Protein folding stabilizing time measurement: a direct folding process and three-dimensional random walk simulation

Protein particles undergo Brownian motion and collisions in solution. The diffusive collisions may lead to aggregation. For proteins to fold successfully the process has to occur quickly and before significant collision takes place. The speed of protein folding was deduced by studying the correlation time of a lysozyme refolding process from autocorrelation function analysis of the mean collision time and aggregation/soluble ratio of protein. It is a measure of time before which an aggregate can be formed and also is the time measure for a protein to fold into a stable state. We report on the protein folding stabilizing time of a lysozyme system to be 25.5-27.5 micros (<+/-4%) between 295 and 279K via direct folding experimental studies, supported by a three-dimensional random walk simulation of diffusion-limited aggregation model. Aggregation is suppressed when the protein is folded to a stable form. Spontaneous folding and diffusion-limited aggregation are antagonistic in nature. Meanwhile, the resultant aggresome, suggested by Raman and mass spectroscopy, may be formed by cross-linkages of disulfide bonds and hydrophobic interactions.     

对生物入侵的几点思考

生物入侵涉及异地迁徙及建群等复杂问题,涉及个体、种群、群落、生态系统等生态学的各个层次,又必不可少地要深入地去探索生物入侵过程中的快速进化和分子生态学基础。生物系统的超级复杂性加上环境和人为因素的极度随机性,充分显示了在这一领域从事研究的艰巨性和挑战性。入侵种具有两面性,因此,预防比治理更为关键。为了应对生物入侵,有待建立完善的国家和地区的防控系统、提高技术水平并加强有关诸多经济因素对生物入侵的影响的研究。     

Protein folding: a problem with multiple solutions

There is continued interest in predicting the structure of proteins either at the simplest level of identifying their fold class or persevering all the way to an atomic resolution structure. Protein folding methods have become very sophisticated and many successes have been recorded with claims to have solved the native structure of the protein. But for any given protein, there may be more than one solution. Many proteins can exist in one of the other two (or more) different forms and some populate multiple metastable states. Here, the two-state case is considered and the key structural changes that take place when the protein switches from one state to the other are identified. Analysis of these results show that hydrogen bonding patterns and hydrophobic contacts vary considerably between different conformers. Contrary to what has often been assumed previously, these two types of interaction operate essentially independently of one another. Core packing is critical for proper protein structure and function and it is shown that there are considerable changes in internal cavity volumes in many cases. The way in which these switches are made is fold dependent. Considerations such as these need to be taken into account in protein structure prediction.     

Protein folding

The importance of protein folding in the biosynthesis of proteins is reviewed.     

Protein folding

The problem of protein folding is that how proteins acquire their native unique three‐dimensional structure in the physiological milieu. To solve the problem, the following key questions should be answered: do proteins fold co‐ or post‐translationally, i.e. during or after biosynthesis, what is the mechanism of protein folding, and what is the explanation for fast folding of proteins? The two first questions are discussed in the current review. The general lines are to show that the opinion, that proteins fold after they are synthesized is hardly substantiated and suitable for solving the problem of protein folding and why proteins should fold cotranslationally. A possible tentative model for the mechanism of protein folding is also suggested. To this end, a thorough analysis is made of the biosynthesis, delivery to the folding compartments, and the rates of the biosynthesis, translocation and folding of proteins. A cursory attention is assigned to the role of GroEL/ES‐like chaperonins in protein folding.     

Protein folding disorders: Toward a basic biological paradigm

Mechanistic ‘physics’ models of protein folding fail to account for the observed spectrum and rate of protein folding and aggregation disorders in human populations, showing that more appropriately in vivo paradigms reflecting biological and other embedding contexts are needed for understanding the etiology, prevention, and treatment of these diseases. Here, a topological rate distortion analysis is applied to the problem that is analogous to Tlusty (2007) elegant exploration of the genetic code. A ‘developmental’ perspective sees the rate distortion function as a temperature analog in a spontaneous symmetry breaking argument, and permits incorporation of external factors as catalysts, driving the system to different possible outcomes via a nonequilibrium empirical Onsager treatment, viewed as a kind of dynamic regression equation. The formalism produces large-scale, quasi-equilibrium ‘resilience’ states representing normal and pathological protein folding. Generalization to long times produces diffusion models of protein folding disorders in which epigenetic or life history factors determine the rate of onset of dysfunction.     

Protein folding by 'levels of separation': a hypothesis

The protein folding process has been studied both computationally and experimentally for over 30 years. To date there is no detailed mechanism to explain the formation of long-range interactions between the transition and native states. Long-range interactions are the principle determinants of the tertiary structure. We present a theoretical model which proposes a mechanism for the acquisition of these interactions as they form in a modified version of 'degrees of separation', that we term 'levels of separation'. It is based on the integration of network science and biochemistry.     

Protein folding: simple models for a complex process

Twenty-eight years after its original publication, the diffusion-collision model has successfully been applied to describe the folding kinetics of two proteins with the same native structure but different sequences (Islam et al., this issue of Structure). The calculations show the relative importance of the primary and tertiary structure on the sequence of events and folding. For both proteins, the model suggests parallel folding pathways, a finding which has wide implications for the interpretations of experiments.     

Protein structure and folding: a new start.

Standard building blocks of proteins--closed loops of 25-30 amino acid residues--have been recently discovered and further characterized by combined efforts of several laboratories. New challenging views on the protein structure, folding, and evolution are introduced by these studies. In particular, the role of van der Waals contacts in protein stability is better understood. They can be considered as locks closing the polypeptide chain returns and forming the loop-n-lock elements. The linearity of the arrangement of the standard loops in the proteins has important evolutionary implications. Selection pressure to maintain the loops of nearly standard size is reflected in the protein sequences as characteristic distance between hydrophobic residues, equal to the loop end-to-end distance. Further characterization of the loop-n-lock units reveals several sequence/structure prototypes, which suggests a new basis for protein classification. The following is a review of these studies.     

Protein folding in the cell: reshaping the folding funnel

Models of protein folding have historically focused on a subset of 'well-behaved' proteins that can be successfully refolded from denaturants in vitro. Energy landscapes, including folding funnel 'cartoons', describe the largely uncomplicated folding of these isolated chains at infinite dilution. However, the frequent failure of many polypeptides to fold to their native state requires more comprehensive models of folding to accommodate the crucial role of interactions between partially folded intermediates. By incorporating additional deep minima, which reflect off-pathway interchain interactions, the folding funnel concept can be extended to describe the behavior of a more diverse set of proteins under more physiologically relevant conditions. In particular, the effects of ribosomes (translation), molecular chaperones and other aspects of the cellular environment on early chain conformations can be included to account for the folding behavior of polypeptide chains in cells.     

Protein folding: in vitro studies

Protein folding is a topic of fundamental interest since it concerns the mechanisms by which the genetic information is translated into the three-dimensional and functional structure of proteins. In these post-genomic times, the knowledge of the fundamental principles is required in the exploitation of the information contained in the increasing number of sequenced genomes. Protein folding also has a practical application in the understanding of different pathologies associated with protein misfolding and aggregation. Significant advances have been made ranging from the Anfinsen postulate to the "new view" which describes the folding process in terms of an energy landscape. These insights arise from both theoretical and experimental studies. Unravelling the mechanisms of protein folding represents one of the most challenging problems to day. This is an extremely active field of research involving aspects of biology, chemistry, biochemistry, computer science and physics.     

Protein folding forces

We investigate the average inter-residue folding forces derived from mutational data of the 15 proteins: barstar, barnase, chymotrypsin inhibitor 2 (CI2), Src SH3 domain, spectrin R16 domain, Arc repressor, apo-azurin, cold shock protein B (cspB), C-terminal domain of ribosomal protein L9 (CTL9), FKBP12, α-lactalbumin, colicin E7 immunity protein 7 (IM7), colicin E9 immunity protein 9 (IM9), spectrin R17 domain, and ubiquitin. The residue-specific contributions to folding in most of the 15 protein molecules are highly non-uniformly distributed and are typically about 1 piconewton (pN) per interaction. The strongest folding forces often occur in some of the helices and strands of folding nuclei which suggests that folding nucleation−condensation is partially directed by formation of some secondary structure interactions. The correlation of the energy changes of mutants with inter-residue contact maps of the protein molecules provides a higher resolution than assigning the mutant data to certain positions in the polypeptide strand alone. In contrast to previous Φ-value analysis, we now can partially resolve folding motions. Compaction of at least one α-helix along its axis mediated by internal hydrogen bonds and stabilized by diffuse tertiary structure interactions appears to be one important molecular event during early folding in barstar, CI2, spectrin R16 domain, Arc repressor, α-lactalbumin, IM7, IM9, and spectrin R17 domain. A lateral movement of at least two strands neighbored in sequence towards each other appears to be involved in early folding of the SH3 domain, cspB, CTL9, and FKBP12.