The Sensitivity of Computational Protein Folding to Contact Map Perturbations: The Case of Ubiquitin Folding and Function

Abstract

Ubiquitin is a small model protein, commonly used in protein folding experiments and simulations. We simulated ubiquitin using a well-tested structure-based model coarse-grained to a C α level (C α -SBM) and found that the simulated folding route did not agree with the experimentally observed one. Simulating the C α -SBM with a cutoff contact map, instead of a screened contact map, switched the folding route with the new route matching the experimental route. Thus, the simulated folding of ubiquitin is sensitive to contact map definition. The screened contact map, which is used in folding simulations because it captures protein folding cooperativity, removes contacts in which the atoms in contact are occluded by a third atom and is less sensitive to the value of the cutoff distance in well-packed regions of the protein. In sparsely packed regions, the larger cutoff distance creates bridging contacts between atoms which are separated by voids. Such contacts do not seem to affect the folding of most proteins, including those of the ubiquitin fold. However, the surface of ubiquitin has several protruding functional side chains which naturally create bridging contacts. Together, our results show that subtle structural features of a protein that may not be apparent by mere observation can be identified by comparing folding simulations of SBMs in which these features are differently encoded. When such structural features are preserved for functional reasons, differences in computational folding can be leveraged to identify functional features. Notably, such features are accessible to a gradation of SBMs even in commonly studied proteins such as ubiquitin.

Understanding the Folding Mediated Assembly of the Bacteriophage MS2 Coat Protein Dimers

“…Several single-domain globular proteins similar in size to the CP monomer fold cooperatively, ,− that is, only two equi-free-energetic basins (folded and unfolded) are populated at T f with a barrier separating them. However, simulations of CP (Figure A) showed that a single partially folded basin (Figure C), whose position shifted with simulation temperature (Figure S1), was populated.…”

Intersubunit Assisted Folding of DNA Binding Domains in Dimeric Catabolite Activator Protein

“…The criteria used to generate the contact map have been known to influence the folding pathway. 43 The native state contact map was generated for the crystal structure of apo CAP stored in PDB ID 3FWE (Figure 1), after mutating the leucine at position 138 to aspartic acid using VMD. The structure of wild type apo CAP (3HIF) was not chosen because of its lower resolution and missing electron density for the important hinge region residues.…”

“…The geometric occlusion criteria consider all residues (only Cα atoms in this case) within a cutoff distance of 6 Å to be in contact and then removes any contact which is geometrically obstructed (where atoms are interacting via intervening atoms). The criteria used to generate the contact map have been known to influence the folding pathway . The native state contact map was generated for the crystal structure of apo CAP stored in PDB ID 3FWE (Figure ), after mutating the leucine at position 138 to aspartic acid using VMD.…”

Successes and challenges in simulating the folding of large proteins

“…Different flavors of Gō models have been tested on a few proteins, and for the most part, as long as little to no frustration in the form of nonnative interactions is encoded, diverse features of protein folding calculated from the different models are both similar to each other and to experimental results (15,60,61). However, functional regions of proteins can be either energetically or topologically frustrated, and in such cases, different unfrustrated Gō models can give different folding features (62,63), and energetic frustration in the form of nonnative interactions ( Fig. 2) needs to be explicitly included in the model (54, 64 -66).…”