Using molecular principal axes for structural comparison: determining the tertiary changes of a FAB antibody domain induced by antigenic binding

Evidence for ligandable sites in structured RNA throughout the Protein Data Bank

RNA has attracted considerable attention as a target for small molecules. However, methods to identify, study, and characterize suitable RNA targets have lagged behind strategies for protein targets. One approach that has received considerable attention for protein targets has been to utilize computational analysis to investigate ligandable "pockets" on proteins that are amenable to small molecule binding. These studies have shown that selected physical properties of pockets are important parameters that govern the ability of a structure to bind to small molecules. This work describes a similar analysis to study pockets on all RNAs in the Protein Data Bank (PDB). Using parameters such as buriedness, hydrophobicity, volume, and other properties, the set of all RNAs is analyzed and compared to all proteins. Considerable overlap is observed between the properties of pockets on RNAs and proteins. Thus, many RNAs are capable of populating conformations with pockets that are likely suitable for small molecule binding. Further, principal moment of inertia (PMI) calculations reveal that liganded RNAs exist in diverse structural space, much of which overlaps with protein structural space. Taken together, these results suggest that complex folded RNAs adopt unique structures with pockets that may represent viable opportunities for small molecule targeting.

Antibody modeling using the prediction of immunoglobulin structure (PIGS) web server [corrected]

Antibodies (or immunoglobulins) are crucial for defending organisms from pathogens, but they are also key players in many medical, diagnostic and biotechnological applications. The ability to predict their structure and the specific residues involved in antigen recognition has several useful applications in all of these areas. Over the years, we have developed or collaborated in developing a strategy that enables researchers to predict the 3D structure of antibodies with a very satisfactory accuracy. The strategy is completely automated and extremely fast, requiring only a few minutes (∼10 min on average) to build a structural model of an antibody. It is based on the concept of canonical structures of antibody loops and on our understanding of the way light and heavy chains pack together.

A systematic comparison of free and bound antibodies reveals binding-related conformational changes

To study structural changes that occur in Abs upon Ag binding, we systematically compared free and bound structures of all 141 crystal structures of the 49 Abs that were solved in these two forms. We found that many structural changes occur far from the Ag binding site. Some of them may constitute a mechanism for the recently suggested allosteric effects in Abs. Within the binding site itself, CDR-H3 is the only element that shows significant binding-related conformational changes; however, this occurs in only one third of the Abs. Beyond the binding site, Ag binding is associated with changes in the relative orientation of the H and L chains in both the variable and constant domains. An even larger change occurs in the elbow angle between the variable and the constant domains, and it is significantly larger for binding of big Ags than for binding of small ones. The most consistent and substantial conformational changes occur in a loop in the H chain constant domain. This loop is implicated in the interaction between the H and L chains, is often intrinsically disordered, and is involved in complement binding. Hence, we suggest that it may have a role in Ab function. These findings provide structural insight into the recently proposed allosteric effects in Abs.