scholarly journals New Charge-Bearing Amino Acid Residues That Promote β-Sheet Secondary Structure

2014 ◽  
Vol 136 (47) ◽  
pp. 16683-16688 ◽  
Author(s):  
Stacy J. Maynard ◽  
Aaron M. Almeida ◽  
Yasuharu Yoshimi ◽  
Samuel H. Gellman
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Amino Acid Residues ◽  
Β Sheet

scholarly journals Analysis of the Secondary Structure of β-Amyloid (Aβ42) Fibrils by Systematic Proline Replacement

2004 ◽  
Vol 279 (50) ◽  
pp. 52781-52788 ◽  
Author(s):  
Akira Morimoto ◽  
Kazuhiro Irie ◽  
Kazuma Murakami ◽  
Yuichi Masuda ◽  
Hajime Ohigashi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Amyloid Fibrils ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Aβ Peptides ◽  
Amyloid Peptides ◽  
Aggregation Inhibitors ◽  
Β Amyloid ◽  
Β Sheet

Amyloid fibrils in Alzheimer's disease mainly consist of 40- and 42-mer β-amyloid peptides (Aβ40 and Aβ42) that exhibit aggregative ability and neurotoxicity. Although the aggregates of Aβ peptides are rich in intermolecular β-sheet, the precise secondary structure of Aβ in the aggregates remains unclear. To identify the amino acid residues involved in the β-sheet formation, 34 proline-substituted mutants of Aβ42 were synthesized and their aggregative ability and neurotoxicity on PC12 cells were examined. Prolines are rarely present in β-sheet, whereas they are easily accommodated in β-turn as a Pro-Xcorner. Among the mutants at positions 15-32, only E22P-Aβ42 extensively aggregated with stronger neurotoxicity than wild-type Aβ42, suggesting that the residues at positions 15-21 and 24-32 are involved in the β-sheet and that the turn at positions 22 and 23 plays a crucial role in the aggregation and neurotoxicity of Aβ42. The C-terminal proline mutants (A42P-, I41P-, and V40P-Aβ42) hardly aggregated with extremely weak cytotoxicity, whereas the C-terminal threonine mutants (A42T- and I41T-Aβ42) aggregated potently with significant cytotoxicity. These results indicate that the hydrophobicity of the C-terminal two residues of Aβ42 is not related to its aggregative ability and neurotoxicity, rather the C-terminal three residues adopt the β-sheet. These results demonstrate well the large difference in aggregative ability and neurotoxicity between Aβ42 and Aβ40. In contrast, the proline mutants at the N-terminal 13 residues showed potent aggregative ability and neurotoxicity similar to those of wild-type Aβ42. The identification of the β-sheet region of Aβ42 is a basis for designing new aggregation inhibitors of Aβ peptides.

Amino acid sequence restriction in relation to proteolysis

1983 ◽  
Vol 3 (3) ◽  
pp. 225-232 ◽  
Author(s):  
Hans Jórnvall ◽  
Bengt Persson
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Amino Acid Sequence ◽  
Distribution Patterns ◽  
Amino Acid Residues ◽  
Individual Protein ◽  
Proteolytic Cleavages ◽  
N Proteins

Distributions of amino acid residues in proteins show that proline is overrepresented in sequence positions following two basic residues ({LysArg}−{LysArg}), i.e. at sites similar to those susceptible to proteolytic cleavages of hormonal pro-forms. Conformational correlations further show that {LysArg}−{LysArg}-Pro sequences are often (8/11) not adiacent to elements of secondary structure, whereas the opposite applies to {LysArg}−{LysArg}-nonPro sequences (82/103 adjacent to elements of secondary structure). These distribution patterns from proteins in general also seem applicable in individual protein groups as demonstrated for some dehydrogenases. It appears possible that {LysArg}−{LysArg}-nonPro constitutes a restricted sequence, n proteins, and that proline, in addition to elements of secondary structure, contributes a means of avoiding unacceptable proteolytic processings of proteins in general.

Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation

2020 ◽  
Vol 17 (2) ◽  
pp. 95-106
Author(s):  
Neerja Thakur ◽  
Nikhil Sharma ◽  
Vijay Kumar ◽  
Tek Chand Bhalla
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
In Silico Analysis ◽  
Amino Acid Residues ◽  
Aliphatic Amino Acid ◽  
Physiochemical Properties ◽  
Commodity Chemicals ◽  
Acid Tolerant ◽  
Ph Adaptation ◽  
Silico Analysis

Background: Amidases are ubiquitous enzymes and biological functions of these enzymes vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals synthesis, pharmaceuticals agrochemicals and wastewater treatments. Methods: They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides, arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic site and preferred substrate. Despite their economic importance, we lack knowledge as to how these amidases withstand elevated pH and temperature whereas others cannot. Results: The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic organisms revealed some striking trends as to how amino acid composition varies significantly. Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L) in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant and alkali tolerant amidases. Conclusion: The present investigation insights physiochemical properties and dominance of some crucial amino acid residues in the primary and secondary structure of some amidases from acid-tolerant, alkali tolerant and neutrophilic microorganisms.

УРОВНИ ИЕРАРХИЧЕСКОЙ ОРГАНИЗАЦИИ БЕЛКОВЫХ ПОСЛЕДОВАТЕЛЬНОСТЕЙ. АНАЛИЗ ЭНТРОПИЙНЫХ ХАРАКТЕРИСТИК

2020 ◽  
Vol 65 (6) ◽  
pp. 1065-1071
Author(s):  
А.Н. Некрасов ◽  
◽  
Ю.П. Козмин ◽  
С.В. Козырев ◽  
Н.Г. Есипова ◽  
...  
Keyword(s):  
Mathematical Method ◽  
Amino Acid ◽  
Secondary Structure ◽  
Protein Sequences ◽  
Amino Acid Residues ◽  
Homologous Protein ◽  
Levels Of Organization

This research investigates 24 647 non-homologous protein sequences. The occurrence profile of peptapeptides was constructed for every sequence and hierarchically organized elements of various sizes were revealed by a special mathematical method in each profile. The correlations between these hierarchical elements were analyzed and it was shown that in a tested set of protein sequences there are 11 levels of protein organization with elements ranging in length from 7 to 56 amino acid residues. It was suggested that the identified levels of organization correspond to elements of a super-secondary structure with different topology.

scholarly journals Biochemical and Structural Insights into RNA Binding by Ssh10b, a Member of the Highly Conserved Sac10b Protein Family in Archaea

2013 ◽  
Vol 289 (3) ◽  
pp. 1478-1490 ◽  
Author(s):  
Li Guo ◽  
Jingjin Ding ◽  
Rong Guo ◽  
Yanjie Hou ◽  
Da-Cheng Wang ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Rna Binding ◽  
Amino Acid Residues ◽  
Sulfolobus Shibatae ◽  
Β Sheet ◽  
Structural Insights ◽  
Dsdna Binding ◽  
Local Distortions

Proteins of the Sac10b family are highly conserved in Archaea. Ssh10b, a member of the Sac10b family from the hyperthermophilic crenarchaeon Sulfolobus shibatae, binds to RNA in vivo. Here we show that binding by Ssh10b destabilizes RNA secondary structure. Structural analysis of Ssh10b in complex with a 25-bp RNA duplex containing local distortions reveals that Ssh10b binds the two RNA strands symmetrically as a tetramer with each dimer bound asymmetrically to a single RNA strand. Amino acid residues involved in double-stranded RNA binding are similar, but non-identical, to those in dsDNA binding. The dimer-dimer interaction mediated by the intermolecular β-sheet appears to facilitate the destabilization of base pairing in the secondary structure of RNA. Our results suggest that proteins of the Sac10b family may play important roles in RNA transactions requiring destabilization of RNA secondary structure in Sulfolobus.

What vibrations tell about proteins

2002 ◽  
Vol 35 (4) ◽  
pp. 369-430 ◽  
Author(s):  
Andreas Barth ◽  
Christian Zscherp
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Ir Spectroscopy ◽  
Reaction Mechanisms ◽  
Amino Acid Side Chain ◽  
Difference Spectroscopy ◽  
Transition Dipole ◽  
Dipole Coupling ◽  
Α Helix ◽  
Β Sheet

1. Introduction 3702. Infrared (IR) spectroscopy – general principles 3722.1 Vibrations 3722.2 Information that can be derived from the vibrational spectrum 3722.3 Absorption of IR light 3753. Protein IR absorption 3763.1 Amino-acid side-chain absorption 3763.2 Normal modes of the amide group 3814. Interactions that shape the amide I band 3824.1 Overview 3824.2 Through-bond coupling 3834.3 Hydrogen bonding 3834.4 Transition dipole coupling (TDC) 3835. The polarization and IR activity of amide I modes 3875.1 The coupled oscillator system 3875.2 Optically allowed transitions 3885.3 The infinite parallel β-sheet 3885.4 The infinite antiparallel β-sheet 3895.5 The infinite α-helix 3906. Calculation of the amide I band 3916.1 Overview 3916.2 Perturbation treatment by Miyazawa 3936.3 The parallel β-sheet 3946.4 The antiparallel β-sheet 3956.5 The α-helix 3966.6 Other secondary structures 3987. Experimental analysis of protein secondary structure 3987.1 Band fitting 3987.2 Methods using calibration sets 4017.3 Prediction quality 4038. Protein stability 4048.1 Thermal stability 4048.2 1H/2H exchange 4069. Molecular reaction mechanisms of proteins 4089.1 Reaction-induced IR difference spectroscopy 4089.2 The origin of difference bands 4099.3 The difference spectrum seen as a fingerprint of conformational change 4109.4 Molecular interpretation: strategies of band assignment 41610. Outlook 41911. Acknowledgements 42012. References 420This review deals with current concepts of vibrational spectroscopy for the investigation of protein structure and function. While the focus is on infrared (IR) spectroscopy, some of the general aspects also apply to Raman spectroscopy. Special emphasis is on the amide I vibration of the polypeptide backbone that is used for secondary-structure analysis. Theoretical as well as experimental aspects are covered including transition dipole coupling. Further topics are discussed, namely the absorption of amino-acid side-chains, 1H/2H exchange to study the conformational flexibility and reaction-induced difference spectroscopy for the investigation of reaction mechanisms with a focus on interpretation tools.

scholarly journals Conformation of dehydropentapeptides containing four achiral amino acid residues – controlling the role of L-valine

2014 ◽  
Vol 10 ◽  
pp. 660-666 ◽  
Author(s):  
Michał Jewgiński ◽  
Joanna Krzciuk-Gula ◽  
Maciej Makowski ◽  
Rafał Latajka ◽  
Paweł Kafarski
Keyword(s):  
Amino Acid ◽  
Nmr Spectroscopy ◽  
Secondary Structure ◽  
Helical Conformation ◽  
Structural Studies ◽  
Amino Acid Residues ◽  
Terminal Position ◽  
Dehydroamino Acid

Structural studies of pentapeptides containing an achiral block, built from two dehydroamino acid residues (ΔZPhe and ΔAla) and two glycines, as well as one chiral L-Val residue were performed using NMR spectroscopy. The key role of the L-Val residue in the generation of the secondary structure of peptides is discussed. The obtained results suggest that the strongest influence on the conformation of peptides arises from a valine residue inserted at the C-terminal position. The most ordered conformation was found for peptide Boc-Gly-ΔAla-Gly-ΔZPhe-Val-OMe (3), which adopts a right-handed helical conformation.

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