Physiological Chemistry

Surveying the floodgates: Estimating protein flux into the endoplasmic reticulum lumen in Saccharomyces cerevisiae

Endoplasmic reticulum resident proteins, along with all proteins traveling through the secretory pathway must enter endoplasmic reticulum lumen through membrane-embedded translocons. In Saccharomyces cerevisiae the heterotrimeric endoplasmic …

Unravelling the impact of obstacles in diffusion and kinetics of an enzyme catalysed reaction

Lattice gas automata simulations of diffusion-limited reactions in heterogeneous media exhibit fractal-like kinetics, which is a generalised mass action kinetics with time-dependent rate constants. We develop a two dimensional lattice gas automata …

Single-molecule enzymology a la Michaelis-Menten

Over the past 100years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted invitro. In recent years, sophisticated …

Effects of protein quality control machinery on protein homeostasis

In the endoplasmic reticulum, protein production occurs through a complex set of reaction networks which synthesize and fold protein polypeptides. Proteins can misfold due to mutation or cellular stress. Accumulation of misfolded proteins can lead to …

A model of the unfolded protein response: Pancreatic beta-cell as a case study

Pancreatic β-cell failure is increasingly recognized as central to the progression of diabetes mellitus. Different causes are implicated in the onset of β-cell stress, dysfunction or death. Recent genetic and biochemical evidence both in humans and …

Modelling reaction kinetics inside cells

In the past decade, advances in molecular biology such as the development of non-invasive single molecule imaging techniques have given Lis a window into the intricate biochemical activities that occur inside cells. in this chapter we review four …

A mesoscopic simulation approach for modeling intracellular reactions

Reactions in the intracellular medium occur in a highly organized and heterogenous environment rendering invalid modeling approaches based on the law of mass action or its stochastic counter-part. This has led to the recent development of a variety …

A systematic investigation of the rate laws valid in intracellular environments

Recently there has been significant interest in deducing the form of the rate laws for chemical reactions occurring in the intracellular environment. This environment is typically characterized by low-dimensionality and a high macromolecular content; …

How reaction kinetics with time-dependent rate coefficients differs from generalized mass action

**Take caution!** The two distinct theoretical descriptions of non‐classical kinetics: fractal‐like kinetics (kinetics with time‐dependent rate coefficients) and the power law approximation (generalized mass action kinetics) are shown to be …

Stochastic approaches for modelling in vivo reactions

In recent years, stochastic modelling has emerged as a physically more realistic alternative for modelling in vivo reactions. There are numerous stochastic approaches available in the literature; most of these assume that observed random fluctuations …