Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

Navigating Among Known Structures in Protein Space

Present-day protein space is the result of 3.7 billion years of evolution, constrained by the underlying physicochemical qualities of the proteins. It is difficult to differentiate between evolutionary traces and effects of physicochemical constraints. Nonetheless, as a rule of thumb, instances of structural reuse, or focusing on structural similarity, are likely attributable to physicochemical constraints, whereas sequence reuse, or focusing on sequence similarity, may be more indicative of evolutionary relationships. Both types of relationships have been studied and can provide meaningful insights to protein biophysics and evolution, which in turn can lead to better algorithms for protein search, annotation, and maybe even design.In broad strokes, studies of protein space vary in the entities they represent, the similarity measure comparing these entities, and the representation used. The entities can be, for example, protein chains, domains, supra-domains, or smaller protein sub-parts denoted themes. The measures of similarity between the entities can be based on sequence, structure, function, or any combination of these. The representation can be global, encompassing the whole space, or local, focusing on a particular region surrounding protein(s) of interest. Global representations include lists of grouped proteins, protein networks, and maps. Networks are the abstraction that is derived most directly from the similarity data: each node is the protein entity (e.g., a domain), and edges connect similar domains. Selecting the entities, the similarity measure, and the abstraction are three intertwined decisions: the similarity measures allow us to identify the entities, and the selection of entities influences what is a meaningful similarity measure. Similarly, we seek entities that are related to each other in a way, for which a simple representation describes their relationships succinctly and accurately. This chapter will cover studies that rely on different entities, similarity measures, and a range of representations to better understand protein structure space. Scholars may use publicly available navigators offering a global representation, and in particular the hierarchical classifications SCOP, CATH, and ECOD, or a local representation, which encompass structural alignment algorithms. Alternatively, scholars can configure their own navigator using existing tools. To demonstrate this DIY (do it yourself) approach for navigating in protein space, we investigate substrate-binding proteins. By presenting sequence similarities among this large and diverse protein family as a network, we can infer that one member (pdb ID 4ntl; of yet unknown function) may bind methionine and suggest a putative binding mechanism.

Correlating topology and thermodynamics to predict protein structure sensitivity to point mutations

The relation between distribution of hydrophobic amino acids along with protein chains and their structure is far from being completely understood. No reliable method allowsab initioprediction of the folded structure from this distribution of physicochemical properties, even when they are highly degenerated by considering only two classes: hydrophobic and polar. Establishment of long-range hydrophobic three dimension (3D) contacts is essential for the formation of the nucleus, a key process in the early steps of protein folding. Thus, a large number of 3D simulation studies were developed to challenge this issue. They are nowadays evaluated in a specific chapter of the molecular modeling competition, Critical Assessment of Protein Structure Prediction. We present here a simulation of the early steps of the folding process for 850 proteins, performed in a discrete 3D space, which results in peaks in the predicted distribution of intra-chain noncovalent contacts. The residues located at these peak positions tend to be buried in the core of the protein and are expected to correspond to critical positions in the sequence, important both for folding and structural (or similarly, energetic in the thermodynamic hypothesis) stability. The degree of stabilization or destabilization due to a point mutation at the critical positions involved in numerous contacts is estimated from the calculated folding free energy difference between mutated and native structures. The results show that these critical positions are not tolerant towards mutation. This simulation of the noncovalent contacts only needs a sequence as input, and this paper proposes a validation of the method by comparison with the prediction of stability by well-established programs.

Strategies for designing non-natural enzymes and binders

The design of tailor-made enzymes is a major goal in biochemical research that can result in wide-range applications and will lead to a better understanding of how proteins fold and function. In this review we highlight recent advances in enzyme and small molecule binder design. A focus is placed on novel strategies for the design of scaffolds, developments in computational methods, and recent applications of these techniques on receptors, sensors, and enzymes. Further, the integration of computational and experimental methodologies is discussed. The outlined examples of designed enzymes and binders for various purposes highlight the importance of this topic and underline the need for tailor-made proteins.

Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold

There are around 100 varieties of outer membrane proteins in each Gram-negative bacteria. All of these proteins have the same fold-an up-down β-barrel. It has been suggested that all membrane β-barrels excluding lysins are homologous. Here we suggest that β-barrels of efflux pumps have converged on this fold as well. By grouping structurally solved outer membrane β-barrels (OMBBs) by sequence we find that the membrane environment may have led to convergent evolution of the barrel fold. Specifically, the lack of sequence linkage to other barrels coupled with distinctive structural differences, such as differences in strand tilt and barrel radius, suggest that the outer membrane factor of efflux pumps evolutionarily converged on the barrel. Rather than being related to other OMBBs, sequence and structural similarity in the periplasmic region of the outer membrane factor of efflux pumps suggests an evolutionary link to the periplasmic subunit of the same pump complex.

Diversity and motif conservation in protein 3D structural landscape: exploration by a new multivariate simulation method

In this paper, diversity and conservation in the 'landscape' of random variation of protein tertiary structures are explored for quantitative feature-vector models of major types of functionally important 3D structural motifs. For this, I have deployed a recently developed nonparametric regression (NPR)-based multidimensional copula method of simulation. Apart from improved accuracy of multidimensional random sample generation, the simulation provides additional insight into diversity in the protein structural landscape in terms of random variation in the feature-vector. It shows the relative importance of several features, with biological implications, in conservation of motifs. Mapping of this landscape in distance-preserving 2D eigenspace also shows consistency in demarcation of different motif classes and preservation of their characteristic patterns in this 2D space.