Influence of Repeats in the Protein Chain on its Aggregation Capacity for ALS-Associated Proteins

Studies of diseases associated with pathological irreversible aggregation of proteins have become of special relevance and attracted the attention of researchers throughout the world because of the appearance of a new conceptual model based on the capacity of some proteins to self-assemble by the prion mechanism. Along with direct prion diseases, such as bovine rabies and Creutzfeldt-Jakob disease in humans, a great number of neurodegenerative disorders associated with the formation of aggregates through the prion mechanism are revealed. These disorders include Alzheimer’s and Parkinson’s diseases, amyotrophic lateral sclerosis, Huntington disease, and mucoviscidosis, some types of diabetes and hereditary cataracts. The listed diseases are caused by transition of a “healthy” protein or peptide molecule from the native conformation to a very stable “pathological” form. In this case, molecules in the “pathological” conformation aggregate specifically, forming amyloid fibrils that can multiply infinitely. An important result of studying the molecular mechanisms of prion diseases and different proteinopathies, associated with the formation of pathological aggregations by the prion mechanism, is the discovery of protein chain regions responsible for their aggregation. The ability to regulate aggregation (fibrillation) of proteins can be the focal tool for the drug development. Herein by the example of 29 RNA-binding proteins with prion-like domains, we demonstrate what role the amino acid repeats in prion-like domains can play. For these proteins, quite different repeats are revealed in the disordered part of the protein chain predicted with bioinformatics methods. Ten proteins of the 29 RNA-binding proteins are involved in the development of some diseases. The prion-like domains of FUS, TAF15, and EWS are critical for the aggregation of proteins associated with human neurodegenerative diseases. Proteins of this family are involved not only in neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS), Huntington disease, spinocerebral ataxy, and dentatorubral pallidoluysian atrophy, but also in the formation of human mixoid liposarcoma. It can be suggested that the presence of a great number of repeats in prion-like domains of RNA-binding proteins can accelerate the formation of a dynamic beta-structure and pathological aggregates, which are crucibles of amyotrophic lateral sclerosis (ALS) pathogenesis

Regions which are Responsible for Swapping are also Responsible for Folding and Misfolding

Domain swapping is a term used to describe a process when two or more protein chains exchange identical structural elements. Some cases of amyloid formation can be explained through a domain swapping mechanism therefore this deserves theoretical consideration and studying. It has been demonstrated that diverse proteins in sequence and structure are able to oligomerize via domain swapping. This allows us to suggest that the exchangeable regions are important in folding and misfolding processes of proteins, i.e. the residues from the swapping regions are typically incorporated into the native structure early during its formation. The modeling of folding of the proteins with swapped domains demonstrates that the regions exchanged in the oligomeric form in most cases are also responsible for folding and misfolding. For 11 out of 17 proteins, swapping regions intersect with the predicted amyloidogenic regions. Moreover, for 10 out of 17 proteins, high Φ-values (>0.5) belong to residues from the swapping regions. Our data confirm that the exchangeable regions are important in folding, misfolding, and domain swapping processes of the proteins, therefore the suggestion that domain swapping can serve as a mechanism for functional interconversion between monomers and oligomers is likely to be correct

KineticDB: a database of protein folding kinetics

We propose here KineticDB, a systematically compiled database of protein folding kinetics, which contains about 90 unique proteins. The main goal of the KineticDB is to provide users with a diverse set of protein folding rates determined experimentally. The search for determinants of protein folding is still in progress, aimed at obtaining a new understanding of the folding process. Comparison with experimental protein folding rates has been the main tool for validation of both theoretical models and empirical relationships during the last 10 years. It is, therefore, necessary to provide a researcher with as much data as possible in a simple and easy-to-use way. At present, the KineticDB contains the results of folding kinetics measurements of single-domain proteins and separate protein domains as well as short peptides without disulfide bonds. It includes data on about 90 unique proteins and many mutants that have been systematically accumulated over the last 10 years and is the largest collection of protein folding kinetic data presented as a database. The KineticDB is available at http://kineticdb.protres.ru/db/index.pl

Kinetics of Amyloid Formation by Different Proteins and Peptides: Polymorphism and Sizes of Folding Nuclei of Fibrils

Aggregation of peptides and proteins into amyloid structure is one of the most intensively studied biological phenomena at the moment. To date, there is no developed theory that would allow one to determine what kind of mechanism presents in the given experiment on the basis of aggregation kinetic data. Debates concerning the mechanism of the amyloid fibrils formation and, in particular, the size of the amyloidogenic nucleus are still going on. We created such a theory on the basis of the kinetics of amyloid aggregates formation. In the presented chapter, theoretical and experimental approaches were employed for studding the process of amyloid formation by different proteins and peptides. The current kinetic models described in this chapter adequately describe the key features of amyloid nucleation and growth

Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle

The potent immunomodulatory, anti-inflammatory and procoagulant properties of the
protein no. 4 secreted from the rat seminal vesicle epithelium (SV-IV) have been
previously found to be modulated by a supramolecular monomer-trimer equilibrium.
More structural details that integrate experimental data into a predictive framework
have recently been reported. Unfortunately, homology modelling and fold-recognition
strategies were not successful in creating a theoretical model of the structural
organization of SV-IV. It was inferred that the global structure of SV-IV is not similar
to any protein of known three-dimensional structure. Reversing the classical approach
to the sequence-structure-function paradigm, in this paper we report on novel
information obtained by comparing physicochemical parameters of SV-IV with two
datasets made of intrinsically unfolded and ideally globular proteins. In addition, we
have analysed the SV-IV sequence by several publicly available disorder-oriented
predictors. Overall, disorder predictions and a re-examination of existing experimental
data strongly suggest that SV-IV needs large plasticity to efficiently interact with the
different targets that characterize its multifaceted biological function and should be
therefore better classified as an intrinsically disordered protein

Disordered Patterns in Clustered Protein Data Bank and in Eukaryotic and Bacterial Proteomes

We have constructed the clustered Protein Data Bank and obtained clusters of chains of different identity inside each cluster, http://bioinfo.protres.ru/st_pdb/. We have compiled the largest database of disordered patterns (141) from the clustered PDB where identity between chains inside of a cluster is larger or equal to 75% (version of 28 June 2010) by using simple rules of selection. The results of these analyses would help to further our understanding of the physicochemical and structural determinants of intrinsically disordered regions that serve as molecular recognition elements. We have analyzed the occurrence of the selected patterns in 97 eukaryotic and in 26 bacterial proteomes. The disordered patterns appear more often in eukaryotic than in bacterial proteomes. The matrix of correlation coefficients between numbers of proteins where a disordered pattern from the library of 141 disordered patterns appears at least once in 9 kingdoms of eukaryota and 5 phyla of bacteria have been calculated. As a rule, the correlation coefficients are higher inside of the considered kingdom than between them. The patterns with the frequent occurrence in proteomes have low complexity (PPPPP, GGGGG, EEEED, HHHH, KKKKK, SSTSS, QQQQQP), and the type of patterns vary across different proteomes, http://bioinfo.protres.ru/fp/search_new_pattern.html

Funnels in Energy Landscapes

Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a "folding funnel" that is concisely defined in terms of energy minima and saddle points, while at the same time conforming to a notion of a "folding funnel" as it is discussed in the protein folding literature.Comment: 6 pages, 3 figures, submitted to European Conference on Complex Systems 200

Multiple Unfolding Intermediates Obtained by Molecular Dynamic Simulations under Stretching for Immunoglobulin-Binding Domain of Protein G

We have studied the mechanical properties of the immunoglobulin-binding domain of protein G at the atomic level under stretching at constant velocity using molecular dynamics simulations. We have found that the unfolding process can occur either in a single step or through intermediate states. Analysis of the trajectories from the molecular dynamic simulations showed that the mechanical unfolding of the immunoglobulin-binding domain of protein G is triggered by the separation of the terminal β-strands and the order in which the secondary-structure elements break is practically the same in two- and multi-state events and at the different extension velocities studied. It is seen from our analysis of 24 trajectories that the theoretical pathway of mechanical unfolding for the immunoglobulin-binding domain of protein G does not coincide with that proposed in denaturant studies in the absence of force

How native state topology affects the folding of Dihydrofolate Reductase and Interleukin-1beta

The overall structure of the transition state and intermediate ensembles experimentally observed for Dihydrofolate Reductase and Interleukin-1beta can be obtained utilizing simplified models which have almost no energetic frustration. The predictive power of these models suggest that, even for these very large proteins with completely different folding mechanisms and functions, real protein sequences are sufficiently well designed and much of the structural heterogeneity observed in the intermediates and the transition state ensembles is determined by topological effects.Comment: Proc. Natl. Acad. Sci. USA, in press (11 pages, 4 color PS figures) Higher resolution PS files can be found at http://www-physics.ucsd.edu/~cecilia/pub_list.htm