Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly

Abstract

Conspectus Are all protein interactions fully optimized? Do suboptimal interactions compromise specificity? What is the functional impact of frustration? Why does evolution not optimize some contacts? Proteins and their complexes are best described as ensembles of states populating an energy landscape. These ensembles vary in breadth from narrow ensembles clustered around a single average X-ray structure to broader ensembles encompassing a few different functional “taxonomic” states on to near continua of rapidly interconverting conformations, which are called “fuzzy” or even “intrinsically disordered”. Here we aim to provide a comprehensive framework for confronting the structural and dynamical continuum of protein assemblies by combining the concepts of energetic frustration and interaction fuzziness. The diversity of the protein structural ensemble arises from the frustrated conflicts between the interactions that create the energy landscape. When frustration is minimal after folding, it results in a narrow ensemble, but residual frustrated interactions result in fuzzy ensembles, and this fuzziness allows a versatile repertoire of biological interactions. Here we discuss how fuzziness and frustration play off each other as proteins fold and assemble, viewing their significance from energetic, functional, and evolutionary perspectives. We demonstrate, in particular, that the common physical origin of both concepts is related to the ruggedness of the energy landscapes, intramolecular in the case of frustration and intermolecular in the case of fuzziness. Within this framework, we show that alternative sets of suboptimal contacts may encode specificity without achieving a single structural optimum. Thus, we demonstrate that structured complexes may not be optimized, and energetic frustration is realized via different sets of contacts leading to multiplicity of specific complexes. Furthermore, we propose that these suboptimal, frustrated, or fuzzy interactions are under evolutionary selection and expand the biological repertoire by providing a multiplicity of biological activities. In accord, we show that non-native interactions in folding or interaction landscapes can cooperate to generate diverse functional states, which are essential to facilitate adaptation to different cellular conditions. Thus, we propose that not fully optimized structures may actually be beneficial for biological activities of proteins via an alternative set of suboptimal interactions. The importance of such variability has not been recognized across different areas of biology. This account provides a modern view on folding, function, and assembly across the protein universe. The physical framework presented here is applicable to the structure and dynamics continuum of proteins and opens up new perspectives for drug design involving not fully structured, highly dynamic protein assemblies.

Fuzzy RNA-recognition by theTrypanosoma bruceieditosome

“…Especially in situations in which proteins or protein complexes are required to respond to changing cellular conditions by scanning large ensembles of different RNA-molecules (Järvelin et al, 2016). As such, our finding represents a logical extension of the fuzzy protein theory for disordered proteins (Fuxreiter, 2020) by merging the fuzziness and frustration concepts in the energy landscape of proteins with that of RNA-molecules (Gianni et al, 2021). As much as frustration in fuzzy protein/protein complexes causes a multiplicity of specific interactions (Freiberger et al, 2021; Ferreiro et al, 2014) it is conceivable that frustration in RNA/protein complexes is responsible for the observed non-binary pre-mRNA-binding characteristics of the T. brucei editosome.…”

A Glimpse into the Structural Properties of the Intermediate and Transition State in the Folding of Bromodomain 2 Domain 2 by Φ Value Analysis

“…Although, for two of them (A380G and L381A), the ΔΔ G was very low (<0.6 kcal/mol), thus precluding a reliable interpretation, the high Φ values of A439G (located in the C-terminal helix αC and establishing contacts with F372 in the ZA loop) observed for both the intermediate and TS2 suggest that this residue is involved in non-native interactions in both of these meta-stable states. Non-native interactions, as probed by unusual Φ values, have been found in other proteins, and it has been observed that they are often present in regions stabilizing folding intermediates [ 19 ] or in regions that are crucial for the function of the protein, such as the protein surfaces involved in recognition and binding [ 18 , 20 ]. In this context, it is interesting to note that the conformational plasticity of the ZA loop of BRDs, evidenced by molecular dynamics simulations, has been recently proposed to provide the necessary malleable interaction surface of the BRD domains to interact with their different target peptides [ 21 ].…”

The dynamic properties of a nuclear coactivator binding domain are evolutionarily conserved

“…Going into details of the NMR model, we note that while overall structure is robust to errors in the predicted sequence as shown by the comparison of the NMR models of free NCBD D/P ML and NCBD D/P AltAll , there are differences in for example helix orientations. Globular domains with a sequence identity as high as these NCBD variants (77-88%) would typically have identical structures due to a highly funneled energy landscape ( 40, 41 ), while proteins with larger structural heterogeneity have less funneled landscapes ( 1 ). Indeed, the differences between the structures of NCBD Human , NCBD D/P ML and NCBD D/P AltAll , in particular regarding the angles of the helices in relation to each other, are consistent with a less funneled energy landscape resulting in conformational heterogeneity ( 11 ).…”

“…Evolution has shaped proteins into a wide spectrum of structure, stability and dynamics, with fully disordered proteins at one end of the scale and well-folded globular proteins at the other one ( 1 ). It is becoming clear that dynamic properties per se are important for protein function ( 1–3 ) but it is not trivial to prove that the dynamics are essential for biological function and not merely a general property of proteins. The Nuclear Coactivator Binding Domain (NCBD) is a small (approximately 50 residues) domain from CREB-binding protein (CBP, also called CREBBP), which is a transcriptional coactivator with histone acetylase activity and present in all animals ( 4 ).…”