Hydrophobic Interactions at the Ccap Position of the C-capping Motif of α-Helices

Ermolenko, Dmitri N.; Thomas, Susan T.; Aurora, Rajeev; Gronenborn, Angela M.; Makhatadze, George I.

doi:10.1016/s0022-2836(02)00734-9

Cited by 39 publications

(50 citation statements)

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“…91 It was pointed out that the short side chain of serine does not contain enough non-polar atoms to be engaged in strong hydrophobic interactions and these relatively weak hydrophobic interactions are frequently compensated for by a local hydrogen bond of this side-chain back onto the helix (typically with one of the 4 nearest neighboring residues along the sequence). 91 Finally, a systematic analysis of a-helical propensity of a series of dodecapeptides containing alanine, asparagine, aspartate, glutamine, glutamate, and serine at the N-terminus and arginine, lysine, and alanine at the C-terminus, it was concluded that the a-helix-stabilizing abilities of these residues can be ranged as follows: aspartate > asparagine > serine > glutamate > glutamine > alanine at the N-terminus and arginine > lysine > alanine at the Cterminus. 92 As it was already mentioned, serine is a perfect residue for tight turns, where it can make hydrogen bonds to the neighboring backbone >NÀ ÀH and >CDO groups.…”

Section: Biological Significance Of Free Serinementioning

confidence: 99%

The intrinsic disorder alphabet. III. Dual personality of serine

Uversky

2015

Intrinsically Disordered Proteins

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Proteins are natural polypeptides consisting of 20 major amino acid residues, content and order of which in a given amino acid sequence defines the ability of a related protein to fold into unique functional state or to stay intrinsically disordered. Amino acid sequences code for both foldable (ordered) proteins/domains and for intrinsically disordered proteins (IDPs) and IDP regions (IDPRs), but these sequence codes are dramatically different. This difference starts with a very general property of the corresponding amino acid sequences, namely, their compositions. IDPs/IDPRs are enriched in specific disorder-promoting residues, whereas amino acid sequences of ordered proteins/domains typically contain more order-promoting residues. Therefore, the relative abundances of various amino acids in ordered and disordered proteins can be used to scale amino acids according to their disorder promoting potentials. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and represents serine, which is the third most disorder-promoting residue. Similar to previous publications, this review represents some physico-chemical properties of serine and the roles of this residue in structures and functions of ordered proteins, describes major posttranslational modifications tailored to serine, and finally gives an overview of roles of serine in structure and functions of intrinsically disordered proteins.

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Section: Biological Significance Of Free Serinementioning

confidence: 99%

The intrinsic disorder alphabet. III. Dual personality of serine

Uversky

2015

Intrinsically Disordered Proteins

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“…α-helices extremities have specific amino acid propensities [18][19][20][21][22] and specific physicochemical stabilizations [23]. For instance, C-capping motifs of α-helices are often stabilized by hydrophobic interactions between helical residues and residues outside the repetitive structures [24], e.g. the Pro C-capping motif [25].…”

Section: Secondary Structuresmentioning

confidence: 99%

Local Protein Structures

Offmann¹,

Tyagi²,

Brevern

2007

CBIO

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Protein structures are classically described as composed of two regular states, the α-helices and the β-strands and one non-regular and variable state, the coil. Nonetheless, this simple definition of secondary structures hides numerous limitations. In fact, the rules for secondary structure assignment are complex. Thus, numerous assignment methods based on different criteria have emerged leading to heterogeneous and diverging results. In the same way, 3 states may over-simplify the description of protein structure; 50% of all residues, i.e., the coil, are not genuinely described even when it encompass precise local protein structures.Description of local protein structures have hence focused on the elaboration of complete sets of small prototypes or "structural alphabets", able to analyze local protein structures and to approximate every part of the protein backbone. They have also been used to predict the protein backbone conformation and in ab initio / de novo methods. In this paper, we review different approaches towards the description of local structures, mainly through their description in terms of secondary structures and in terms of structural alphabets. We provide some insights into their potential applications.

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“…The presence of the desired mutations was confirmed by sequencing the entire gene. Proteins were expressed from plasmid carrying the ubiquitin gene under control of the T7 promoter in BL21(DE3) or JM109 (DE3) and purified as described previously [1]. Protein concentration was measured spectrophotometrically using a molar extinction coefficient of 1480 at 276 nm [1].…”

Section: Protein Mutagenesis Expression and Purificationmentioning

confidence: 99%

“…Proteins were expressed from plasmid carrying the ubiquitin gene under control of the T7 promoter in BL21(DE3) or JM109 (DE3) and purified as described previously [1]. Protein concentration was measured spectrophotometrically using a molar extinction coefficient of 1480 at 276 nm [1]. Correction for the light scattering was done as described [2].…”

Section: Protein Mutagenesis Expression and Purificationmentioning

confidence: 99%

“…The first residue proceeding the helix (C-cap residue) in the wild type ubiquitin is E34. Effects of amino acid substitution with all 20 naturally occurring amino acid at the C-cap on the stability of the ubiquitin variants revealed a number of interesting properties [1]. First, it was observed that stability changes correlate with the hydrophobic nature of residue 34.…”

Section: Introductionmentioning

confidence: 99%

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