Non-local residue-residue contacts in proteins are more conserved than local ones.

Non-covalent residue-residue contacts drive the folding of proteins and stabilize them. They may be local-i.e. involve residues that are close in sequence, or non-local. It has been suggested that, in most proteins, local contacts drive protein folding by providing crucial constraints of the conformational space, thus allowing proteins to fold. We compared residues that are involved in local contacts to residues that are involved in non-local contacts and found that, in most proteins, residues in non-local contacts are significantly more conserved evolutionarily than residues in local contacts. Moreover, non-local contacts are more structurally conserved: a contact between positions that are distant in sequence is more likely to exist in many structural homologues compared with a contact between positions that are close in sequence. These results provide new insights into the mechanisms of protein folding and may allow for better prediction of critical intra-chain contacts.

Trade-off between positive and negative design of protein stability: from lattice models to real proteins.

Two different strategies for stabilizing proteins are (i) positive design in which the native state is stabilized and (ii) negative design in which competing non-native conformations are destabilized. Here, the circumstances under which one strategy might be favored over the other are explored in the case of lattice models of proteins and then generalized and discussed with regard to real proteins. The balance between positive and negative design of proteins is found to be determined by their average "contact-frequency", a property that corresponds to the fraction of states in the conformational ensemble of the sequence in which a pair of residues is in contact. Lattice model proteins with a high average contact-frequency are found to use negative design more than model proteins with a low average contact-frequency. A mathematical derivation of this result indicates that it is general and likely to hold also for real proteins. Comparison of the results of correlated mutation analysis for real proteins with typical contact-frequencies to those of proteins likely to have high contact-frequencies (such as disordered proteins and proteins that are dependent on chaperonins for their folding) indicates that the latter tend to have stronger interactions between residues that are not in contact in their native conformation. Hence, our work indicates that negative design is employed when insufficient stabilization is achieved via positive design owing to high contact-frequencies.

Assessment of CASP8 structure predictions for template free targets.

The biennial CASP experiment is a crucial way to evaluate, in an unbiased way, the progress in predicting novel 3D protein structures. In this article, we assess the quality of prediction of template free models, that is, ab initio prediction of 3D structures of proteins based solely on the amino acid sequences, that is, proteins that did not have significant sequence identity to any protein in the Protein Data Bank. There were 13 targets in this category and 102 groups submitted predictions. Analysis was based on the GDT_TS analysis, which has been used in previous CASP experiments, together with a newly developed method, the OK_Rank, as well as by visual inspection. There is no doubt that in recent years many obstacles have been removed on the long and elusive way to deciphering the protein-folding problem. Out of the 13 targets, six were predicted well by a number of groups. On the other hand, it must be stressed that for four targets, none of the models were judged to be satisfactory. Thus, for template free model prediction, as evaluated in this CASP, successes have been achieved for most targets; however, a great deal of research is still required, both in improving the existing methods and in development of new approaches.

Assessment of disorder predictions in CASP8.

The interest in intrinsically disordered proteins has greatly increased, as it has become clear that they are very widespread, especially in eukaryotic organisms. Functionally, they appear to play a significant role in the control of many cellular processes and signalling pathways and have been, also, associated with a number of diseases ranging from cancer to Alzheimer's. Thus, there is enormous interest in attempts to predict disordered regions in proteins solely from knowledge of their amino acid sequences. In this study, we assess the quality of predictions for 25 groups on predicting disordered regions in 122 target proteins. In addition, we suggest the need of a "knowledge-independent" measure that would enable one to normalize the results of the different CASP experiments and to determine whether the disorder prediction field had improved across the years.

Analysing the origin of long-range interactions in proteins using lattice models.

BACKGROUND: Long-range communication is very common in proteins but the physical basis of this phenomenon remains unclear. In order to gain insight into this problem, we decided to explore whether long-range interactions exist in lattice models of proteins. Lattice models of proteins have proven to capture some of the basic properties of real proteins and, thus, can be used for elucidating general principles of protein stability and folding. RESULTS: Using a computational version of double-mutant cycle analysis, we show that long-range interactions emerge in lattice models even though they are not an input feature of them. The coupling energy of both short- and long-range pairwise interactions is found to become more positive (destabilizing) in a linear fashion with increasing 'contact-frequency', an entropic term that corresponds to the fraction of states in the conformational ensemble of the sequence in which the pair of residues is in contact. A mathematical derivation of the linear dependence of the coupling energy on 'contact-frequency' is provided. CONCLUSION: Our work shows how 'contact-frequency' should be taken into account in attempts to stabilize proteins by introducing (or stabilizing) contacts in the native state and/or through 'negative design' of non-native contacts.

Low folding propensity and high translation efficiency distinguish in vivo substrates of GroEL from other Escherichia coli proteins.

MOTIVATION: Theoretical considerations have indicated that the amount of chaperonin GroEL in Escherichia coli cells is sufficient to fold only approximately 2-5% of newly synthesized proteins under normal physiological conditions, thereby suggesting that only a subset of E.coli proteins fold in vivo in a GroEL-dependent manner. Recently, members of this subset were identified in two independent studies that resulted in two partially overlapping lists of GroEL-interacting proteins. The objective of the work described here was to identify sequence-based features of GroEL-interacting proteins that distinguish them from other E.coli proteins and that may account for their dependence on the chaperonin system. RESULTS: Our analysis shows that GroEL-interacting proteins have, on average, low folding propensities and high translation efficiencies. These two properties in combination can increase the risk of aggregation of these proteins and, thus, cause their folding to be chaperonin-dependent. Strikingly, we find that these properties are absent in proteins homologous to the E.coli GroEL-interacting proteins in Ureaplasma urealyticum, an organism that lacks a chaperonin system, thereby confirming our conclusions.