Intrinsically Disordered Proteins—Relation to General Model Expressing the Active Role of the Water Environment

Kalinowska, Barbara; Banach, Mateusz; Konieczny, Leszek; Marchewka, Damian; Roterman, Irena

doi:10.1016/b978-0-12-800168-4.00008-1

Cited by 11 publications

(9 citation statements)

References 39 publications

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“…The parameters based on FOD calculated for different scales differ but the overall status of the molecule remains the same for all analyzed proteins. In conclusion, the choice of intrinsic hydrophobicity scale [31][32][33][34][35][36][37][38][39][40][41] does not appear to affect the outcome of fuzzy oil drop analysis. The comparative analysis was performed for hydrophobic parameters applying the KyteDoolittle scale [35] and shown in appropriate tables.…”

Section: The Real Hydrophobic Distribution In a Protein Moleculementioning

confidence: 99%

“…It can also be used to identify the location of ligand binding cavities [27,28], protein complexation areas [29,30], the structure of large protein complexes (such as chaperonin) [31] and the properties of proteins which include intrinsically disordered fragments [32] or share certain structural characteristics (e.g., immunoglobulin-like domains) [33]. In this work we apply the model to a set of relatively small proteins whose biological function involves interaction with DNA via a specific loop.…”

Section: Introductionmentioning

confidence: 99%

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

Kalinowska

Banach

Konieczny

et al. 2015

Entropy

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Abstract: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.

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Section: The Real Hydrophobic Distribution In a Protein Moleculementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Kalinowska

Banach

Konieczny

et al. 2015

Entropy

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“…or a disordered fragment [9]. This, however, requires normalization (rescaling) of H t , H o and H r (hydrophobicity yielded by distribution R) so that the sum of all values assigned to a given section is equal to 1.…”

Section: Summary Of the Modelmentioning

confidence: 99%

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

Banach

Kalinowska

Konieczny

et al. 2016

Entropy

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Abstract: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.

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“…The applicability of FOD was tested on few selected sets of proteins of small size [38], structural similarity [39], protein complexes [40] and intrinsically disordered proteins [41].…”

Section: Discussionmentioning

confidence: 99%

“…This molecule also contains a loop (38)(39)(40)(41). The β-fragment at 42-46 and the loop both diverge from the model even though in G A 88 the same residues form parts of an accordant helix.…”

Section: De Novo Designed Proteinsmentioning

confidence: 99%

Structural Role of Hydrophobic Core in Proteins-Selected Examples

Banach¹,

Kalinowska²,

Konieczny³

et al. 2016

J Proteomics Bioinform

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This paper discusses the sequence/structure relation. The core question concerns the degree to which similar sequences produce similar structures and vice versa. A mechanism by which similar sequences may result in dissimilar structures is proposed, based on the Fuzzy Oil Drop (FOD) model in which structural similarity is estimated by analyzing the protein's hydrophobic core. We show that local changes in amino acid sequences, in addition to producing local structural alterations at the substitution site, may also change the shape of the hydrophobic core, significantly affecting the overall tertiary conformation of the protein. Our analysis focuses on four sets of proteins: 1) Pair of designer proteins with specially prepared sequences; 2) Pair of natural proteins modified (mutated) to converge to a point of high-level sequence identity while retaining their respective wild-type tertiary folds; 3) Pair of natural proteins with common ancestry but with differing structures and biological profiles shaped by divergent evolution; and 4) Pair of natural proteins of high structural similarity with no sequence similarity and different biological function. with even higher levels of sequence identity (95%) and differing folds. Thus, conformational switching to an alternative monomeric fold of comparable stability can be effected with just a handful of mutations in a small protein. This result has implications for understanding not only the folding code but also the evolution of new folds. The CATH [18] classification for these two proteins is as follows: 1.10.8.40-Mainly Alpha Orthogonal Bundle for 2JWS and 3.10.20.10.-R-Alpha Beta Roll for 2JWU. Wild type proteins with aim-oriented mutationsTwo proteins: G311 (1ZXG) and A219 (1ZXH) are modified versions of wild-type proteins designated G and A (IgG binding domains, source: Staphylococcus aureus for 1ZXG and Streptococcus sp. for 1ZXH) respectively [19]. The series of mutations aimed at achieving a high level of sequence identity while preserving wild-type 3D structures. Both proteins (G311 vs. G and A219 vs. A) represent backbone RMS-D 1.4 Å, maintaining wild-type secondary structures: α/β for G311 and helical for A219. The final sequence identity of both modified proteins is on the level of 59%. All relevant data was taken from a paper describing experimental results of protein modifications [19]. Homologous proteinsThe next pair comprises two proteins with common ancestry but different folds and functions: 2PIJ (Pfl 6 BETA) (source: Pseudomonas fluorescens) Cro protein from prophage pfl 6 in P. fluorescens pf-5 [20] and 3BD1 (Xfaso 1) Cro protein from putative prophage element X. fastidiosa strain ann-1 [20] (source: Xylella fastidiosa). Both proteins share an identical CATH classification: 1.10.260.40-Mainly Alpha Orthogonal Bundle.The differences between homologous proteins are due to evolutionary pressure. In the presented case the sequence identity is 40%, yet the α-helix is replaced by a β-sheet in the C-terminal region spanning approximately 25 residu...

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Intrinsically Disordered Proteins—Relation to General Model Expressing the Active Role of the Water Environment

Cited by 11 publications

References 39 publications

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

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

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

Structural Role of Hydrophobic Core in Proteins-Selected Examples

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