Hydrophobic clusters in protein structures

Arunachalam, J.; Gautham, N.

doi:10.1002/prot.21881

Cited by 17 publications

(14 citation statements)

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“…We considered hydrophobic groups within 4.5 Å of each other as interacting. Other researchers have used the same cutoff distance to identify interacting hydrophobic groups [ 20 , 21 ].…”

Section: Methodsmentioning

confidence: 99%

The origin of β-strand bending in globular proteins

et al. 2015

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BackgroundMany β-strands are not flat but bend and/or twist. However, although almost all β-strands have a twist, not all have a bend, suggesting that the underlying force(s) driving β-strand bending is distinct from that for the twist. We, therefore, investigated the physical origin(s) of β-strand bends.MethodsWe calculated rotation, twist and bend angles for a four-residue short frame. Fixed-length fragments consisting of six residues found in three consecutive short frames were used to evaluate the twist and bend angles of full-length β-strands.ResultsWe calculated and statistically analyzed the twist and bend angles of β-strands found in globular proteins with known three-dimensional structures. The results show that full-length β-strand bend angles are related to the nearby aromatic residue content, whereas local bend angles are related to the nearby aliphatic residue content. Furthermore, it appears that β-strands bend to maximize their hydrophobic contacts with an abutting hydrophobic surface or to form a hydrophobic side-chain cluster when an abutting hydrophobic surface is absent.ConclusionsWe conclude that the dominant driving force for full-length β-strand bends is the hydrophobic interaction involving aromatic residues, whereas that for local β-strand bends is the hydrophobic interaction involving aliphatic residues.Electronic supplementary materialThe online version of this article (doi:10.1186/s12900-015-0048-y) contains supplementary material, which is available to authorized users.

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“…We considered hydrophobic groups within 4.5 Å of each other as interacting. Other researchers have used the same cutoff distance to identify interacting hydrophobic groups [ 20 , 21 ].…”

Section: Methodsmentioning

confidence: 99%

The origin of β-strand bending in globular proteins

et al. 2015

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“…As other caseins do not form hydrophobic interaction, so there is no dissociation upon cooling. According to amino acid concentrations, 28% of κ casein, 30% of α s2 casein, 32% of α s1 casein and 34% of β casein residues are hydrophobic, or about 1 in 3 [51,65]. Hydrophobic Clustering Analysis (HCA) was carried out by Horne, 2017 to explore the hydrophobic residues along the caseins sequence.…”

Section: Hydrophobic Clustering Of Caseinsmentioning

confidence: 99%

Casein Micelles as an Emerging Delivery System for Bioactive Food Components

Sadiq

Gill

Chandrapala

2021

Foods

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Bioactive food components have potential health benefits but are highly susceptible for degradation under adverse conditions such as light, pH, temperature and oxygen. Furthermore, they are known to have poor solubilities, low stabilities and low bioavailabilities in the gastrointestinal tract. Hence, technologies that can retain, protect and enable their targeted delivery are significant to the food industry. Amongst these, microencapsulation of bioactives has emerged as a promising technology. The present review evaluates the potential use of casein micelles (CMs) as a bioactive delivery system. The review discusses in depth how physicochemical and techno-functional properties of CMs can be modified by secondary processing parameters in making them a choice for the delivery of food bioactives in functional foods. CMs are an assembly of four types of caseins, (αs1, αs2, β and κ casein) with calcium phosphate. They possess hydrophobic and hydrophilic properties that make them ideal for encapsulation of food bioactives. In addition, CMs have a self-assembling nature to incorporate bioactives, remarkable surface activity to stabilise emulsions and the ability to bind hydrophobic components when heated. Moreover, CMs can act as natural hydrogels to encapsulate minerals, bind with polymers to form nano capsules and possess pH swelling behaviour for targeted and controlled release of bioactives in the GI tract. Although numerous novel advancements of employing CMs as an effective delivery have been reported in recent years, more comprehensive studies are required to increase the understanding of how variation in structural properties of CMs be utilised to deliver bioactives with different physical, chemical and structural properties.

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“…The Bigelow scale is no longer used; it contains a number of errors and omissions, including an unusually high hydrophobicity for the Pro residue compared with the more widely accepted value, close to that of the hydrophilic residue His, in the scale of Kyte and Doolittle (1982). Proline is not classified as a hydrophobic residue; it is seldom found in the core of globular proteins (Macarthur and Thornton, 1991;Le Questel et al, 1993) or in clusters of hydrophobic residues (Arunachalam and Gautham, 2008), partly because of the restricted range of Ramachandran angles accessible to imino acids and partly because the backbone carbonyl moiety is an excellent H-bond acceptor, making the residue more hydrophilic than its hydrophobicity would suggest, even on the scale of Kyte and Doolittle (1982). Likewise, the side chain of Gln can act as an H-bond acceptor and donor so the energetic cost of desolvating Gln is high.…”

Section: Quaternary Structures and The Hydrophobic Effectmentioning

confidence: 99%

Invited review: Caseins and the casein micelle: Their biological functions, structures, and behavior in foods

Holt

Carver

Ecroyd

et al. 2013

Journal of Dairy Science

386

240

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A typical casein micelle contains thousands of casein molecules, most of which form thermodynamically stable complexes with nanoclusters of amorphous calcium phosphate. Like many other unfolded proteins, caseins have an actual or potential tendency to assemble into toxic amyloid fibrils, particularly at the high concentrations found in milk. Fibrils do not form in milk because an alternative aggregation pathway is followed that results in formation of the casein micelle. As a result of forming micelles, nutritious milk can be secreted and stored without causing either pathological calcification or amyloidosis of the mother's mammary tissue. The ability to sequester nanoclusters of amorphous calcium phosphate in a stable complex is not unique to caseins. It has been demonstrated using a number of noncasein secreted phosphoproteins and may be of general physiological importance in preventing calcification of other biofluids and soft tissues. Thus, competent noncasein phosphoproteins have similar patterns of phosphorylation and the same type of flexible, unfolded conformation as caseins. The ability to suppress amyloid fibril formation by forming an alternative amorphous aggregate is also not unique to caseins and underlies the action of molecular chaperones such as the small heat-shock proteins. The open structure of the protein matrix of casein micelles is fragile and easily perturbed by changes in its environment. Perturbations can cause the polypeptide chains to segregate into regions of greater and lesser density. As a result, the reliable determination of the native structure of casein micelles continues to be extremely challenging. The biological functions of caseins, such as their chaperone activity, are determined by their composition and flexible conformation and by how the casein polypeptide chains interact with each other. These same properties determine how caseins behave in the manufacture of many dairy products and how they can be used as functional ingredients in other foods. aBStraCtA typical casein micelle contains thousands of casein molecules, most of which form thermodynamically stable complexes with nanoclusters of amorphous calcium phosphate. Like many other unfolded proteins, caseins have an actual or potential tendency to assemble into toxic amyloid fibrils, particularly at the high concentrations found in milk. Fibrils do not form in milk because an alternative aggregation pathway is followed that results in formation of the casein micelle. As a result of forming micelles, nutritious milk can be secreted and stored without causing either pathological calcification or amyloidosis of the mother's mammary tissue. The ability to sequester nanoclusters of amorphous calcium phosphate in a stable complex is not unique to caseins. It has been demonstrated using a number of noncasein secreted phosphoproteins and may be of general physiological importance in preventing calcification of other biofluids and soft tissues. Thus, competent noncasein phosphoproteins have similar patterns of phosp...

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Hydrophobic clusters in protein structures

Cited by 17 publications

References 50 publications

The origin of β-strand bending in globular proteins

The origin of β-strand bending in globular proteins

Casein Micelles as an Emerging Delivery System for Bioactive Food Components

Invited review: Caseins and the casein micelle: Their biological functions, structures, and behavior in foods

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