Protein Is an Intelligent Micelle

Chameleon sequences-Structural effects

The predisposition of amino acids towards accepting the appropriate secondary structure form is ambiguous. The identified sequences (6-12 aa in length - ChSeq data base) of the chameleon type (the same sequence accepting different secondary structures) constitute a puzzle that makes it difficult to indicate the initial conformation in a chain with a given amino acid sequence. The analysis of proteins presented in this paper uses the hydrophobicity distribution in protein body as the criterion for comaparable analysis of the status of helica/Beta-structural chameleon fragments in pairs of proteins. The sub-base is the object of analysis containg the proteins representing the organisation of hydrophobicity in one protein of the pair as ordered according to micelle-like organisation (hydrophobic core with polar surface) and the second one in pair with disordered hydrophobicity organisation. The status of chameleon sections appears to represent local organisation of hydrophobicity highly accordant in both proteins in chameleon pair independently on the status of the structural unit they belong to. The fuzzy oil drop model (FOD) in its modified form (FOD-M) is applied for analysis. This work aims to verify the hypothesis assuming the subordination of the form of secondary structure to the superior goal of obtaining a hydrophobicity distribution suitable for the given biological activity of the protein, ensuring biological functionality. Secondary structure is not an aim by itself. It is shown, that the main goal is to reach the structure representing specific activity. Secondary structure is a means to achieve this goal.

Aquaporins as Membrane Proteins: The Current Status

BACKGROUND

The ambient conditions that ensure the expected protein folding activity are important in directing the protein folding process. Water favors the formation of a centrally located hydrophobic protein nucleus with exposed polar residues for preferable contact with polar water molecules. Different ambient conditions are created by the hydrophobic cell membrane, which also provides an environment for the activity of proteins, including channels responsible for transporting multiple molecules, the concentration of which is controlled as part of homeostasis. Aquaporins are transmembrane proteins responsible for primarily transporting water and low-molecular-weight compounds.

METHODS

The fuzzy oil drop (FOD) model was applied in its modified form, FOD-M, for the analysis. The FOD model allows quantitative assessment of protein structure adaptation to external conditions, ensuring its biological activity.

RESULTS

The aquaporins studied in this work revealed adaptations for stabilizing hydrophobic environments and transporting polar molecules.

CONCLUSIONS

A significant degree of similarity was demonstrated in the structure of human aquaporins using FOD-M. This model enabled a quantitative assessment of the degree of adaptation to biological function achieved through an appropriate balance between micelle-like decomposition and appropriate modification due to the specificity of the environment that ensures adequate activity.

Protein folding: Funnel model revised

The spatial structure of proteins, largely determined by their amino acid sequences, is also dependent on the environmental conditions under which the folding process takes place. In aqueous environments, exposure of polar amino acids is the driving factor, whereas protein stabilization in amphipathic membranes requires exposure to hydrophobic residues. This observation can be extended to all other environmental conditions under which proteins exhibit biological activity and, most importantly, to the folding process. The fuzzy oil drop (FOD) model assumes a centric location of hydrophobic residues (hydrophobic core) with exposure of polar residues towards the aqueous environment, as the influence of the aqueous environment is extended to include the contribution of other non-aqueous factors, enabling the assessment of their influence on protein structuring. The application of the modified FOD model (FOD-M) we have developed allows the environment to be represented as an external force field in the form of a continuum. The role of environmental conditions allows modification of the funnel model expressing the localization of the energy minimum as dependent on external conditions expressed by the K scale, where K measures the degree of other than polar water factors participating in folding process.

Domain swapping: a mathematical model for quantitative assessment of structural effects

The domain-swapping mechanism involves the exchange of structural elements within a secondary or supersecondary structure between two (or more) proteins. The present paper proposes to interpret the domain-swapping mechanism using a model that assesses the structure of proteins (and complexes) based on building the structure of a common hydrophobic core in a micelle-like arrangement (a central hydrophobic core with a polar shell in contact with polar water), which has a considerable impact on the stabilisation of the domain structure built by domain swapping. Domains with a hydrophobicity system that is incompatible with the micelle-like structure have also been identified. This incompatibility is the form of structural codes related to biological function.

Chameleon Sequences-Structural Effects in Proteins Characterized by Hydrophobicity Disorder

Repeated protein folding processes both in vivo and in vitro leading to the same structure for a specific amino acid sequence prove that the amino acid sequence determines protein structuring. This is also evidenced by the variability of structuring, dependent on the introduced mutations. An important phenomenon in this regard is the presence of a differentiated secondary structure for chain fragments of identical sequence representing distinct forms of the secondary-order structure. Proteins termed chameleon proteins contain polypeptide chain fragments of identical sequence (length 6-12 aa) showing structural differentiation: helix versus β-structure. In the present paper, it was shown that these fragments represent components matching the structural status dictated by the physicochemical properties of the entire structural unit. This structural matching is related to achieving the goal of the biological function of the structural unit. The corresponding secondary structure represents a means to achieving this goal, not an end in itself. A selected set of proteins from the ChSeq database have been analyzed using a fuzzy oil drop model (FOD-M) identifying the uniqueness of the hydrophobicity distribution taken as a medium for recording the specificity of a given protein and a given chameleon section in particular. It was shown that in the vast majority, the status of chameleon sections turns out to be comparable regardless of the represented secondary structure.

Transmembrane proteins-Different anchoring systems

Transmembrane proteins are active in amphipathic environments. To stabilize the protein in such surrounding the exposure of hydrophobic residues on the protein surface is required. Transmembrane proteins are responsible for the transport of various molecules. Therefore, they often represent structures in the form of channels. This analysis focused on the stability and local flexibility of transmembrane proteins, particularly those related to their biological activity. Different forms of anchorage were identified using the fuzzy oil-drop model (FOD) and its modified form, FOD-M. The mainly helical as well as β-barrel structural forms are compared with respect to the mechanism of stabilization in the cell membrane. The different anchoring system was found to stabilize protein molecules with possible local fluctuation.

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.

Model of the external force field for the protein folding process-the role of prefoldin

Introduction: The protein folding process is very sensitive to environmental conditions. Many possibilities in the form of numerous pathways for this process can-if an incorrect one is chosen-lead to the creation of forms described as misfolded. The aqueous environment is the natural one for the protein folding process. Nonetheless, other factors such as the cell membrane and the presence of specific molecules (chaperones) affect this process, ensuring the correct expected structural form to guarantee biological activity. All these factors can be considered components of the external force field for this process. Methods: The fuzzy oil drop-modified (FOD-M) model makes possible the quantitative evaluation of the modification of the external field, treating the aqueous environment as a reference. The FOD-M model (tested on membrane proteins) includes the component modifying the water environment, allowing the assessment of the external force field generated by prefoldin. Results: In this work, prefoldin was treated as the provider of a specific external force field for actin and tubulin. The discussed model can be applied to any folding process simulation, taking into account the changed external conditions. Hence, it can help simulate the in silico protein folding process under defined external conditions determined by the respective external force field. In this work, the structures of prefoldin and protein folded with the participation of prefoldin were analyzed. Discussion: Thus, the role of prefoldin can be treated as a provider of an external field comparable to other environmental factors affecting the protein folding process.

Hydrophobicity-Based Force Field In Enzymes

The biocatalysis process takes place with the participation of enzymes, which, depending on the reaction carried out, require, apart from the appropriate arrangement of catalytic residues, an appropriate external force field. It is generated by the protein body. The relatively small size of the part directly involved in the process itself is supported by the presence of an often complex structure of the protein body, the purpose of which is to provide an appropriate local force field, eliminating the influence of water. Very often, the large size of the enzyme is an expression of the complex form of this field. In this paper, a comparative analysis of arbitrarily selected enzymes, representatives of different enzyme classes, was carried out, focusing on the measurement of the diversity of the force field provided by a given protein. This analysis was based on the fuzzy oil drop model (FOD) and its modified version (FOD-M), which takes into account the participation of nonaqueous external factors in shaping the structure and thus the force field within the protein. The degree and type of ordering of the hydrophobicity distribution in the protein molecule is the result of the influence of the environment but also the supplier of the local environment for a given process, including the catalysis process in particular. Determining the share of a nonaqueous environment is important due to the ubiquity of polar water, whose participation in processes with high specificity requires control. It can be assumed that some enzymes in their composition have a permanently built-in part, the role of which is reduced to that of a permanent chaperone. It provides a specific external force field needed for the process. The proposed model, generalized to other types of proteins, may also provide a form of recording the environment model for the simulation of the in silico protein folding process, taking into account the impact of its differentiation.

Role of environmental specificity in CASP results

BACKGROUND

Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical Assessment of Structure Prediction) competition. However, the question of the mechanism behind the protein folding process itself remains unanswered. Correctly predicting the structure also does not solve the problem of, for example, amyloid proteins, where a polypeptide chain with an unaltered sequence adopts a different 3D structure.

RESULTS

This work was an attempt at explaining the structural variation by considering the contribution of the environment to protein structuring. The application of the fuzzy oil drop (FOD) model to assess the validity of the selected models provided in the CASP13, CASP14 and CASP15 projects reveals the need for an environmental factor to determine the 3D structure of proteins. Consideration of the external force field in the form of polar water (Fuzzy Oil Drop) and a version modified by the presence of the hydrophobic compounds, FOD-M (FOD-Modified) reveals that the protein folding process is environmentally dependent. An analysis of selected models from the CASP competitions indicates the need for structure prediction as dependent on the consideration of the protein folding environment.

CONCLUSIONS

The conditions governed by the environment direct the protein folding process occurring in a certain environment. Therefore, the variation of the external force field should be taken into account in the models used in protein structure prediction.

Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone

BACKGROUND

The aqueous environment directs the protein folding process towards the generation of micelle-type structures, which results in the exposure of hydrophilic residues on the surface (polarity) and the concentration of hydrophobic residues in the center (hydrophobic core). Obtaining a structure without a hydrophobic core requires a different type of external force field than those generated by a water. The examples are membrane proteins, where the distribution of hydrophobicity is opposite to that of water-soluble proteins. Apart from these two extreme examples, the process of protein folding can be directed by chaperones, resulting in a structure devoid of a hydrophobic core.

RESULTS

The current work presents such example: DnaJ Hsp40 in complex with alkaline phosphatase PhoA-U (PDB ID-6PSI)-the client molecule. The availability of WT form of the folding protein-alkaline phosphatase (PDB ID-1EW8) enables a comparative analysis of the structures: at the stage of interaction with the chaperone and the final, folded structure of this biologically active protein. The fuzzy oil drop model in its modified FOD-M version was used in this analysis, taking into account the influence of an external force field, in this case coming from a chaperone.

CONCLUSIONS

The FOD-M model identifies the external force field introduced by chaperon influencing the folding proces. The identified specific external force field can be applied in Ab Initio protein structure prediction as the environmental conditioning the folding proces.