Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding

Molecular Dynamics Simulation Study on Allosteric Regulation of CD44-Hyaluronan Binding as a Force Sensing Mechanism

CD44 protein exists on surfaces of a variety of human cells, acts as a receptor for the hyaluronan (HA) molecule, and mediates cell adhesion via the HA binding in leukocyte trafficking, cell rolling, and so on. The molecular structures of both CD44 and HA are well known, and the previous work shows that the external-mechanical force induces the partially disordered (PD) conformation from the ordered (O) conformation of CD44. The PD conformation has the higher HA affinity compared to the O conformation. However, the details of force-sensing mechanics have remained unclear. This study provides new insights into allosteric regulation of HA binding by conformational shift from the O to the PD conformation of the CD44 HA binding domain by using the classical molecular dynamics simulations. The O conformation was more favorable than the PD conformation under the equilibrium state, and the O conformation showed weak HA-binding affinity. Our simulation suggests that the PD conformation induced by the external force can refold to a compact structure similar to the O conformation keeping the bound HA. This new conformation showed a higher affinity than the O and PD conformations. Our results show that the unfolding of a remote disordered region from the ligand binding site by the external force allosterically regulates the HA affinity. This study promotes understanding not only the mechanism of CD44-mediated cell rolling but also the allosteric regulation induced by the external mechanical force.

Computer-aided antibody design

Recent clinical trials using antibodies with low toxicity and high efficiency have raised expectations for the development of next-generation protein therapeutics. However, the process of obtaining therapeutic antibodies remains time consuming and empirical. This review summarizes recent progresses in the field of computer-aided antibody development mainly focusing on antibody modeling, which is divided essentially into two parts: (i) modeling the antigen-binding site, also called the complementarity determining regions (CDRs), and (ii) predicting the relative orientations of the variable heavy (V(H)) and light (V(L)) chains. Among the six CDR loops, the greatest challenge is predicting the conformation of CDR-H3, which is the most important in antigen recognition. Further computational methods could be used in drug development based on crystal structures or homology models, including antibody-antigen dockings and energy calculations with approximate potential functions. These methods should guide experimental studies to improve the affinities and physicochemical properties of antibodies. Finally, several successful examples of in silico structure-based antibody designs are reviewed. We also briefly review structure-based antigen or immunogen design, with application to rational vaccine development.

Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

The human APOBEC3G protein (A3G) is a single-stranded DNA deaminase that inhibits the replication of retrotransposons and retroviruses, including HIV-1. Atomic details of A3G’s catalytic mechanism have started to emerge, as the structure of its catalytic domain (A3Gctd) has been revealed by NMR and X-ray crystallography. The NMR and crystal structures are similar overall; however, differences are apparent for β2 strand (β2) and loops close to the catalytic site. To add some insight into these differences and to better characterize A3Gctd dynamics, we calculated its free energy profile by using the Generalized-Born surface area (GBSA) method accompanied with a molecular dynamics simulation. The GBSA method yielded an enthalpy term for A3Gctd’s free energy, and we developed a new method that takes into account the distribution of the protein’s dihedral angles to calculate its entropy term. The structure solved by NMR was found to have a lower energy than that of the crystal structure, suggesting that this conformation is dominant in solution. In addition, β2-loop-β2’ configuration was stable throughout a 20-ns molecular dynamics (MD) simulation. This finding suggests that in solution A3Gctd is not likely to adopt the continuous β2 strand configuration present in the APOBEC2 crystal structure. In the NMR structure, the solvent water accessibility of the catalytic Zn²⁺ was limited throughout the 20-ns MD simulation. This result explains previous observations in which A3G did not bind or catalyze single cytosine nucleotide, even when at excessive concentrations.