The fuzzy oil drop model, a tool which can be used to study the structure of hydrophobic core in proteins, has been applied analysis proteins belonging jumonji group—JARID2, JARID1A, JARID1B and JARID1D—proteins that share property being able interact with DNA. Their ARID PHD domains, when analyzed context are found exhibit structural variability regarding status their secondary folds, including β-hairpin determines biological function. Additionally, disordered fragments present (as...

The presented analysis concerns the inter-domain and inter-protein interface in protein complexes. We propose extending traditional understanding of domain as a function local compactness with an additional criterion which refers to presence well-defined hydrophobic core. Interface areas selected homodimers vary respect their contribution share well individual (domain-specific) cores. basic definition domain, i.e., structural unit characterized by tighter packing than its immediate...

Four de novo proteins differing in single mutation positions, with a chain length of 56 amino acids, represent diverse 3D structures: monomeric 3α and 4β + α folds. The reason for this diversity is seen the different structure hydrophobic core as result synergy leading to generation system which polypeptide whole participates. On basis fuzzy oil drop model, where expressed by means distribution function form Gaussian distribution, it has been shown that composition these two structural forms...

Reactive oxygen intermediates and serine proteases are important components of host defense systems but can produce injury if not tightly regulated. To determine whether these be coordinately controlled, we investigated regulation superoxide generation by physiologically relevant concentrations a) highly purified serum-derived antichymotrypsin (ACT), b) recombinant, wild-type ACT, c) rACT in which amino acid substitutions were engineered into the reactive center, d) chymotrypsin/ACT...

In this paper we show that the fuzzy oil drop model represents a general framework for describing generation of hydrophobic cores in proteins and thus provides insight into influence water environment upon protein structure stability. The has been successfully applied study wide range proteins, however focuses specifically on domains representing immunoglobulin-like folds. Here provide evidence domains, despite being structurally similar, differ with respect to their participation core. It...

One of the factors responsible for tertiary structural stabilization in proteins is presence hydrophobic core—a result interactions within protein body. In some (especially extracellular ones) additional provided by covalent bonds between selected Cys residues, commonly referred to as disulfide bonds. The mutual interplay both and their respective contributions are focus this work. assessment effects isinterpreted Fuzzy Oil Drop (FOD) model which individual polypeptide chain fragments...

Research on the protein folding problem differentiates process with respect to duration of this process. The current structure encoded in sequence dogma seems be clearly justified, especially case proteins referred as fast-folding, ultra-fast-folding or downhill. In present work, an attempt determine characteristics group using fuzzy oil drop model is undertaken. According model, a specific micelle composed bi-polar molecules such amino acids. Protein regarded spherical formation presence...

The water environment determines the activity of biological processes. role such an interpreted in form external field expressed by 3D Gaussian distribution fuzzy oil drop model directs folding process towards generation a centrally located hydrophobic core with simultaneous exposure polar residues on surface. In addition to proteins soluble environment, there is significant group membrane that act as receptors or channels, including ion channels particular. change (water) into highly...

Proteins whose presence prevents water from freezing in living organisms at temperatures below 0 °C are referred to as antifreeze proteins. This group includes molecules of varying size (from 30 over 300 aa) and variable secondary/supersecondary conformation. Some these proteins also contain peculiar structural motifs called solenoids. We have applied the fuzzy oil drop model analysis four categories proteins: 1 - very small proteins, i.e. helical peptides (below 40 aa); 2 globular (40-100 3...

Mutations in proteins introduce structural changes and influence biological activity: the specific effects depend on location of mutation. The simple method proposed present paper is based a two-step model silico protein folding. structure first intermediate assumed to be determined solely by backbone conformation. second one presence hydrophobic center. comparable analysis set mutants performed identify mutant-induced changes. core organization measured divergence entropy allows...

We propose a mathematical model describing the formation of micellar forms—whether spherical, globular, cylindrical, or ribbonlike—as well as its adaptation to protein structure. Our model, based on fuzzy oil drop paradigm, assumes that in spherical micelle distribution hydrophobicity produced by alignment polar molecules with external water environment can be modeled 3D Gaussian function. Perturbing this function changing values sigma parameters leads variety conformations—the is therefore...

The aqueous environment is a pervasive factor which, in many ways, determines the protein folding process and consequently activity of proteins. Proteins are unable to perform their function unless immersed water (membrane proteins excluded from this statement). Tertiary conformational stabilization dependent on presence internal force fields (nonbonding interactions between atoms), as well an external field generated by water. hitherto unknown structuralization may be elucidated analyzing...

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

Protein solubility is based on the compatibility of specific protein surface with polar aquatic environment. The exposure residues to promotes protein’s in environment also influences folding process by favoring centralization hydrophobic simultaneous residues. degree residue distribution, model concentration center molecule, determined sequence amino acids chain. fuzzy oil drop enables quantification hydrophobicity distribution observed a form fully consistent Gaussian 3D function, which...

The Aβ42 amyloid is the causative factor behind various neurodegenerative processes. It forms elongated fibrils which cause structural devastation in brain tissue. structure of an seems to be a contradiction protein folding principles. Our work focuses on Aβ(15-40) containing D23N mutation (also known as "Iowa mutation"), upon silico experiment based. Models generated using I-Tasser software well fuzzy oil drop model - regarded alternatives conformation are compared terms their respective...

The issue of changing the structure globular proteins into an amyloid form is in focus researchers' attention. Numerous experimental studies are carried out, and mathematical models to define essence transformation sought. present work focuses on hydrophobic core amyloids. ordering described by a 3D Gaussian distribution analog hydrophobicity spherical micelle. Amyloid fibril ribbon-like micelle made up numerous individual chains, each representing flat structure. within single chain...

Background Folding nucleus of globular proteins formation starts by the mutual interaction a group hydrophobic amino acids whose close contacts allow subsequent and stability 3D structure. These early steps can be predicted simulation folding process through Monte Carlo (MC) coarse grain model in discrete space. We previously defined MIRs (Most Interacting Residues), as set residues presenting large number non-covalent neighbour interactions during such simulation. are good candidates to...