology was developed to fix two antiparallel ?-chains and obtain backbone angles (?,?).

Hydrogen bonding arrangements were defined with new parameters.

Calculations with methyl groups (representing alanyl residues) showed that regular ?-structures and both right- and left-handed twisted ?-structures are stereochemically possible.

Key Theoretical Result: The energy minimum occurs to the right of the n=2 line, corresponding to the right-handed twisted ?-structure. This preference arises mainly from interchain side-chain interactions, especially between methyl groups.

This agrees well with experimental data on globular proteins, where right-handed twisted ?-sheets are commonly observed.