The N-terminus of MIF regulates the dynamic profile of residues involved in CD74 activation.

Macrophage migration inhibitory factor (MIF) is an immunomodulatory protein with a pathogenic activity in various inflammatory disorders, autoimmune diseases, and cancer. The majority of MIF-triggered pathological conditions are associated with activation of the cell surface receptor CD74. In the absence of small molecule antagonists that directly target CD74, MIF variants and MIF-ligand complexes have served as modulators of CD74 activity. These molecules have been reported to have either antagonistic or agonistic effects against the receptor, although the mechanistic parameters that distinguish the two groups are largely unknown. Through molecular dynamics simulations and NMR experiments, we explored the relationship between MIF's catalytically active N-terminus and the surface residues important for the activation of CD74. We found that the two sites are connected via backbone dynamics that are propagated to the CD74 activation surface of MIF, from the ß2 and ß4 strands. Our results also provide mechanistic evidence that explain the functional characteristics of MIF variants, serving as CD74 agonists or antagonists. Such findings are of high importance for understanding the MIF-induced activation of CD74 as well as for the development of highly potent CD74 therapeutics.

Observation of Magic Number Clusters from Thermal Dissociation Molecular Dynamics Simulations of Lithium Formate Ionic Clusters.

Molecular dynamics (MD) simulations are well positioned to elucidate the aspects of electrospray ionization (ESI) and high-energy collision dissociation (HCD), as well as give insight into processes that involve neutral species that cannot be observed experimentally in ESI, HCD, and collision-induced dissociation (CID). Here, we utilize temperature dissociation molecular dynamics (TDMD) to model the HCD/CID of lithium formate clusters carrying a single positive charge. These simulations successfully reproduce the experimental ESI HCD spectra of lithium formate solutions and also support the existence of magic number clusters (MNCs) that have been observed. The simulations also provide strong evidence that the main fragmentation channel of such clusters involves neutral (LiHCOO)2 dimers.

Fine grained sampling of residue characteristics using molecular dynamics simulation.

In a fine-grained computational analysis of protein structure, we investigated the relationships between a residue's backbone conformations and its side-chain packing as well as conformations. To produce continuous distributions in high resolution, we ran molecular dynamics simulations over a set of protein folds (dynameome). In effect, the dynameome dataset samples not only the states well represented in the PDB but also the known states that are not well represented in the structural database. In our analysis, we characterized the mutual influence among the backbone phi,psi angles with the first side-chain torsion angles (chi(1)) and the volumes occupied by the side-chains. The dependencies of these relationships on side-chain environment and amino acids are further explored. We found that residue volumes exhibit dependency on backbone 2 degrees structure conformation: side-chains pack more densely in extended beta-sheet than in alpha-helical structures. As expected, residue volumes on the protein surface were larger than those in the interior. The first side-chain torsion angles are found to be dependent on the backbone conformations in agreement with previous studies, but the dynameome dataset provides higher resolution of rotamer preferences based on the backbone conformation. All three gauche(-), gauche(+), and trans rotamers show different patterns of phi,psi dependency, and variations in chi(1) value are skewed from their canonical values to relieve the steric strains. By demonstrating the utility of dynameomic modeling on the native state ensemble, this study reveals details of the interplay among backbone conformations, residue volumes and side-chain conformations.

Stabilizing helical polyalanine peptides with negative polarity or charge: capping with cysteine.

Alanine-based peptides are widely known for their propensity to form helices, whether in the gas phase or in aqueous solution. Interactions of substituent groups or peptides with the helical macrodipole may either encourage or discourage the formation or stability of a helix, depending upon the placement of these groups. We report the first study of the inductive stabilization of a number of peptides through electronegative or anionic N-terminal residue capping. Using Charmm27/CMAP equilibrium and replica-exchange (REX) molecular dynamics (MD) simulations with Generalized Born implicit solvation methods, we find that the N-terminal cysteine capping of alanine peptides strongly enhances the helicity, even allowing the helical moiety to remain at temperatures beyond the denaturing temperature. Though the overall number of hydrogen bonds is enhanced, this stabilization seems to occur indirectly through interaction with the helical macrodipole rather than as a direct result of hydrogen bonding involving the cysteine, though the nature of the hydrogen bonding changes.