Protein Unfolding and Disordered Proteins

IDP Force Field Development

Intrinsically disordered proteins (IDPs) are notoriously challenging to study both experimentally and computationally. Our findings highlight how IDPs, with their rugged energy landscapes, are highly sensitive test systems that are capable of revealing force field deficiencies and, therefore, contributing to force field development. more

SESCA: Semi-Empirical-Spectrum-Calculation-Algorithm

SESCA is a computational method that allows rapid and accurate prediction of CD spectra from three-dimensional protein model structures. Calculations allow a direct comparison between the measured CD spectrum of a target protein and the predicted CD spectra based on model structures or structural ensembles to determine the model quality. more

Tension Induced Titin Kinase Activation

Activation of the titin kinase, the catalytic domain of the muscle protein titin, requires major conformational rearrangements resulting in the exposure of its phosphorylation site. Force probe MD simulations can give a detailed description of the activation mechanism and can test the hypothesis that it is the force sensor for the muscle cell.

Simulation of Ion Mobility Spectrometry Experiments

Mass spectrometry based proteomics is becoming an invaluable analysis tool of complex samples like human cell lysates and allows the identification and quantification of thousands of proteins. To enhance the coverage and accuracy of complete proteomes the digested proteins are initially separated with HPLC and in latest devices additionally by trapped ion mobility spectrometry (TIMS). [more]

Altered Kinetics of p53 Caused by the Mutation P27A

The protein p53 is also called the ‘guardian of the genome’ due to its central role in genetic stability. It interacts with numerous other proteins, mainly via its disordered N-terminal transactivation domain (NTAD). It has been shown that an α-helix can fold in the unbound NTAD from residue T18 to L26 which serves as one of the main interaction sites. [more]

Transient Kinetics of the Intrinsically Disordered Protein α-Synuclein: from Picosecond to Millisecond Time Scales

The internal kinetics of intrinsically disordered proteins (IDPs) determine the transient formation of secondary structure elements as well as tertiary contacts within the monomer. This internal kinetics influences the aggregation of monomers into neurotoxic higher molecular weight oligomers and further on the formation of fibrillar structures. [more]

Aqueous Urea Solution: Structure, Energetics, and Urea Aggregation

In virtually every biochemistry lab, urea is used as protein denaturant. However, despite its ubiquiteous use, only little is known about the molecular mechanism underlying urea-induced protein denaturation.To study structure and energetics of aqueous urea solutions, we have carried out molecular dynamics (MD) simulations. [more]

Light Driven Polymer Switching

Nanomechanical devices or molecular machines will, for a broad range of applications, most likely be powered by light or other kinds of electromagnetic radiation. The major reasons are ease of addressability, picosecond reaction times to external stimuli, and compatibility with a broad range of ambient substances, such as solvents, electrolytes, or gases. [more]

Ubiquitin Unfolding and Refolding

Proteins enable living organisms to move, metabolize and sense, in short, to function. To fulfill such diverse tasks, proteins take up a specific fold, their native structure.The factors driving the complex folding process are not yet fully understood. [more]

Hindered Refolding as Mechanism for Urea Induced Denaturation of the Cold Shock protein

Some proteins such as the Cold Shock protein Bc-CsP are not strongly affected by the presence of urea in molecular dynamics (MD) simulations within reachable simulation times. To study urea-induced unfolding for the Cold Shock protein, we generate partially unfolded states by high-temperature unfolding and simulate these at different conditions. [more]