ChemInform Abstract: The Impact of the Amino Acid Sequence on the Specificity of Copper(II) Interactions with Peptides Having Non-Coordinating Side-Chains

ChemInform ◽  
2010 ◽  
Vol 29 (22) ◽  
pp. no-no
Author(s):  
W. BAL ◽  
M. DYBA ◽  
H. KOZLOWSKI
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Side Chains ◽  
The Impact

scholarly journals Expression, purification and crystallization of a protein resulting from the inversion of the amino-acid sequence of a helical bundle

2017 ◽  
Vol 73 (1) ◽  
pp. 51-53
Author(s):  
Aikaterini Kefala ◽  
Dina Kotsifaki ◽  
Mary Providaki ◽  
Maria Amprazi ◽  
Michael Kokkinidis
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Three Dimensional ◽  
Unfolded Proteins ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Helical Bundle ◽  
Sequence Inversion ◽  
The Impact

Earlier studies have found that the occurrence of inverse sequence identity in proteins is not indicative of three-dimensional similarity, but rather leads to different folds or unfolded proteins. Short helices, however, frequently keep their conformations when their sequences are inverted. To explore the impact of sequence inversion on long helices, revRM6, with the inverse amino-acid sequence relative to RM6, a highly stable variant of the ColE1 Rop protein, was engineered. RM6 is a highly regular four-α-helical bundle that serves as a model system for protein-folding studies. Here, the crystallization and preliminary crystallographic characterization of revRM6 are reported. The protein was overexpressed inEscherichia coli, purified to homogeneity and crystallized. The crystals belonged to space groupP41212, with unit-cell parametersa=b= 44.98,c= 159.74 Å, and diffracted to a resolution of 3.45 Å.

Weitere Untersuchungen zur Aminosäuresequenz des Melittins, II.

1969 ◽  
Vol 24 (4) ◽  
pp. 415-418 ◽  
Author(s):  
Joachim Jentsch
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
High Specificity ◽  
Bee Venom ◽  
Side Chains ◽  
Amino Groups ◽  
Crotalus Atrox ◽  
Peptide Bonds ◽  
Rattlesnake Venom

Degradation of melittin with α-Protease from Crotalus atrox venom (rattlesnake) confirmed the amino acid sequence of the toxic main peptide from bee venom. Hydrolysis occured mainly at the peptide bonds whose amino groups were provided by hydrophobic side chains such as valine, leucine and isoleucine bonds. However, on the contrary one glutamine bond was cleaved. Neverthelness, regarding the relatively high specificity, rattlesnake venom protease may be a valuable reagent for further sequence studies.

scholarly journals Functional Characterization of the N-Terminal C2 Domain fromArabidopsis thalianaPhospholipase Dαand Dβ

2016 ◽  
Vol 2016 ◽  
pp. 1-15 ◽  
Author(s):  
Renaud Rahier ◽  
Alexandre Noiriel ◽  
Abdelkarim Abousalham
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Functional Characterization ◽  
Resonance Energy ◽  
Lipid Binding ◽  
C2 Domain ◽  
Dot Blot ◽  
Independent Manner ◽  
C2 Domains ◽  
The Impact

Most of plant phospholipases D (PLD) exhibit a C2-lipid binding domain of around 130 amino acid residues at their N-terminal region, involved in their Ca2+-dependent membrane binding. In this study, we expressed and partially purified catalytically active PLDαfromArabidopsis thaliana(AtPLDα) in the yeastPichia pastoris. The N-terminal amino acid sequence of the recombinant AtPLDαwas found to be NVEETIGV and thus to lack the first 35 amino acid belonging to the C2 domain, as found in other recombinant or plant purified PLDs. To investigate the impact of such a cleavage on the functionality of C2 domains, we expressed, inE. coli, purified, and refolded the mature-like form of the C2 domain of the AtPLDαalong with its equivalent C2 domain of the AtPLDβ, for the sake of comparison. Using Förster Resonance Energy Transfer and dot-blot assays, both C2 domains were shown to bind phosphatidylglycerol in a Ca2+-independent manner while phosphatidic acid and phosphatidylserine binding were found to be enhanced in the presence of Ca2+. Amino acid sequence alignment and molecular modeling of both C2 domains with known C2 domain structures revealed the presence of a novel Ca2+-binding site within the C2 domain of AtPLDα.

Synthesis and chiroptical properties of heterodetic cyclic hexapeptides related to oxytocin ring moiety

1980 ◽  
Vol 45 (4) ◽  
pp. 1109-1131 ◽  
Author(s):  
Ivo Frič ◽  
Lyudmila I. Leonteva ◽  
Petr Maloň ◽  
Karel Jošt ◽  
Karel Bláha
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Peptide Synthesis ◽  
Spatial Arrangement ◽  
Cd Spectroscopy ◽  
Side Chains ◽  
Peptide Backbone ◽  
Chiroptical Properties ◽  
Disulfide Group ◽  
Cyclic Hexapeptides

Cyclic disulfides of cysteinyl-tetraglycyl-cysteine (Ia), cysteinyl-tyrosyl-triglycyl-cysteine (Ib) and cysteinyl-tyrosyl-isoleucyl-diglycyl-cysteine (Ic) were synthesized by classical methods of peptide synthesis. The actions of solvent and of side chains in the positions 2 and 3 on the conformational arrangement of the peptide backbone and the disulfide group were investigated by means of CD spectroscopy. Some mechanisms which co-operate in stabilizing the oxytocin conformation were identified. Hence, it may be deduced, that the amino acid sequence in the positions 1-3 determines the spatial arrangement characteristic for oxytocin, at least in a protonating medium.

scholarly journals Role of pKA in Charge Regulation and Conformation of Various Peptide Sequences

Polymers ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 214
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Zdeněk Tošner ◽  
Miroslav Štěpánek ◽  
Peter Košovan
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Total Charge ◽  
Side Chains ◽  
Intrinsically Disordered ◽  
Acid And Base ◽  
Base Side

Peptides containing amino acids with ionisable side chains represent a typical example of weak ampholytes, that is, molecules with multiple titratable acid and base groups, which generally exhibit charge regulating properties upon changes in pH. Charged groups on an ampholyte interact electrostatically with each other, and their interaction is coupled to conformation of the (macro)molecule, resulting in a complex feedback loop. Their charge-regulating properties are primarily determined by the pKA of individual ionisable side-chains, modulated by electrostatic interactions between the charged groups. The latter is determined by the amino acid sequence in the peptide chain. In our previous work we introduced a simple coarse-grained model of a flexible peptide. We validated it against experiments, demonstrating its ability to quantitatively predict charge on various peptides in a broad range of pH. In the current work, we investigated two types of peptide sequences: diblock and alternating, each of them consisting of an equal number of amino acids with acid and base side-chains. We showed that changing the sequence while keeping the same overall composition has a profound effect on the conformation, whereas it practically does not affect total charge on the peptide. Nevertheless, the sequence significantly affects the charge state of individual groups, showing that the zero net effect on the total charge is a consequence of unexpected cancellation of effects. Furthermore, we investigated how the difference between the pKA of acid and base side chains affects the charge and conformation of the peptide, showing that it is possible to tune the charge-regulating properties by following simple guiding principles based on the pKA and on the amino acid sequence. Our current results provide a theoretical basis for understanding of the complex coupling between the ionisation and conformation in flexible polyampholytes, including synthetic polymers, biomimetic materials and biological molecules, such as intrinsically disordered proteins, whose function can be regulated by changes in the pH.

scholarly journals Passaging impact of H9N2 avian influenza virus in hamsters on its pathogenicity and genetic variability

2014 ◽  
Vol 8 (05) ◽  
pp. 570-580 ◽  
Author(s):  
Houssam A. Shaib ◽  
Nelly Cochet ◽  
Thierry Ribeiro ◽  
Afif M Abdel Nour ◽  
Georges Nemer ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Avian Influenza ◽  
Mammalian Cells ◽  
Pcr Amplification ◽  
Amino Acid Sequences ◽  
Influenza Viruses ◽  
H9n2 Virus ◽  
World Health ◽  
The Impact

Introduction: Avian influenza viruses of the H9N2 subtype have been reported to cause human infections. This study demonstrates the impact of nasal viral passaging of avian H9N2 in hamsters on its cross species-pathogenic adaptability and variability of amino acid sequences of the hemagglutinin (HA) and neuraminidase (NA) stalk. Methodology: Three intranasal passagings of avian H9N2 in hamsters P1, P2, and P3 were accomplished. Morbidity signs and lesions were observed three days post viral inoculation. The HA test was used for presumptive detection of H9N2 virus in the trachea and lungs of the hamsters challenged with the differently passaged viruses. Different primers were used for PCR amplification of the HA1 and NA stalk regions of the differently passaged H9N2 viruses, followed by sequence alignment. Results: The morbidity signs indicated low pathogenicity of the differently passaged H9N2 viruses in hamsters. The frequency of gross and microscopic lesions in the tracheas and lungs were insignificantly different among hamsters challenged with the differently passaged H9N2 viruses (p > 0.05). There was 100% similarity in the amino acid sequence of the HA gene of most passaged viruses. The amino acid sequence of the neuraminidase in the third passaged H9N2 virus recovered from lungs showed a R46P mutation that might have a role in the pathogenic adaptability of P3 viruses in hamsters’ lungs. Conclusions: The apparent adaptation of avian H9N2 virus to mammalian cells is in agreement with the World Health Organization’s alertness for a possible public health threat by this adaptable virus.

scholarly journals Aminopeptidase C of Aspergillus niger Is a Novel Phenylalanine Aminopeptidase

2003 ◽  
Vol 69 (2) ◽  
pp. 1246-1250 ◽  
Author(s):  
Daniëlle E. J. W. Basten ◽  
Peter J. T. Dekker ◽  
Peter J. Schaap
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aspergillus Niger ◽  
Amino Acid Sequence ◽  
Aminopeptidase Activity ◽  
Side Chains ◽  
Peptide Hydrolase ◽  
Peptide Hydrolases ◽  
Aromatic Side Chains

ABSTRACT A novel enzyme with a specific phenylalanine aminopeptidase activity (ApsC) from Aspergillus niger (CBS 120.49) has been characterized. The derived amino acid sequence is not similar to any previously characterized aminopeptidase sequence but does share similarity with some mammalian acyl-peptide hydrolase sequences. ApsC was found to be most active towards phenylalanine β-naphthylamide (F-βNA) and phenylalanine para-nitroanilide (F-pNA), but it also displayed activity towards other amino acids with aromatic side chains coupled to βNA; other amino acids with nonaromatic side chains coupled to either pNA or βNA were not hydrolyzed or were poorly hydrolyzed. ApsC was not able to hydrolyze N-acetylalanine-pNA, a substrate for acyl-peptide hydrolases.

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.

Paris I Dysfibrinogenemia: A Point Mutation in Intron 8 Results in Insertion of a 15 Amino Acid Sequence in the Fibrinogen γ-Chain

1993 ◽  
Vol 69 (03) ◽  
pp. 217-220 ◽  
Author(s):  
Jonathan B Rosenberg ◽  
Peter J Newman ◽  
Michael W Mosesson ◽  
Marie-Claude Guillin ◽  
David L Amrani
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Point Mutation ◽  
Genomic Dna ◽  
Comparative Sequence Analysis ◽  
Chain Gene ◽  
Molecular Defect ◽  
Nucleotide Position ◽  
Normal Individuals ◽  
Polymerase Chain

SummaryParis I dysfibrinogenemia results in the production of a fibrinogen molecule containing a functionally abnormal γ-chain. We determined the basis of the molecular defect using polymerase chain reaction (PCR) to amplify the γ-chain region of the Paris I subject’s genomic DNA. Comparative sequence analysis of cloned PCR segments of normal and Paris I genomic DNA revealed only an A→G point mutation occurring at nucleotide position 6588 within intron 8 of the Paris I γ-chain gene. We examined six normal individuals and found only normal sequence in this region, indicating that this change is not likely to represent a normal polymorphism. This nucleotide change leads to a 45 bp fragment being inserted between exons 8 and 9 in the mature γparis I chain mRNA, and encodes a 15 amino acid insert after γ350 [M-C-G-E-A-L-P-M-L-K-D-P-C-Y]. Alternative splicing of this region from intron 8 into the mature Paris I γ-chain mRNA also results after translation into a substitution of S for G at position γ351. Biochemical studies of 14C-iodoacetamide incorporation into disulfide-reduced Paris I and normal fibrinogen corroborated the molecular biologic predictions that two additional cysteine residues exist within the γpariS I chain. We conclude that the insertion of this amino acid sequence leads to a conformationallyaltered, and dysfunctional γ-chain in Paris I fibrinogen.

Sign in / Sign up

Export Citation Format

Share Document