Who solved the protein folding problem?

For the third time, techniques for the prediction of three-dimensional structures of proteins were critically assessed in a worldwide blind test. Steady progress is undeniable. How did this happen and what are the implications?     

The posttranslational concept of protein folding: how valid is it?

Two concepts of protein folding are known. One of them, the cotranslational concept, states that a protein folds during the synthesis of the polypeptide chain on the ribosome. According to the other, the posttranslational concept, the protein starts to fold just after the synthesis of its polypeptide chain. This article attempts to show that the posttranslational concept is hardly suited to solve the problem of protein folding. In our opinion, polypeptide chains cannot be represented as random coils. They are stiff chain-like macromolecules rather than flexible ones: the single bond rotational barriers of a polypeptide substantially exceed the accepted standard values; even in strong denaturing conditions, a protein possesses a considerable amount of residual folded structures. We believe that the popular "hierarchical" models for the protein folding mechanism are not realistic because the formation of secondary and tertiary structures of proteins occurs simultaneously and cooperatively. The time for the elongation of a polypeptide chain by one amino acid residue during biosynthesis exceeds considerably the time of the formation of alpha-helices and beta-sheets in proteins as well as the time supposed for the spatial structure formation of a native protein during renaturation. Thus, we believe that the mechanism of protein folding in vivo cannot be clarified by denaturation-renaturation experiments. In our opinion, the phenomenon of protein renaturation is no more than the restoration of native protein conformation (which initially forms cotranslationally) disrupted during denaturation, and thus denaturation-renaturation experiments cannot serve as a model to clarify the mechanism of protein folding.     

Are synthetic proteins relevant to the problem of protein folding?

The possibility to derive the analogs of native proteins by the chemical synthesis is considered to be a serious argument for the concept of posttranslational protein folding. The present paper analyzes for the first time chemically synthesized proteins to reveal whether they are relevant to the problem of protein folding. The results enable the following conclusions to be drawn. The acquisition of the peculiar conformations by the chemically synthesized proteins to exhibit the specific functions is conditioned by the highly marked features of the secondary and tertiary structures of the corresponding native proteins. These features will make themselves evident only if favorable conditions are carefully chosen during the experiments for each individual protein. Thus, in our opinion, the possibility to derive a synthetic protein is hardly evidence for the posttranslational folding of proteins.     

2D protein electrophoresis: can it be perfected?

23 years after O'Farrel developed two-dimensional gel electrophoresis we still debate if the technique can be improved, or if there are other alternative separation technologies that can challenge its central position in proteomic projects. These questions are relevant as the pharmaceutical industry expects proteomic studies to provide novel protein targets for drug discovery and diagnostics. In our opinion, there are various aspects of the technology that can be improved, including resolution, sample preparation and detection, but so far there is no alternative technique(s) available, or any under development, that can replace it.     

SH2 domain inhibition: a problem solved?

The past two years have witnessed a number of significant advances in the design of SH2 inhibitors of both Src and Grb2. For Src, several non-peptide templates have been developed with high affinity, and one case, in the context of bone-binding phosphotyrosine bioisostere, has yielded an in vivo active antiresorptive agent. Similarly, high-affinity Grb2 SH2 inhibitors with novel phosphotyrosine replacements have now been reported that demonstrate, for the first time, cellular activities consistent with an anticancer agent.     

The PacELF programme: will mass drug administration be enough?

The Pacific Programme to Eliminate Lymphatic Filariasis is a regional, mass drug administration-based campaign in 22 countries and territories with the aim of eliminating filariasis transmission and alleviating the suffering caused by Wuchereria bancrofti. The challenges to filariasis elimination campaigns based on mass drug-administration alone are reviewed in this article. These challenges together with the previous successes of mosquito control campaigns in eliminating filariasis from regions in the Pacific argue for inclusion of entomology components in the control of filariasis and the monitoring of filariasis elimination programs.     

The protein folding transition state: what are Phi-values really telling us?

Protein engineering-based studies of the folding transition state have accelerated significantly in the last decade, and more than a half dozen proteins have been subjected to extensive Phi-value analysis. A general picture is emerging from these studies of a transition state in which the large majority of experimentally characterized side chains participate in relatively homogeneous and energetically weak interactions playing only a relatively small role in defining relative folding rates.     

Is the unfolded state the Rosetta Stone of the protein folding problem?

Solving the protein folding problem is one of the most challenging tasks in the post genomic era. Identification of folding-initiation sites is very important in order to understand the protein folding mechanism. Detection of residual structure in unfolded proteins can yield important clues to the initiation sites in protein folding. A substantial number of studied proteins possess residual structure in hydrophobic regions clustered together in the protein core. These stable structures can work as seeds in the folding process. In addition, local preferences for secondary structure in the form of turns for beta-sheet initiation and helical turns for alpha-helix formation can guide the folding reaction. In this respect the unfolded states, studied at increasing structural resolution, can be the Rosetta Stone of the protein folding problem.     

Is protein folding rate dependent on number of folding stages? Modeling of protein folding with ferredoxin-like fold

Statistical analysis of protein folding rates has been done for 84 proteins with available experimental data. A surprising result is that the proteins with multi-state kinetics from the size range of 50–100 amino acid residues (a.a.) fold as fast as proteins with two-state kinetics from the same size range. At the same time, the proteins with two-state kinetics from the size range 101–151 a.a. fold faster than those from the size range 50–100 a.a. Moreover, it turns out unexpectedly that usually in the group of structural homologs from the size range 50–100 a.a., proteins with multi-state kinetics fold faster than those with two-state kinetics. The protein folding for six proteins with a ferredoxin-like fold and with a similar size has been modeled using Monte Carlo simulations and dynamic programming. Good correlation between experimental folding rates, some structural parameters, and the number of Monte Carlo steps has been obtained. It is shown that a protein with multi-state kinetics actually folds three times faster than its structural homologs.     

Testing the intermediate disturbance hypothesis: when will there be two peaks of diversity?

Succession after disturbances generates a mosaic of patches in different successional stages. The intermediate disturbance hypothesis predicts that intermediate disturbances lead to the highest diversity of these stages on a regional scale resulting in a hump‐shaped diversity–disturbance curve. We tested this prediction using field data of forest succession and hypothetical succession scenarios in combination with analytical and simulation models. According to our study the main factors shaping the diversity–disturbance curve and the position of the diversity maximum were the transition times between the successional stages, the transition type, neighbourhood effects and the choice of diversity measure. Although many scenarios confirmed the intermediate disturbance hypothesis we found that deviations in the form of two diversity maximums were possible. Such bimodal diversity–disturbance curves occurred when early and late successional stages were separated by one or more long‐lived (compared to the early stages) intermediate successional stages. Although the field data which met these conditions among all those tested were rare (one of six), the consequences of detecting two peaks are fundamental. The impact of disturbances on biodiversity can be complex and deviate from a hump‐shaped curve.     

How do cofactors modulate protein folding?

Cofactors are essential components of many proteins for biological activity. Characterization of several cofactor-binding proteins has shown that cofactors often have the ability to interact specifically with the unfolded polypeptides. This suggests that cofactor-coordination prior to polypeptide folding may be a relevant path in vivo. By binding before folding, the cofactor may affect both the mechanism and speed of folding. Here, we discuss three different cofactors that modulate protein-folding processes in vitro.     

Lateral gene transfer: when will adolescence end?

The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fuelled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints probably stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Here, we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.