Predicting Protein Surface Property with its Surface Hydrophobicity

2021 ◽  
Vol 28 ◽  
Author(s):  
Sen Tang ◽  
Junsheng Li ◽  
Guoxia Huang ◽  
Liujuan Yan
Keyword(s):  
Molecular Structure ◽  
Surface Properties ◽  
Surface Property ◽  
Hydrophobic Interactions ◽  
Surface Hydrophobicity ◽  
Molecular Surface ◽  
Spatial Structures ◽  
Actual Distribution ◽  
Hydrophobic Residues ◽  
Key Indicator

: This article reviews and discusses the relationship between surface hydrophobicity and other surface properties of proteins and the possibility of using surface hydrophobicity as a key indicator to predict and evaluate the changes in the surface properties of a protein. Hydrophobicity is the main driving force of protein folding; it affects the structure and functions. Surface hydrophobicity and other surface properties of proteins are controlled by their spatial structures. Due to the hydrophobic interactions, most proteins fold into their globular structures, and they lack sufficient hydrophobic residues on the molecular surface; thus, they do not exhibit excellent surface properties. Surface hydrophobicity is closely related to the changes in the surface property of proteins because it directly reflects the actual distribution of the hydrophobic residues on the surface of a protein. The molecular structure of a protein can be changed or modified to remove the constraints of spatial structures and expose more hydrophobic residues on the molecular surface, which may improve the surface properties of proteins. Therefore, the changes in the surface hydrophobicity caused by changes in the molecular structure can be an ideal key indicator to predict and evaluate the changes in the surface properties of a protein.

scholarly journals The contribution of hydrophobic residues in the pore-forming region of the ryanodine receptor channel to block by large tetraalkylammonium cations and Shaker B inactivation peptides

2012 ◽  
Vol 140 (3) ◽  
pp. 325-339 ◽  
Author(s):  
Sammy A. Mason ◽  
Cedric Viero ◽  
Joanne Euden ◽  
Mark Bannister ◽  
Duncan West ◽  
...  
Keyword(s):  
Ryanodine Receptor ◽  
Hydrophobic Interactions ◽  
Structural Information ◽  
Dissociation Rate ◽  
Structural Components ◽  
Hydrophobic Residues ◽  
K Channels ◽  
New Information ◽  
Tetraalkylammonium Cations ◽  
Cytosolic Side

Although no high-resolution structural information is available for the ryanodine receptor (RyR) channel pore-forming region (PFR), molecular modeling has revealed broad structural similarities between this region and the equivalent region of K+ channels. This study predicts that, as is the case in K+ channels, RyR has a cytosolic vestibule lined with predominantly hydrophobic residues of transmembrane helices (TM10). In K+ channels, this vestibule is the binding site for blocking tetraalkylammonium (TAA) cations and Shaker B inactivation peptides (ShBPs), which are stabilized by hydrophobic interactions involving specific residues of the lining helices. We have tested the hypothesis that the cytosolic vestibule of RyR fulfils a similar role and that TAAs and ShBPs are stabilized by hydrophobic interactions with residues of TM10. Both TAAs and ShBPs block RyR from the cytosolic side of the channel. By varying the composition of TAAs and ShBPs, we demonstrate that the affinity of both species is determined by their hydrophobicity, with variations reflecting alterations in the dissociation rate of the bound blockers. We investigated the role of TM10 residues of RyR by monitoring block by TAAs and ShBPs in channels in which the hydrophobicity of individual TM10 residues was lowered by alanine substitution. Although substitutions changed the kinetics of TAA interaction, they produced no significant changes in ShBP kinetics, indicating the absence of specific hydrophobic sites of interactions between RyR and these peptides. Our investigations (a) provide significant new information on both the mechanisms and structural components of the RyR PFR involved in block by TAAs and ShBPs, (b) highlight important differences in the mechanisms and structures determining TAA and ShBP block in RyR and K+ channels, and (c) demonstrate that although the PFRs of these channels contain analogous structural components, significant differences in structure determine the distinct ion-handling properties of the two species of channel.

In situ detection of cell surface hydrophobicity of probe-defined bacteria in activated sludge

2001 ◽  
Vol 43 (6) ◽  
pp. 97-103 ◽  
Author(s):  
J. L. Nielsen ◽  
L. H. Mikkelsen ◽  
P. H. Nielsen
Keyword(s):  
Activated Sludge ◽  
Surface Properties ◽  
Treatment Plant ◽  
Cell Surface Hydrophobicity ◽  
Surface Hydrophobicity ◽  
Substrate Uptake ◽  
Filamentous Bacteria ◽  
In Situ Conditions ◽  
Bacterial Surfaces

The surface hydrophobicity of different types of bacteria in activated sludge were investigated under in situ conditions by following the adhesion of fluorescent microspheres with defined surface properties to bacterial surfaces (the MAC-method). This technique was combined with identification of the bacteria with fluorescence in situ hybridization with rRNA-targeted oligonucleotides (FISH) and could thus be used for characterization of surface properties of probe-defined bacteria directly in a complex system without prior enrichment or isolation. This MAC-FISH technique could be used for single bacteria as well as filamentous bacteria. In the investigated activated sludge from an industrial wastewater treatment plant, two types of filamentous bacteria dominated. One morphotype consistently attracted only very few hydrophobic microspheres, indicating that the thin sheath of exopolymers around the cells had a hydrophilic surface. Use of a hierarchical set of gene probes revealed that these filaments were sulphide oxidising Thiothrix spp. The other predominating filamentous morphotype had a thick, very hydrophobic exopolymeric sheath. This filamentous bacterium was found to belong to the alpha-Proteobacteria. The relevance of the significant differences in surface hydrophobicity for the two morphotypes in respect to substrate uptake and floc formation is discussed.

scholarly journals New Assay for Measuring Cell Surface Hydrophobicities of Candida dubliniensis andCandida albicans

2001 ◽  
Vol 8 (3) ◽  
pp. 585-587 ◽  
Author(s):  
M. A. Jabra-Rizk ◽  
W. A. Falkler ◽  
W. G. Merz ◽  
T. F. Meiller
Keyword(s):  
Cell Surface ◽  
Anaerobic Bacterium ◽  
Hydrophobic Interactions ◽  
Cell Surface Hydrophobicity ◽  
Fusobacterium Nucleatum ◽  
Surface Hydrophobicity ◽  
Yeast Cells ◽  
Pathogenic Yeast ◽  
Yeast Cell Surface ◽  
The Many

ABSTRACT Hydrophobic interactions, based on cell surface hydrophobicity (CSH), are among the many and varied mechanisms of adherence deployed by the pathogenic yeast Candida albicans. Recently it was shown that, unlike C. albicans, C. dubliniensisis a species that exhibits an outer fibrillar layer consistent with constant CSH. Previously, C. dubliniensis grown at 25 or 37°C was shown to coaggregate with the oral anaerobic bacteriumFusobacterium nucleatum. C. albicans, however, demonstrated similar coaggregation only when hydrophobic or grown at 25°C. This observation implied that coaggregation of Candida cells with F. nucleatum is associated with a hydrophobic yeast cell surface. To test this hypothesis, 42 C. albicans and 40 C. dubliniensis clinical isolates, including a C. albicans hydrophobic variant, were grown at 25 and 37°C and tested with the established hydrophobicity microsphere assay, which determines CSH levels based on the number of microspheres attached to the yeast cells. The coaggregation assay was performed in parallel experiments. All C. dubliniensis isolates grown at either temperature, hydrophobic 25°C-grown C. albicans isolates, and the C. albicans hydrophobic variant, unlike the 37°C-hydrophilic C. albicans isolates, exhibited hydrophobic CSH levels with the microsphere assay and simultaneously showed maximum, 4+, coaggregation with F. nucleatum. The parallel results obtained for C. dubliniensis using both assays support the use of the CoAg assay both as a rapid assay to determine CSH and to differentiate between C. dubliniensisand C. albicans.

Impact of pH on molecular structure and surface properties of lentil legumin-like protein and its application as foam stabilizer

2015 ◽  
Vol 132 ◽  
pp. 45-53 ◽  
Author(s):  
M. Jarpa-Parra ◽  
F. Bamdad ◽  
Z. Tian ◽  
Hongbo Zeng ◽  
Feral Temelli ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Surface Properties ◽  
Foam Stabilizer

Relationship between Measured Diffusion Coefficients and Calculated Molecular Surface Properties

1996 ◽  
Vol 100 (13) ◽  
pp. 5538-5540 ◽  
Author(s):  
Peter Politzer ◽  
Jane S. Murray ◽  
Pär Flodmark
Keyword(s):  
Surface Properties ◽  
Diffusion Coefficients ◽  
Molecular Surface

scholarly journals Defining the Ail Ligand-Binding Surface: Hydrophobic Residues in Two Extracellular Loops Mediate Cell and Extracellular Matrix Binding To Facilitate Yop Delivery

2017 ◽  
Vol 85 (4) ◽  
Author(s):  
Tiffany M. Tsang ◽  
Jeffrey S. Wiese ◽  
Jamal A. Alhabeil ◽  
Lisa D. Usselman ◽  
Joshua J. Thomson ◽  
...  
Keyword(s):  
Hydrophobic Interactions ◽  
Binding Activity ◽  
Host Cells ◽  
Cell Binding ◽  
Content Type ◽  
Mutant Proteins ◽  
Hydrophobic Residues ◽  
Extracellular Loops ◽  
Binding Surface ◽  
Mediate Cell

ABSTRACT Yersinia pestis, the causative agent of plague, binds host cells to deliver cytotoxic Yop proteins into the cytoplasm that prevent phagocytosis and generation of proinflammatory cytokines. Ail is an eight-stranded β-barrel outer membrane protein with four extracellular loops that mediates cell binding and resistance to human serum. Following the deletion of each of the four extracellular loops that potentially interact with host cells, the Ail-Δloop 2 and Ail-Δloop 3 mutant proteins had no cell-binding activity while Ail-Δloop 4 maintained cell binding (the Ail-Δloop 1 protein was unstable). Using the codon mutagenesis scheme SWIM (selection without isolation of mutants), we identified individual residues in loops 1, 2, and 3 that contribute to host cell binding. While several residues contributed to the binding of host cells and purified fibronectin and laminin, as well as Yop delivery, three mutations, F80A (loop 2), S128A (loop 3), and F130A (loop 3), produced particularly severe defects in cell binding. Combining these mutations led to an even greater reduction in cell binding and severely impaired Yop delivery with only a slight defect in serum resistance. These findings demonstrate that Y. pestis Ail uses multiple extracellular loops to interact with substrates important for adhesion via polyvalent hydrophobic interactions.

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