External Force Field for Protein Folding in Chaperonins-Potential Application in In Silico Protein Folding.

The present study discusses the influence of the TRiC chaperonin involved in the folding of the component of reovirus mu1/σ3. The TRiC chaperone is treated as a provider of a specific external force field in the fuzzy oil drop model during the structural formation of a target folded protein. The model also determines the status of the final product, which represents the structure directed by an external force field in the form of a chaperonin. This can be used for in silico folding as the process is environment-dependent. The application of the model enables the quantitative assessment of the folding dependence of an external force field, which appears to have universal application.

Secondary structure in polymorphic forms of alpha-synuclein amyloids.

Numerous Alpha-synuclein amyloid structures available in PDB enable their comparative analysis. They are all characterized by a flat structure of each individual chain with an extensive network of inter-chain hydrogen bonds. The identification of such amyloid fibril structures requires determining the special conditions imposed on the torsion angles. Such conditions have already been formulated by the Authors resulting in the model of idealised amyloid. Here, we investigate the fit of this model in the group of A-Syn amyloid fibrils. We identify and describe the characteristic supersecondary structures in amyloids. Generally, the amyloid transformation is suggested to be the 3D to 2D transformation engaging mostly the loops linking Beta-structural fragments. The loop structure introducing the 3D organisation of Beta-sheet change to flat form (2D) introduces the mutual reorientation of Beta-strands enabling the large-scale H-bonds generation with the water molecules. Based on the model of idealised amyloid we postulate the hypothesis for amyloid fibril formation based on the shaking, an experimental procedure producing the amyloids.

The Possible Mechanism of Amyloid Transformation Based on the Geometrical Parameters of Early-Stage Intermediate in Silico Model for Protein Folding.

The specificity of the available experimentally determined structures of amyloid forms is expressed primarily by the two- and not three-dimensional forms of a single polypeptide chain. Such a flat structure is possible due to the ß structure, which occurs predominantly. The stabilization of the fibril in this structure is achieved due to the presence of the numerous hydrogen bonds between the adjacent chains. Together with the different forms of twists created by the single R- or L-handed α-helices, they form the hydrogen bond network. The specificity of the arrangement of these hydrogen bonds lies in their joint orientation in a system perpendicular to the plane formed by the chain and parallel to the fibril axis. The present work proposes the possible mechanism for obtaining such a structure based on the geometric characterization of the polypeptide chain constituting the basis of our early intermediate model for protein folding introduced formerly. This model, being the conformational subspace of Ramachandran plot (the ellipse path), was developed on the basis of the backbone conformation, with the side-chain interactions excluded. Our proposal is also based on the results from molecular dynamics available in the literature leading to the unfolding of α-helical sections, resulting in the ß-structural forms. Both techniques used provide a similar suggestion in a search for a mechanism of conformational changes leading to a formation of the amyloid form. The potential mechanism of amyloid transformation is presented here using the fragment of the transthyretin as well as amyloid Aß.

Alternative Structures of α-Synuclein.

The object of our analysis is the structure of alpha-synuclein (ASyn), which, under in vivo conditions, associates with presynaptic vesicles. Misfolding of ASyn is known to be implicated in Parkinson's disease. The availability of structural information for both the micelle-bound and amyloid form of ASyn enables us to speculate on the specific mechanism of amyloid transformation. This analysis is all the more interesting given the fact that-Unlike in Aß(1-42) amyloids-only the central fragment (30-100) of ASyn has a fibrillar structure, whereas, its N- and C-terminal fragments (1-30 and 100-140, respectively) are described as random coils. Our work addresses the following question: Can the ASyn chain-as well as the aforementioned individual fragments-adopt globular conformations? In order to provide an answer, we subjected the corresponding sequences to simulations carried out using Robetta and I-Tasser, both of which are regarded as accurate protein structure predictors. In addition, we also applied the fuzzy oil drop (FOD) model, which, in addition to optimizing the protein's internal free energy, acknowledges the presence of an external force field contributed by the aqueous solvent. This field directs hydrophobic residues to congregate near the center of the protein body while exposing hydrophilic residues on its surface. Comparative analysis of the obtained models suggests that fragments which do not participate in forming the amyloid fibril (i.e., 1-30 and 100-140) can indeed attain globular conformations. We also explain the influence of mutations observed in vivo upon the susceptibility of ASyn to undergo amyloid transformation. In particular, the 30-100 fragment (which adopts a fibrillar structure in PDB) is not predicted to produce a centralized hydrophobic core by any of the applied toolkits (Robetta, I-Tasser, and FOD). This means that in order to minimize the entropically disadvantageous contact between hydrophobic residues and the polar solvent, ASyn adopts the form of a ribbonlike micelle (rather than a spherical one). In other words, the ribbonlike micelle represents a synergy between the conformational preferences of the protein chain and the influence of its environment.

Structural analysis of the Aß(11-42) amyloid fibril based on hydrophobicity distribution.

The structure of the Aß(11-42) amyloid available in PDB makes possible the molecular analysis of the specificity of amyloid formation. This molecule (PDB ID 2MVX) is the object of analysis. This work presents the outcome of in silico experiments involving various alternative conformations of the Aß(11-42) sequence, providing clues as to the amylodogenecity of its constituent fragments. The reference structure (PDB) has been compared with folds generated using I-Tasser and Robetta-the strongest contenders in the CASP challenge. Additionally, a polypeptide which matches the Aß(11-42) sequence has been subjected to folding simulations based on the fuzzy oil drop model, which favors the production of a monocentric hydrophobic core. Computer simulations yielded 15 distinct structural forma (five per software package), which, when compared to the experimentally determined structure, allow us to study the role of structural elements which cause an otherwise globular protein to transform into an amyloid. The unusual positions of hydrophilic residues disrupting the expected hydrophobic core and propagating linearly along the long axis of fibril is recognized as the seed for amyloidogenic transformation in this polypeptide. This paper discusses the structure of the Aß(11-42) amyloid fibril, listed in PDB under ID 2MXU (fragment od Aß(1-42) amyloid).

The aqueous environment as an active participant in the protein folding process.

Existing computational models applied in the protein structure prediction process do not sufficiently account for the presence of the aqueous solvent. The solvent is usually represented by a predetermined number of H2O molecules in the bounding box which contains the target chain. The fuzzy oil drop (FOD) model, presented in this paper, follows an alternative approach, with the solvent assuming the form of a continuous external hydrophobic force field, with a Gaussian distribution. The effect of this force field is to guide hydrophobic residues towards the center of the protein body, while promoting exposure of hydrophilic residues on its surface. This work focuses on the following sample proteins: Engrailed homeodomain (RCSB: 1enh), Chicken villin subdomain hp-35, n68h (RCSB: 1yrf), Chicken villin subdomain hp-35, k65(nle), n68h, k70(nle) (RCSB: 2f4k), Thermostable subdomain from chicken villin headpiece (RCSB: 1vii), de novo designed single chain three-helix bundle (a3d) (RCSB: 2a3d), albumin-binding domain (RCSB: 1prb) and lambda repressor-operator complex (RCSB: 1lmb).

Structural analysis of the Aß(15-40) amyloid fibril based on hydrophobicity distribution.

The Aß42 amyloid is the causative factor behind various neurodegenerative processes. It forms elongated fibrils which cause structural devastation in brain tissue. The structure of an amyloid seems to be a contradiction of protein folding principles. Our work focuses on the Aß(15-40) amyloid containing the D23N mutation (also known as the "Iowa mutation"), upon which an in silico experiment is based. Models generated using I-Tasser software as well as the fuzzy oil drop model - regarded as alternatives to the amyloid conformation - are compared in terms of their respective distributions of hydrophobicity (i.e. the existence of a hydrophobic core). In this process, fuzzy oil drop model parameters are applied in assessing the propensity of selected fragments for undergoing amyloid transformation.

Filamentous Aggregates of Tau Proteins Fulfil Standard Amyloid Criteria Provided by the Fuzzy Oil Drop (FOD) Model.

Abnormal filamentous aggregates that are formed by tangled tau protein turn out to be classic amyloid fibrils, meeting all the criteria defined under the fuzzy oil drop model in the context of amyloid characterization. The model recognizes amyloids as linear structures where local hydrophobicity minima and maxima propagate in an alternating manner along the fibril's long axis. This distribution of hydrophobicity differs greatly from the classic monocentric hydrophobic core observed in globular proteins. Rather than becoming a globule, the amyloid instead forms a ribbonlike (or cylindrical) structure.