How Do Rotameric Conformations Influence the Time-Resolved Fluorescence of Tryptophan in Proteins? A Perspective Based on Molecular Modeling and Quantum Chemistry

Abstract

We discuss the dynamics of tryptophan rotamers in the context of the non-exponential fluorescence decay in proteins. The central question is: how does the ground-state conformational heterogeneity influence the time evolution of tryptophan fluorescence? This problem is examined here from the theoretical perspective. Three methods at different levels of theory, and with different scopes and computational requirements are reviewed. The Dead-end elimination method is limited to side-chain dynamics and provides an efficient way to detect the stable tryptophan rotamers in a protein. Its application to the study of heterogeneous emission characteristics is illustrated. Molecular dynamics is aimed at the full phase space of the macromolecule in solution, but must rely on classical force fields and laws of evolution. We examine to what extent the molecular mechanics paradigm yields sufficiently accurate thermodynamic results, and what are the possible kinetic implications. Finally Quantum Chemistry is the only theoretical method that allows a direct assessment of the excited states. It is necessarily restricted to small molecular systems, and thus must be used in a hybrid combination with classical methods and electrostatic models. So far understanding of the emitting state has greatly progressed as a result of these calculations, but the actual treatment of the photophysical decay processes at the quantum level has not yet really started.

Orientation of tyrosine side chain in neurotoxic Aβ differs in two different secondary structures of the peptide

“…The tyrosyl moiety in each rotameric orientation/state experiences a different microenvironment; it remained at different distances from the adjacent peptide linkages, some of which may contribute to the fluorescence quenching. Fluorescence quenching via excited state charge transfer often depends on the rotameric structure of the fluorophore moiety [40][41][42][43][44][45][46][47]. Three different fluorescence lifetimes were suggested for each of the rotameric states of the tyrosyl group in aqueous buffer at low (micromolar range) peptide concentration [39].…”

“…The time-resolved fluorescence decay analysis often found that fluorescence decay fit to multi-component lifetime components and with different amplitudes. Some experimental and theoretical investigation with tryptophan-and tyrosine-containing proteins and peptides suggested the existence of rotameric states as the source of different fluorescence components [40][41][42][43][44][45][46][47][53][54][55]. Different degrees of fluorescence quenching are possible as the excited state charge transfer depends on the rotameric structure of the aromatic component, an indole ring in the case of tryptophan residue and phenole ring for tyrosine residue.…”

Reorientations of Aromatic Amino Acids and Their Side Chain Models: Anisotropy Measurements and Molecular Dynamics Simulations

“…Studies of molecular reorientations in solution provide the most direct access to the rates of nanosecond and subnanosecond molecular motions and interactions with the environment. − To interpret dynamics of larger systems such as peptides and proteins, , it is important to understand motions of the simplest building blocks: individual aromatic amino acids and their side-chain models. The goal of our work is to perform a systematic study of these systems, presenting both basic experimental data to quantify the time scales of the occurring processes and results of molecular dynamics simulations and continuum modeling aimed at providing insights into the microscopic underpinnings of the observations.…”

Tryptophan Conformations Associated with Partial Unfolding in Ribonuclease T1

“…The interpretation of the time-resolved fluorescence decay of tryptophan in proteins continues to challenge both experimentalists and theoreticians. The most often cited model, known as the rotamer model, provides a simple explanation for the ubiquitous multiplicity of fluorescence lifetimes (1)(2)(3). According to this model, each lifetime component is associated with a single rotamer state or a narrow distribution of rotamer states, which, upon excitation, decays at a characteristic exponential rate.…”