The unfolding transition state of ubiquitin with charged residues has higher energy than that with hydrophobic residues

2020 ◽  
Vol 22 (40) ◽  
pp. 23158-23168
Author(s):  
Tathagata Nandi ◽  
Amogh Desai ◽  
Sri Rama Koti Ainavarapu
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Transition State ◽  
State Structure ◽  
Native State ◽  
Hydrophobic Residues ◽  
Folding Pathways ◽  
Charged Residues

The native-state structure and folding pathways of a protein are encoded in its amino acid sequence.

scholarly journals Purification and partial characterization of a lectin from Caesalpinia tinctoria Domb, ex Dc fruits

2003 ◽  
Vol 15 (2) ◽  
pp. 119-122 ◽  
Author(s):  
Marli Lourdes de Oliveira ◽  
Leila Maria Beltramini ◽  
Salvatore Giovanni de Simone ◽  
Maria Helena Nasser Brumano ◽  
Rosemeire Aparecida Silva-Lucca ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Terminal Amino Acid ◽  
Saline Extract ◽  
Hydrophobic Residues ◽  
Terminal Amino ◽  
Helix Conformation ◽  
Far Ultraviolet ◽  
Terminal Amino Acid Sequence

A lectin was isolated from the pod saline extract of Caesalpinia tinctoria by dialoconcentration on Centripep-10 and affinity chromatography on chitin column. The purified lectin was partially characterized with respect to its biochemical and structural properties. It contains 8.3 % of carbohydrate and exhibited an agglutinating activity against human erythrocytes (ABO groups). Its amino acid composition was characterized by a great number of acidic and hydrophobic residues and the estimated molecular mass was 12.5 kDa. The presence of only one N-terminal amino acid sequence (D¹-V-P-A-Y-V-Y-V-H-F10-G-F-G-E-E-H-R -D-V-F20-D), showed the homogeneity of the purified lectin. The far-ultraviolet circular dichroism (CD) spectrum of lectin indicated that it contains 10 % a-helix, 38 % b-sheet, 28 % unordered form and 6 % of P II (poly-L-proline II helix conformation).

Axially projected collagen structures

1974 ◽  
Vol 187 (1086) ◽  
pp. 37-46 ◽  
Keyword(s):  
Electron Microscope ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Optical Diffraction ◽  
X Ray ◽  
Symmetric Structure ◽  
Charged Residues ◽  
Precise Version

The positively stained bands of the segment long spacing (s. l. s.) pattern of collagen are shown to be accounted for by the distribution of charged residues in the sequence of the α 1 chain. The native tendon pattern can be constructed by repeated stagger of 234 residues between adjacent molecules, as in the Hodge-Petruska model. The relation of the precise version of this model to negatively stained patterns is shown and the part played by the teleopeptides revealed. A brief discussion of the meridional X-ray reflexions in terms of amino acid sequence is presented and related to electron microscope patterns. Optical diffraction suggests an approximate thirding of the D period. Finally a symmetric structure formed by reconstituting chick cartilage collagen is analysed and its origins revealed as an elaboration of the Hodge-Petruska model. It is shown to be related to the fibrous long spacing (f. l. s. I) structure.

scholarly journals Complete nucleotide sequence and deduced polypeptide sequence of a nonmuscle myosin heavy chain gene from Acanthamoeba: evidence of a hinge in the rodlike tail.

1987 ◽  
Vol 105 (2) ◽  
pp. 913-925 ◽  
Author(s):  
J A Hammer ◽  
B Bowers ◽  
B M Paterson ◽  
E D Korn
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Heavy Chain ◽  
Myosin Ii ◽  
Myosin Filament ◽  
Chain Gene ◽  
Nonmuscle Myosin ◽  
Heavy Chain Gene ◽  
Charged Residues ◽  
Globular Head

We have completely sequenced a gene encoding the heavy chain of myosin II, a nonmuscle myosin from the soil ameba Acanthamoeba castellanii. The gene spans 6 kb, is split by three small introns, and encodes a 1,509-residue heavy chain polypeptide. The positions of the three introns are largely conserved relative to characterized vertebrate and invertebrate muscle myosin genes. The deduced myosin II globular head amino acid sequence shows a high degree of similarity with the globular head sequences of the rat embryonic skeletal muscle and nematode unc 54 muscle myosins. By contrast, there is no unique way to align the deduced myosin II rod amino acid sequence with the rod sequence of these muscle myosins. Nevertheless, the periodicities of hydrophobic and charged residues in the myosin II rod sequence, which dictate the coiled-coil structure of the rod and its associations within the myosin filament, are very similar to those of the muscle myosins. We conclude that this ameba nonmuscle myosin shares with the muscle myosins of vertebrates and invertebrates an ancestral heavy chain gene. The low level of direct sequence similarity between the rod sequences of myosin II and muscle myosins probably reflects a general tolerance for residue changes in the rod domain (as long as the periodicities of hydrophobic and charged residues are largely maintained), the relative evolutionary "ages" of these myosins, and specific differences between the filament properties of myosin II and muscle myosins. Finally, sequence analysis and electron microscopy reveal the presence within the myosin II rodlike tail of a well-defined hinge region where sharp bending can occur. We speculate that this hinge may play a key role in mediating the effect of heavy chain phosphorylation on enzymatic activity.

The Histidine and Methionine Sequences of Rabbit Skeletal Tropomyosin

1972 ◽  
Vol 50 (3) ◽  
pp. 312-329 ◽  
Author(s):  
R. S. Hodges ◽  
L. B. Smillie
Keyword(s):  
Amino Acid ◽  
Sequence Analysis ◽  
Amino Acid Sequence ◽  
Coiled Coil ◽  
Sequence Information ◽  
Chain Packing ◽  
Hydrophobic Residues ◽  
Coil Structure ◽  
Methionine Residues ◽  
Polypeptide Chains

Amino acid analyses of tropomyosin have previously shown four histidine and 13–14 methionine residues per mole (70 000 daltons) of tropomyosin. The isolation of two unique histidyl and five unique methionyl sequences is described. The number of unique methionyl peptides will undoubtedly be increased when more extensive sequence information becomes available although the value of 2 for the unique histidine sequences is considered to be a maximal one. These data support the conclusion that the two subunits of tropomyosin are similar in amino acid sequence. Both the acetylated NH2-terminal and COOH-terminal sequences of the protein have been determined in this study. The isolation and sequence analysis of two varieties of peptides arising from the COOH-terminus of the protein indicates either a degree of proteolysis during its isolation or a difference in the constituent polypeptide chains of tropomyosin in this region of their structures. The limited sequences reported indicate a repeat of hydrophobic residues as required by the inter-chain packing of a coiled-coil structure.

scholarly journals Apical targeting of the P2Y4 receptor is directed by hydrophobic and basic residues in the cytoplasmic tail

2013 ◽  
Vol 304 (3) ◽  
pp. C228-C239 ◽  
Author(s):  
D. Ross DuBose ◽  
Samuel C. Wolff ◽  
Ai-Dong Qi ◽  
Izabela Naruszewicz ◽  
Robert A. Nicholas
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Basolateral Membrane ◽  
Chloride Secretion ◽  
Common Mechanism ◽  
Main Body ◽  
Sequence Alignments ◽  
Hydrophobic Residues ◽  
Intestinal Chloride Secretion ◽  
Apical Sorting

The P2Y4 receptor is selectively targeted to the apical membrane in polarized epithelial cell lines and has been shown to play a key role in intestinal chloride secretion. In this study, we delimit a 23 amino acid sequence within the P2Y4 receptor C-tail that directs its apical targeting. Using a mutagenesis approach, we found that four hydrophobic residues near the COOH-terminal end of the signal are necessary for apical sorting, whereas two basic residues near the NH2-terminal end of the signal are involved to a lesser extent. Interestingly, mutation of the key hydrophobic residues results in a basolateral enrichment of the receptor construct, suggesting that the apical targeting sequence may prevent insertion or disrupt stability of the receptor at the basolateral membrane. The signal is not sequence specific, as an inversion of the 23 amino acid sequence does not disrupt apical targeting. We also show that the apical targeting sequence is an autonomous signal and is capable of redistributing the normally basolateral P2Y12 receptor, suggesting that the apical signal is dominant over the basolateral signal in the main body of the P2Y12 receptor. The targeting sequence is unique to the P2Y4 receptor, and sequence alignments of the COOH-terminal tail of mammalian orthologs reveal that the hydrophobic residues in the targeting signal are highly conserved. These data define the novel apical sorting signal of the P2Y4 receptor, which may represent a common mechanism for trafficking of epithelial transmembrane proteins.

SEARCH FOR FOLDING INITIATION SITES FROM AMINO ACID SEQUENCE

2008 ◽  
Vol 06 (04) ◽  
pp. 681-691 ◽  
Author(s):  
OXANA V. GALZITSKAYA
Keyword(s):  
Protein Folding ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Transition State ◽  
Initiation Site ◽  
Ribonuclease A ◽  
Fibril Formation ◽  
Protein Chain ◽  
Folding Nucleus ◽  
Key Residues

A crucial event in protein folding is the formation of a folding nucleus, which is a structured part of the protein chain in the transition state. We demonstrate a correlation between locations of residues involved in the folding nuclei and locations of predicted amyloidogenic regions. The average Φ-values are significantly greater inside amyloidogenic regions than outside them. We have found that fibril formation and normal folding involve many of the same key residues, giving an opportunity to outline the folding initiation site in protein chains. The search for folding initiation sites for apomyoglobin and ribonuclease. A coincides with the predictions made by other approaches.

The influence of amino acid sequence on structure and morphology of polydiacetylene containing peptide fibres

Soft Matter ◽  
2015 ◽  
Vol 11 (7) ◽  
pp. 1335-1344 ◽  
Author(s):  
Maaike Nieuwland ◽  
Nicole van Gijzel ◽  
Jan C. M. van Hest ◽  
Dennis W. P. M. Löwik
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Self Assembly ◽  
The Self ◽  
Peptide Amphiphile ◽  
Structure And Morphology ◽  
Charged Residues

The influence of positively and negatively charged residues on the self-assembly and morphology of peptide amphiphile fibres.

scholarly journals The Amino Acid Sequence of a Protein (Apovitellenin I) From the Low-density Lipoprotein of Emu Egg Yolk

1974 ◽  
Vol 27 (1) ◽  
pp. 15 ◽  
Author(s):  
TAA Dopheide ◽  
AS Inglis
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Low Density Lipoprotein ◽  
Density Lipoprotein ◽  
Egg Yolk ◽  
Side Chain ◽  
Low Density ◽  
Hydrophobic Residues ◽  
Polar Residues

The amino acid sequence of apovitellenin I from emu (Dromaius novae-hollandiae) egg yolk has been determined. Difficulties were encountered during sequencing, due to a labile Tyr-Val bond, which was hydrolysed readily by trypsin, chymotrypsin and pepsin. By use of a sequenator, this bond was easily characterized. The protein contains 84 residues and is devoid of half-cystine and histidine. Hydrophobic residues occur in clusters; two very hydrophobic sequences of 12 and 13 residues are present. A very hydrophilic sequence of seven residues contains nearly one-third of all side-chain charges in the molecule; the remainder of the polar residues are scattered throughout the sequence. In a number of instances, residues with opposite charges occur in adjacent positions.

The staining pattern of the tropomyosin sequence is displayed in a new paracrystal

1986 ◽  
Vol 44 ◽  
pp. 150-151
Author(s):  
M.K. Lamvik ◽  
L.L. Klatt
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Staining Pattern ◽  
Banding Patterns ◽  
Mass Thickness ◽  
New Form

Tropomyosin paracrystals have been used extensively as test specimens and magnification standards due to their clear periodic banding patterns. The paracrystal type discovered by Ohtsuki1 has been of particular interest as a test of unstained specimens because of alternating bands that differ by 50% in mass thickness. While producing specimens of this type, we came across a new paracrystal form. Since this new form displays aligned tropomyosin molecules without the overlaps that are characteristic of the Ohtsuki-type paracrystal, it presents a staining pattern that corresponds to the amino acid sequence of the molecule.

Isolation and Structural Charaderization of a Potent Inhibitor of Coagulation Factor Xa from the Leech Haementeria ghilianii

1989 ◽  
Vol 61 (03) ◽  
pp. 437-441 ◽  
Author(s):  
Cindra Condra ◽  
Elka Nutt ◽  
Christopher J Petroski ◽  
Ellen Simpson ◽  
P A Friedman ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Salivary Gland ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Western Blot ◽  
Potent Inhibitor ◽  
Factor Xa ◽  
Coagulation Factor ◽  
Sds Page ◽  
Bovine Factor

SummaryThe present work reports the discovery and charactenzation of an anticoagulant protein in the salivary gland of the giant bloodsucking leech, H. ghilianii, which is a specific and potent inhibitor of coagulation factor Xa. The inhibitor, purified to homogeneity, displayed subnanomolar inhibition of bovine factor Xa and had a molecular weight of approximately 15,000 as deduced by denaturing SDS-PAGE. The amino acid sequence of the first 43 residues of the H. ghilianii derived inhibitor displayed a striking homology to antistasin, the recently described subnanomolar inhibitor of factor Xa isolated from the Mexican leech, H. officinalis. Antisera prepared to antistasin cross-reacted with the H. ghilianii protein in Western Blot analysis. These data indicate that the giant Amazonian leech, H. ghilianii, and the smaller Mexican leech, H. officinalrs, have similar proteins which disrupt the normal hemostatic clotting mechanisms in their mammalian host’s blood.

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