Macromolecular Entropy Can Be Accurately Computed from Force.

A method is presented to evaluate a molecule's entropy from the atomic forces calculated in a molecular dynamics simulation. Specifically, diagonalization of the mass-weighted force covariance matrix produces eigenvalues which in the harmonic approximation can be related to vibrational frequencies. The harmonic oscillator entropies of each vibrational mode may be summed to give the total entropy.

How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: β₂-Adrenergic Receptor in the Spotlight.

Atomistic molecular dynamics (MD) simulations are used extensively to elucidate membrane protein properties. These simulations are based on three-dimensional protein structures that in turn are often based on crystallography. The protein structures resolved in crystallographic studies typically do not correspond to pristine proteins, however.

Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces.

The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of which appears to be largely of entropic nature according to previous experimental studies. We here study at atomic detail the allosteric regulation of CAP with Molecular dynamics (MD) simulations.

Quantitative imaging of the electrostatic field and potential generated by a transmembrane protein pore at subnanometer resolution.

Elucidating the mechanisms by which proteins translocate small molecules and ions through transmembrane pores and channels is of great interest in biology, medicine, and nanotechnology. However, the characterization of pore forming proteins in their native state lacks suitable methods that are capable of high-resolution imaging (~1 nm) while simultaneously mapping physical and chemical properties. Here we report how force-distance (FD) curve-based atomic force microscopy (AFM) imaging can be applied to image the native pore forming outer membrane protein F (OmpF) at subnanometer resolution and to quantify the electrostatic field and potential generated by the transmembrane pore.

Mechanistic explanation of different unfolding behaviors observed for transmembrane and soluble β-barrel proteins.

In response to mechanical stress, membrane proteins progress through sequences of major unfolding barriers, whereas soluble proteins usually must overcome only one major unfolding barrier. To gain insight into these markedly different unfolding behaviors, we applied force-probe molecular dynamics simulations and unfolded two β-barrel proteins, the transmembrane outer membrane protein G (OmpG) and the water-soluble green fluorescent protein (GFP). The simulations mimic with high precision the unfolding experiments and show that OmpG in the absence of a membrane and GFP circumvent high unfolding barriers by rotations and explore alternative unfolding pathways.

Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.

Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs.

Gating of the MlotiK1 potassium channel involves large rearrangements of the cyclic nucleotide-binding domains.

Cyclic nucleotide-regulated ion channels are present in bacteria, plants, vertebrates, and humans. In higher organisms, they are closely involved in signaling networks of vision and olfaction. Binding of cAMP or cGMP favors the activation of these ion channels.

Estimating absolute configurational entropies of macromolecules: the minimally coupled subspace approach.

We develop a general minimally coupled subspace approach (MCSA) to compute absolute entropies of macromolecules, such as proteins, from computer generated canonical ensembles. Our approach overcomes limitations of current estimates such as the quasi-harmonic approximation which neglects non-linear and higher-order correlations as well as multi-minima characteristics of protein energy landscapes. Here, Full Correlation Analysis, adaptive kernel density estimation, and mutual information expansions are combined and high accuracy is demonstrated for a number of test systems ranging from alkanes to a 14 residue peptide.

Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces.

The quasiharmonic approximation is the most widely used estimate for the configurational entropy of macromolecules from configurational ensembles generated from atomistic simulations. This method, however, rests on two assumptions that severely limit its applicability, (i) that a principal component analysis yields sufficiently uncorrelated modes and (ii) that configurational densities can be well approximated by Gaussian functions. In this paper we introduce a nonparametric density estimation method which rests on adaptive anisotropic kernels.

Primary steps of pH-dependent insulin aggregation kinetics are governed by conformational flexibility.

Insulin aggregation critically depends on pH. The underlying energetic and structural determinants are, however, unknown. Here, we measure the kinetics of the primary aggregation steps of the insulin monomer in vitro and relate it to its conformational flexibility.

Mechanoenzymatics of titin kinase.

Biological responses to mechanical stress require strain-sensing molecules, whose mechanically induced conformational changes are relayed to signaling cascades mediating changes in cell and tissue properties. In vertebrate muscle, the giant elastic protein titin is involved in strain sensing via its C-terminal kinase domain (TK) at the sarcomeric M-band and contributes to the adaptation of muscle in response to changes in mechanical strain. TK is regulated in a unique dual autoinhibition mechanism by a C-terminal regulatory tail, blocking the ATP binding site, and tyrosine autoinhibition of the catalytic base.