Basic units of protein structure, folding, and function

Berezovsky, Igor N.; Zheng, Zejun

doi:10.1016/j.pbiomolbio.2016.09.009

Cited by 43 publications

(51 citation statements)

References 165 publications

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“…Whether evolution might take a similar route between folds is a matter of speculation, but an intriguing possibility nonetheless, considering the much greater probability of finding a path in this way. The possibility that disordered sequences may act as a bridge between protein folds is consistent with the role of loops as basic elements of protein structure [21][22][23]. .…”

Section: Fold Bridge Sequences Are Likely To Be Intrinsically Disorderedmentioning

confidence: 63%

“…Such sequences are expected to be very rare, given that the fraction of possible random sequences which actually fold to a specific, stable backbone structure is already extremely tiny [12][13][14][15][16][17][18]. An initial suggestion that such sequences may be possible comes from the context dependence of secondary structure elements [19,20] and since internal loops linking these elements are agnostic to secondary structure, they can also be shared between different topologies [21][22][23].…”

Section: Introductionmentioning

confidence: 99%

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Exploring the sequence fitness landscape of a bridge between protein folds

Tian

Best

2020

PLoS Comput Biol

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Most foldable protein sequences adopt only a single native fold. Recent protein design studies have, however, created protein sequences which fold into different structures apon changes of environment, or single point mutation, the best characterized example being the switch between the folds of the GA and GB binding domains of streptococcal protein G. To obtain further insight into the design of sequences which can switch folds, we have used a computational model for the fitness landscape of a single fold, built from the observed sequence variation of protein homologues. We have recently shown that such coevolutionary models can be used to design novel foldable sequences. By appropriately combining two of these models to describe the joint fitness landscape of GA and GB, we are able to describe the propensity of a given sequence for each of the two folds. We have successfully tested the combined model against the known series of designed GA/GB hybrids. Using Monte Carlo simulations on this landscape, we are able to identify pathways of mutations connecting the two folds. In the absence of a requirement for domain stability, the most frequent paths go via sequences in which neither domain is stably folded, reminiscent of the propensity for certain intrinsically disordered proteins to fold into different structures according to context. Even if the folded state is required to be stable, we find that there is nonetheless still a wide range of sequences which are close to the transition region and therefore likely fold switches, consistent with recent estimates that fold switching may be more widespread than had been thought.

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Section: Fold Bridge Sequences Are Likely To Be Intrinsically Disorderedmentioning

confidence: 63%

Section: Introductionmentioning

confidence: 99%

Exploring the sequence fitness landscape of a bridge between protein folds

Tian

Best

2020

PLoS Comput Biol

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“…The β-sheet structure relies on hydrogen bonds formed between C=O and H in two peptide chains or within one peptide chain to maintain conformational stability. Although all the peptide bonds are involved in the formation of interchain hydrogen bonds in the β-sheet structure, they are not as stable as the α-helix structure [32]. From Table 1, in the ordered structure, the content of α-helix decreased and that of β-sheet increased with the binding of EGCG, which implied that EGCG induced the continuous transformation of the α-helix structure to β-sheet [16].…”

Section: Resultsmentioning

confidence: 99%

The Effect of (−)-Epigallocatechin-3-Gallate Non-Covalent Interaction with the Glycosylated Protein on the Emulsion Property

Feng¹,

Jin²,

Gao³

et al. 2019

Polymers

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The effect of (−)-epigallocatechin-3-gallate (EGCG) on protein structure and emulsion properties of glycosylated black bean protein isolate (BBPI-G) were studied and compared to native black bean protein isolate (BBPI). The binding affinity of BBPI and BBPI-G with EGCG belonged to non-covalent interaction, which was determined by fluorescence quenching. EGCG attachment caused more disordered protein conformation, leading to a higher emulsification property. Among the different EGCG concentrations (0.10, 0.25, 0.50 mg/mL), the result revealed that the highest level of the emulsification property was obtained with 0.25 mg/mL EGCG. Therefore, the BBPI-EGCG and BBPI-G-EGCG prepared by 0.25 mg/mL EGCG were selected to fabricate oil-in-water (O/W) emulsions. After the addition of EGCG, the mean particle size of emulsions decreased with the increasing absolute value of zeta-potential, and more compact interfacial film was formed due to the higher percentage of interfacial protein adsorption (AP%). Meanwhile, EGCG also significantly reduced the lipid oxidation of emulsions.

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“…The protein structure and amino acid composition determine protein properties and function . Here we compared CHER of five different proteins (HSA‐ acidic globular protein of human plasma, lysozyme‐ basic globular antimicrobial enzyme, β‐synuclein ‐ acidic unfolded protein in brain tissue, H2 A and H3 ‐ basic histone proteins involved in chromatin structure in eukaryotic cells) with the aim to know if CPS analysis can provide useful information about the given protein.…”

Section: Comparison Of Individual Amino Acid (Aa) Content In Selectedmentioning

confidence: 99%

“…Proteins are the most versatile macromolecules in living systems, which perform many critical functions in all biological processes . Electroactivity of proteins was firstly described in Prof. J. Heyrovsky's laboratory by direct current (DC) polarography .…”

Section: Comparison Of Individual Amino Acid (Aa) Content In Selectedmentioning

confidence: 99%

Chronopotentiometric Analysis of Proteins at Charged Electrode Surfaces

et al. 2019

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Protein properties and functions are strongly dependent on the structure and amino acid content. In this work, catalytic hydrogen evolution reaction (CHER) of five proteins (human serum albumin, lysozyme, β‐synuclein, H2 A and H3 histones) were studied using constant current chronopotentiometric stripping (CPS) with the aim to find out the association between protein content and its electrochemical response. We have shown that the height and potential of CPS peak H in dependence on accumulation potential differed for the studied proteins, while the CPS peak area was almost the same for all of them. CV and CPS peaks H of Cys‐containing proteins appeared at less negative potentials in comparison to proteins without Cys, suggesting easier CHER. Acidic and basic proteins not containing Cys can be also recognized due to their different CPS response after their adsorption at the positive and negative charged interface.

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Basic units of protein structure, folding, and function

Cited by 43 publications

References 165 publications

Exploring the sequence fitness landscape of a bridge between protein folds

Exploring the sequence fitness landscape of a bridge between protein folds

The Effect of (−)-Epigallocatechin-3-Gallate Non-Covalent Interaction with the Glycosylated Protein on the Emulsion Property

Chronopotentiometric Analysis of Proteins at Charged Electrode Surfaces

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