Mateusz Banach

Fuzzy oil drop model to interpret the structure of antifreeze proteins and their mutants

Mutations in proteins introduce structural changes and influence biological activity: the specific effects depend on the location of the mutation. The simple method proposed in the present paper is based on a two-step model of in silico protein folding. The structure of the first intermediate is assumed to be determined solely by backbone conformation. The structure of the second one is assumed to be determined by the presence of a hydrophobic center. The comparable structural analysis of the set of mutants is performed to identify the mutant-induced structural changes. The changes of the hydrophobic core organization measured by the divergence entropy allows quantitative comparison estimating the relative structural changes upon mutation. The set of antifreeze proteins, which appeared to represent the hydrophobic core structure accordant with “fuzzy oil drop” model was selected for analysis.

Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins

The fuzzy oil drop model, a tool which can be used to study the structure of the hydrophobic core in proteins, has been applied in the analysis of proteins belonging to the jumonji group—JARID2, JARID1A, JARID1B and JARID1D—proteins that share the property of being able to interact with DNA. Their ARID and PHD domains, when analyzed in the context of the fuzzy oil drop model, are found to exhibit structural variability regarding the status of their secondary folds, including the β-hairpin which determines their biological function. Additionally, the structure of disordered fragments which are present in jumonji proteins (as confirmed by the DisProt database) is explained on the grounds of the hydrophobic core model, suggesting that such fragments contribute to tertiary structural stabilization. This conclusion is supported by divergence entropy measurements, expressing the degree of ordering in each protein’s hydrophobic core.

The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function

In this paper we show that the fuzzy oil drop model represents a general framework for describing the generation of hydrophobic cores in proteins and thus provides insight into the influence of the water environment upon protein structure and stability. The model has been successfully applied in the study of a wide range of proteins, however this paper focuses specifically on domains representing immunoglobulin-like folds. Here we provide evidence that immunoglobulin-like domains, despite being structurally similar, differ with respect to their participation in the generation of hydrophobic core. It is shown that β-structural fragments in β-barrels participate in hydrophobic core formation in a highly differentiated manner. Quantitatively measured participation in core formation helps explain the variable stability of proteins and is shown to be related to their biological properties. This also includes the known tendency of immunoglobulin domains to form amyloids, as shown using transthyretin to reveal the clear relation between amyloidogenic properties and structural characteristics based on the fuzzy oil drop model.

Role of Disulfide Bonds in Stabilizing the Conformation of Selected Enzymes—An Approach Based on Divergence Entropy Applied to the Structure of Hydrophobic Core in Proteins

One of the factors responsible for tertiary structural stabilization in proteins is the presence of the hydrophobic core—a result of hydrophobic interactions within the protein body. In some proteins (especially extracellular ones) additional stabilization is provided by covalent bonds between selected Cys residues, commonly referred to as disulfide bonds. The mutual interplay of both factors and their respective contributions to stabilization are the focus of this work. The assessment of the effects of disulfide bonds isinterpreted by Fuzzy Oil Drop (FOD) model in which individual polypeptide chain fragments (including fragments which participate in SS bonds) can be evaluated in the context of their influence upon tertiary structural stabilization by comparing their corresponding theoretical and idealized hydrophobicity density distributions. The proteins were identified with both factors reinforcing each other, as well as proteins where they seem to counteract each other. The analysis presents a number of enzymes, including ribonuclease, lysozyme, disulfide isomerase and phospholipase.

Influence of the Aqueous Environment on Protein Structure—A Plausible Hypothesis Concerning the Mechanism of Amyloidogenesis

The aqueous environment is a pervasive factor which, in many ways, determines the protein folding process and consequently the activity of proteins. Proteins are unable to perform their function unless immersed in water (membrane proteins excluded from this statement). Tertiary conformational stabilization is dependent on the presence of internal force fields (nonbonding interactions between atoms), as well as an external force field generated by water. The hitherto the unknown structuralization of water as the aqueous environment may be elucidated by analyzing its effects on protein structure and function. Our study is based on the fuzzy oil drop model—a mechanism which describes the formation of a hydrophobic core and attempts to explain the emergence of amyloid-like fibrils. A set of proteins which vary with respect to their fuzzy oil drop status (including titin, transthyretin and a prion protein) have been selected for in-depth analysis to suggest the plausible mechanism of amyloidogenesis.

Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes

The presented analysis concerns the inter-domain and inter-protein interface in protein complexes. We propose extending the traditional understanding of the protein domain as a function of local compactness with an additional criterion which refers to the presence of a well-defined hydrophobic core. Interface areas in selected homodimers vary with respect to their contribution to share as well as individual (domain-specific) hydrophobic cores. The basic definition of a protein domain, i.e., a structural unit characterized by tighter packing than its immediate environment, is extended in order to acknowledge the role of a structured hydrophobic core, which includes the interface area. The hydrophobic properties of interfaces vary depending on the status of interacting domains—In this context we can distinguish: (1) Shared hydrophobic cores (spanning the whole dimer); (2) Individual hydrophobic cores present in each monomer irrespective of whether the dimer contains a shared core. Analysis of interfaces in dystrophin and utrophin indicates the presence of an additional quasi-domain with a prominent hydrophobic core, consisting of fragments contributed by both monomers. In addition, we have also attempted to determine the relationship between the type of interface (as categorized above) and the biological function of each complex. This analysis is entirely based on the fuzzy oil drop model.

Prediction of Protein-Protein Binding Interfaces

When it comes to regulating protein activity, complexation mechanisms are just as important as ligand binding. Most proteins never exist in isolation – instead they serve as building blocks for more complex systems. Some proteins form multimers to ensure maintain spatial alignment (required e.g. for phase separation in the dual lipid layer and formation of hydrophilic compartments in ion channels (Unwin 2005; Jasti et al.. 2007)); others may require temporary binding of cofactors (e.g. regulation of transcription factors (Huxford et al. 1998)), or are part of complicated protein machinery (e.g. proton-driven rotors in ATP synthases (Boyer 1997; Oster and Wang 1999, 2003)).

Intermediates in the Protein Folding Process: A Computational Model

The paper presents a model for simulating the protein folding process in silico. The two-step model (which consists of the early stage—ES and the late stage—LS) is verified using two proteins, one of which is treated (according to experimental observations) as the early stage and the second as an example of the LS step. The early stage is based solely on backbone structural preferences, while the LS model takes into account the water environment, treated as an external hydrophobic force field and represented by a 3D Gauss function. The characteristics of 1ZTR (the ES intermediate, as compared with 1ENH, which is the LS intermediate) confirm the link between the gradual disappearance of ES characteristics in LS structural forms and the simultaneous emergence of LS properties in the 1ENH protein. Positive verification of ES and LS characteristics in these two proteins (1ZTR and 1ENH respectively) suggest potential applicability of the presented model to in silico protein folding simulations.

Comparative Analysis of Techniques Oriented on the Recognition of Ligand Binding Area in Proteins

This chapter presents an analysis of the various models implemented by software packages which enable computerized identification of ligand binding sites.

Can the Structure of the Hydrophobic Core Determine the Complexation Site

Stabilization of the tertiary protein structure is most often attributed to hydrophobic interactions, although this type of interaction is not specifically reflected in protein force fields. Initial attempts to extend the analysis of traditional nonbinding interactions with factors representing hydrophobic interactions (Levitt 1976) were not particularly successful, even though the influence of the aqueous environment on molecular dynamics cannot be underestimated in respect to experimental observations.