Characterizing and Predicting Protein Hinges for Mechanistic Insight

Abstract

The functioning of proteins requires highly specific dynamics, which depend critically on the details of how amino acids are packed. Hinge motions are the most common type of large motion, typified by the opening and closing of enzymes around their substrates. The packing and geometries of residues are characterized here by graph theory. This characterization is sufficient to enable reliable hinge predictions from a single static structure, and notably, this can be from either the open or the closed form of a structure. This new method to identify hinges within protein structures is called PACKMAN. The predicted hinges are validated by using permutation tests on B-factors. Hinge prediction results are compared against lists of manually-curated hinge residues, and the results suggest that PACKMAN is robust enough to reproduce the known conformational changes and is able to predict hinge regions equally well from either the open or the closed forms of a protein. A group of 167 protein pairs with open and closed structures has been investigated Examples are shown for several additional proteins, including Zika virus non-structured (NS) proteins where there are 6 hinge regions in the NS5 protein, 5 hinge regions in the NS2B bound in the NS3 protease complex and 5 hinges in the NS3 helicase protein. Results obtained from this method can be important for generating conformational ensembles of protein targets for drug design. PACKMAN is freely accessible at (https://PACKMAN.bb.iastate.edu/).

Structural compliance: A new metric for protein flexibility

“…Protein packing is a multiscale phenomenon, which influences the local and global dynamics of the protein. It is often informative to study which parts of a protein are so densely packed as to be completely immobile and which are less dense, where internal movements are possible, to make conclusions about the mechanism and function of the protein 22 . The compliance and stiffness maps proposed in this paper can serve as another way to study protein packing.…”

“…The compliance and stiffness profiles can help us to determine the dynamic communities 32‐34 and to coarse‐grain them for further analysis. We can use a hinge prediction method (PACKMAN 22 ) based on packing densities to identify the hinges in the parts of the protein that tend to be more flexible, making these sites responsible for the global deformability. Therefore, if these regions are predicted to be hinges and show high compliance values, they can most likely represent global deformability, whereas local deformability occurs otherwise.…”

“…Other comparisons have been made between sets of experimental structures and the computed normal modes 20,21 . Khade et al 22 recently used the experimental B‐factors to verify a packing‐based method for the prediction of the flexible and rigid parts of proteins.…”

“…The software for the calculation of compliance and stiffness values has been inserted into the PACKMAN package, developed by Khade et al, 22 which is an open‐source Python‐based package and can be freely accessed at https://jerniganlab.github.io/Software/PACKMAN/Tutorials/compliance.…”

A novel measure to analyze protein structures: Aspect ratio in protein alpha shapes

“…10,11 In the field of structural biology, earliest applications of alpha shapes are the computations of the molecular area and volume of macromolecules and detection of the inaccessible cavities in proteins. 12,13 Alpha shapes are recently used by Khade et al 14 to identify the hinge locations within protein structures.…”