Evolutionary conservation in protein folding kinetics

The sequence and structural conservation of folding transition states have been predicted on theoretical grounds. Using homologous sequence alignments of proteins previously characterized via coupled mutagenesis/kinetics studies, we tested these predictions experimentally. Only one of the six appropriately characterized proteins exhibits a statistically significant correlation between residues' roles in transition state structure and their evolutionary conservation. However, a significant correlation is observed between the contributions of individual sequence positions to the transition state structure across a set of homologous proteins. Thus the structure of the folding transition state ensemble appears to be more highly conserved than the specific interactions that stabilize it.     

Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation

To what extent does natural selection act to optimize the details of protein folding kinetics? In an effort to address this question, the relationship between an amino acid's evolutionary conservation and its role in protein folding kinetics has been investigated intensively. Despite this effort, no consensus has been reached regarding the degree to which residues involved in native-like transition state structure (the folding nucleus) are conserved. Here we report the results of an exhaustive, systematic study of sequence conservation among residues known to participate in the experimentally (Phi-value) defined folding nuclei of all of the appropriately characterized proteins reported to date. We observe no significant evidence that these residues exhibit any anomalous sequence conservation. We do observe, however, a significant bias in the existing kinetic data: the mean sequence conservation of the residues that have been the subject of kinetic characterization is greater than the mean sequence conservation of all residues in 13 of 14 proteins studied. This systematic experimental bias gives rise to the previous observation that the median conservation of residues reported to participate in the folding nucleus is greater than the median conservation of all of the residues in a protein. When this bias is corrected (by comparing, for example, the conservation of residues known to participate in the folding nucleus with that of other, kinetically characterized residues) the previously reported preferential conservation is effectively eliminated. In contrast to well-established theoretical expectations, both poorly and highly conserved residues are apparently equally likely to participate in the protein-folding nucleus.     

A new method for quantifying residue conservation and its applications to the protein folding nucleus

The conservation of residues in columns of a multiple sequence alignment (MSA) reflects the importance of these residues for maintaining the structure and function of a protein. To date, many scores have been suggested for quantifying residue conservation, but none has achieved the full rigor both in biology and statistics. In this paper, we present a new approach for measuring the evolutionary conservation at aligned positions. Our conservation measure is related to the logarithmic probabilities for aligned positions, and combines the physicochemical properties and the frequencies of amino acids. Such a measure is both biologically and statistically meaningful. For testing the relationship between an amino acid's evolutionary conservation and its role in the Phi-value defined protein folding kinetics, our results indicate that the folding nucleus residues may not be significantly more conserved than other residues by using the biological-relevance weighted statistical scoring method suggested in this paper as an alternative to entropy-based procedures.     

Evolutionary Pareto-optimization of stably folding peptides

Background  

As a rule, peptides are more flexible and unstructured than proteins with their substantial stabilizing hydrophobic cores. Nevertheless, a few stably folding peptides have been discovered. This raises the question whether there may be more such peptides that are unknown as yet. These molecules could be helpful in basic research and medicine.     

Evolutionary conservation of domain-domain interactions

Background

Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs.

Results

Here we map structurally derived DDIs onto the cellular PPI networks of different organisms and demonstrate that there is a catalog of domain pairs that is used to mediate various interactions in the cell. We show that these DDIs occur frequently in protein complexes and that homotypic interactions (of a domain with itself) are abundant. A comparison of the repertoires of DDIs in the networks of Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens shows that many DDIs are evolutionarily conserved.

Conclusion

Our results indicate that different organisms use the same 'building blocks' for PPIs, suggesting that the functionality of many domain pairs in mediating protein interactions is maintained in evolution.     

Evolutionary conservation of microtubule-capture mechanisms

The dynamic nature of microtubules allows them to search the three-dimensional space of the cell. But what are they looking for? During cellular morphogenesis, microtubules are captured at sites just under the plasma membrane, and this polarizes the microtubule array and associated organelles. Recent data indicate that the signalling pathways that are involved in regulating the different microtubule cortical interactions are not only conserved between species, but also that they function in diverse processes.     

Evolutionary conservation of domain-domain interactions

Background  

Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs.     

Evolutionary conservation of the membrane fusion machine

Recent structural studies of proteins mediating membrane fusion reveal intriguing similarities between diverse viral and mammalian systems. Particularly striking is the close similarity between the transmembrane envelope glycoproteins from the retrovirus HTLV-1 and the filovirus Ebola. These similarities suggest similar mechanisms of membrane fusion. The model that fits most currently available data suggests fusion activation in viral systems is driven by a symmetrical conformational change triggered by an activation event such as receptor binding or a pH change. The mammalian vesicle fusion mediated by the SNARE protein complex most likely occurs by a similar mechanism but without symmetry constraints.     

Evolutionary ecology and the conservation of biodiversity

Studies on evolving interactions among species and the coevolutionary process have suggested that the conservation of biodiversity requires a broad geographic perspective, if the `interaction biodiversity' of the earth is to be conserved with its species diversity. Continued maintenance of the geographic mosaic of specialization, defense and population structure appears to be crucial to the coevolutionary process and the long-term persistence of some interspecific interactions.     

Evolutionary aspects of protein structure and folding

Four basic stages of evolution of protein structure are described based on recent work of the authors targeted specifically on reconstruction of the earliest events in the protein evolution. According to this reconstruction, the initial stage of short peptides of, probably, only few amino-acid residues had been followed by formation of closed loops of the size 25-30 residues, which corresponds to the polymer-statistically optimal ring closure size for mixed polypeptide chains. The next stage involved fusion of the respective small linear genes and formation of protein structures consisting of several closed loops of the nearly standard size, up to 4-6 loops (100-200 amino acid residues) in a typical protein fold. The last, modern stage began with combinatorial fusion of the presumably circular 300-600 bp DNA units and, accordingly, formation of multidomain proteins.     

Evolutionary aspects of protein structure and folding

The traditional reconstruction of molecular events of the past based on sequence conservation becomes very vague beyond one to two billion years ago. There are certain molecular features, however, such as polymer flexibility and loop closure, that are conserved merely because of their physical nature. This allows one to penetrate the earliest stages of protein evolution.     

Identifying the protein folding nucleus using molecular dynamics

Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model protein into its folded conformation. Amino acid residues participating in those contacts may serve as "accelerator pedals" used by molecular evolution to control protein folding rate.     

Evolutionary conservation of protein vibrational dynamics

The aim of the present work is to study the evolutionary divergence of vibrational protein dynamics. To this end, we used the Gaussian Network Model to perform a systematic analysis of normal mode conservation on a large dataset of proteins classified into homologous sets of family pairs and superfamily pairs. We found that the lowest most collective normal modes are the most conserved ones. More precisely, there is, on average, a linear correlation between normal mode conservation and mode collectivity. These results imply that the previously observed conservation of backbone flexibility (B-factor) profiles is due to the conservation of the most collective modes, which contribute the most to such profiles. We discuss the possible roles of normal mode robustness and natural selection in the determination of the observed behavior. Finally, we draw some practical implications for dynamics-based protein alignment and classification and discuss possible caveats of the present approach.     

Evolutionary conservation of the substrate-binding cleft of phosphoglycerate kinases

The primary structures of six phosphoglycerate kinases (PGKs) are known: three from mammals, one from yeast, and two from trypanosomes. Comparison of the amino acid sequence of these enzymes reveals 154 invariant positions out of 392 positions in the aligned sequences. Most of the conserved positions fall into the twelve beta-sheets and adjacent peptide regions that form the inner loops surrounding the ATP and 3-phosphoglycerate-binding cleft. The homology between mammalian and yeast PGKs is greater than 94% for the inner-loop region, even though the overall homology is less than 65%. Trypanosome PGK has only 44% overall homology with the mammalian enzyme, but shows 74% homology in the inner-loop region. Trypanosome PGK contains a polypeptide segment in its N-terminal domain that is transposed in comparison with the other species.