Current Physical Chemistry - Volume 2, Issue 1, 2012

The present issue marks the beginning of the second year of Current Physical Chemistry (CPC). Although the Journal is still in its infancy, I shall attempt both to draw up a balance of what it has offered so far, as well as to anticipate what it will offer to its readers in the near future and in the long term. In 2011 CPC has published separate feature articles, as well as series of articles grouped together to form a Special Issue con Read More

Protein Folding Dynamics: Bridging the Gap Between Theory and Experiments Once regarded as a grand challenge, protein folding has seen great progress in recent years [1-3], and the gap between the timescales reachable by experiments and by computer simulations has been significantly reduced due to concurrent advances in both experimental [4-7] and theoretical techniques [8-10]. Scientists can nowadays access to th Read More

We review our joint experimental-theoretical effort on the folding of photo-switchable α-helices. The folding kinetics of these peptides is profoundly non-exponential, which is attributed to a partitioning of the unfolded state into several misfolded traps. These traps are connected to the folded state in a hub-like fashion with folding barriers of different heights. Molecular dynamics simulations reveal a semi-quantitative agreemen Read More

The interactions between the nanoscale particles, such as the carbon nanotubes, and biomolecules are essential to the nanoscale particle based biotechnology and biomedical applications, such as gene delivery, cellular imaging, tumor therapy. However, how the structure changes and whether the functions of the biomolecules are affected due to the existence of nanoscale particles are still poorly understood. In this pa Read More

Many proteins undergo significant structural changes following the hydrolysis of a bound nucleoside triphosphate (NTP) molecule. Davydov has proposed that, in the protein myosin, vibrational excitations are taken advantage of in the energy transduction process following this hydrolysis. Using an atomistic, mixed quantum-classical molecular dynamics model, we have attempted to obtain a more detailed understanding of Read More

α-helix and β-hairpin are the two principal secondary structures in proteins. A large number of experimental and theoretical kinetics and thermodynamics studies of the folding and unfolding of α-helix and β-hairpin structured polypeptides and proteins have been performed. Different theoretical models have been proposed to explain their folding mechanisms. Inconsistencies exist among the various models, which ess Read More

Fast folding techniques use optical spectroscopic tools to monitor protein folding or unfolding dynamics after a fast triggering such as the laser induced temperature jump. These techniques have greatly improved time resolution of experiments and provide new opportunities for comparison between theory and simulations. However, the direct comparison is still difficult due to two main challenges: a gap between folding relev Read More

Since 2000, when they were first identified by Willie Taylor, the number of knotted proteins within the protein database has increased and there are now nearly 300 such structures. The polypeptide chains of these proteins form topologically knotted structures. There are now examples of proteins which form simple 31 trefoil knots, 41, 52 Gordian knots and 61 Stevedore knots. Knotted proteins represent a significant challe Read More

Bias-Exchange Metadynamics is a powerful technique that can be used for reconstructing the free energy and for enhancing the conformational search in complex biological systems. In this method, a large set of collective variables (CVs) is chosen and several metadynamics simulations are performed on different replicas of the system, each replica biasing a different CV. Exchanges between the bias potentials are periodicall Read More

When one studies protein folding and unfolding by molecular simulations, one faces a great difficulty. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in local-minimum-energy states, giving the results in error. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. In this article we review some of powerful Read More

Intrinsically disordered but biologically active proteins, commonly referred to as IDPs, are readily identified in many biological systems and play critical roles in multiple protein regulatory processes. While disordered in their unbound states, IDPs often, but not always, fold upon binding with their protein interaction partners. Here, we discuss how a class of IDPs directs the targeting, specificity and activity of Protein Phosphata Read More

We present the results of high temperature 500 K Molecular Dynamics simulations of a single-stranded DNA i-motif. The unfolding pathways are compared to a biased metadynamics simulation at 300 K. Our results indicate a remarkable agreement between the trajectories. We found that the unfolding process can be described by two main mechanisms with a small number of eigenvectors.