Dipeptide Nanotubes, with N-Terminally Located ω-Amino Acid Residues, That are Stable Proteolytically, Thermally, and Over a Wide Range of pH

2008 ◽  
Vol 20 (6) ◽  
pp. 2282-2290 ◽  
Author(s):  
Samit Guha ◽  
Michael G. B. Drew ◽  
Arindam Banerjee
Keyword(s):  
Amino Acid ◽  
Amino Acid Residues ◽  
Wide Range

scholarly journals pIPredict: a computer tool for predicting isoelectric points of peptides and proteins

2015 ◽  
Vol 61 (1) ◽  
pp. 83-91 ◽  
Author(s):  
V.S. Skvortsov ◽  
N.N. Alekseychuk ◽  
D.V. Khudyakov ◽  
I.V. Romero Reyes
Keyword(s):  
Amino Acid ◽  
Posttranslational Modifications ◽  
Support Vector ◽  
Amino Acid Residues ◽  
Computer Tool ◽  
Wide Range ◽  
Vector Machines ◽  
Isoelectric Points ◽  
Peptide Fractionation ◽  
Made In

The data on approximate values of isoelectric point (pI) of peptides obtained during their fractionation by isoelectric focusing can be successfully used for the calculation of the pKa’s scale for amino acid residues. This scale can be used for pI prediction. The data of peptide fractionation also provides information about various posttranslational modifications (PTM), so that the prediction of pI may be performed for a wide range of protein forms. In this study, pKa values were calculated using a set of 13448 peptides (including 300 peptides with PTMs significant for pI calculation). The pKa constants were calculated for N-terminal, internal and C-terminal amino acid residues separately. The comparative analysis has shown that our scale increases the accuracy of pI prediction for peptides and proteins and successfully competes with traditional scales and such methods as support vector machines and artificial neural networks. The prediction performed by this scale, can be made in our program pIPredict with GUI written in JAVA as executable jar-archive. The program is freely available for academic users at http://www.ibmc.msk.ru/LPCIT/pIPredict. The software has also the possibility of pI predicting by some other scales; it recognizes some PTM and has the ability to use a custom scale.

scholarly journals Identification and Expression Analysis of Snf2 Family Proteins in Tomato (Solanum lycopersicum)

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Dongdong Zhang ◽  
Sujuan Gao ◽  
Ping Yang ◽  
Jie Yang ◽  
Songguang Yang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Solanum Lycopersicum ◽  
Developmental Stages ◽  
Profile Analysis ◽  
Nucleosome Position ◽  
Fruit Fly ◽  
Amino Acid Residues ◽  
Expression Profile Analysis ◽  
Wide Range ◽  
Chromatin Remodeling Complexes

As part of chromatin-remodeling complexes (CRCs), sucrose nonfermenting 2 (Snf2) family proteins alter chromatin structure and nucleosome position by utilizing the energy of ATP, which allows other regulatory proteins to access DNA. Plant genomes encode a large number of Snf2 proteins, and some of them have been shown to be the key regulators at different developmental stages in Arabidopsis. Yet, little is known about the functions of Snf2 proteins in tomato (Solanum lycopersicum). In this study, 45 Snf2s were identified by the homologous search using representative sequences from yeast (S. cerevisiae), fruit fly (D. melanogaster), and Arabidopsis (A. thaliana) against the tomato genome annotation dataset. Tomato Snf2 proteins (also named SlCHRs) could be clustered into 6 groups and distributed on 11 chromosomes. All SlCHRs contained a helicase-C domain with about 80 amino acid residues and a SNF2-N domain with more variable amino acid residues. In addition, other conserved motifs were also identified in SlCHRs by using the MEME program. Expression profile analysis indicated that tomato Snf2 family genes displayed a wide range of expressions in different tissues and some of them were regulated by the environmental stimuli such as salicylic acid, abscisic acid, salt, and cold. Taken together, these results provide insights into the functions of SlCHRs in tomato.

scholarly journals A Superfamily 3 DNA Helicase Encoded by Plasmid pSSVi from the Hyperthermophilic Archaeon Sulfolobus solfataricus Unwinds DNA as a Higher-Order Oligomer and Interacts with Host Primase

2010 ◽  
Vol 192 (7) ◽  
pp. 1853-1864 ◽  
Author(s):  
Xin Guo ◽  
Li Huang
Keyword(s):  
Amino Acid ◽  
Adenine Nucleotide ◽  
Sulfolobus Solfataricus ◽  
Dna Helicase ◽  
Higher Order ◽  
Hyperthermophilic Archaea ◽  
Amino Acid Residues ◽  
Protein Dimerization ◽  
Wide Range ◽  
Large Oligomer

ABSTRACT Replication proteins encoded by nonconjugative plasmids from the hyperthermophilic archaea of the order Sulfolobales show great diversity in amino acid sequence. We have biochemically characterized ORF735, a replication protein from pSSVi, an integrative nonconjugative plasmid from Sulfolobus solfataricus P2. We show that ORF735 is a DNA helicase of superfamily 3. It unwound double-stranded DNA (dsDNA) in a 3′-to-5′ direction in the presence of ATP over a wide range of temperatures, from 37°C to 75°C, and possessed DNA-stimulated ATPase activity. ORF735 existed in solution as a salt-stable dimer and was capable of assembling into a salt-sensitive oligomer that was significantly larger than a hexamer in the presence of a divalent cation (Mg2+) and an adenine nucleotide (ATP, dATP, or ADP) or its analog (ATPγS or AMPPNP). Both N-terminal and C-terminal portions of ORF735 (87 and 160 amino acid residues, respectively, in size) were required for protein dimerization but dispensable for the formation of the higher-order oligomer. The protein unwound DNA only as a large oligomer. Yeast two-hybrid and coimmunoprecipitation assays revealed that ORF735 interacted with the noncatalytic subunit of host primase. These findings provide clues to the functional role of ORF735 in pSSVi DNA replication.

scholarly journals New 19-Residue Peptaibols from Trichoderma Clade Viride

2018 ◽  
Vol 6 (3) ◽  
pp. 85 ◽  
Author(s):  
Tamás Marik ◽  
Chetna Tyagi ◽  
Gordana Racić ◽  
Dávid Rakk ◽  
András Szekeres ◽  
...  
Keyword(s):  
Amino Acid ◽  
Structural Investigation ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Helix Formation ◽  
Left Handed ◽  
Wall Structures ◽  
High Preference ◽  
Wide Range ◽  
Unusual Amino Acid

Trichoderma koningiopsis and T. gamsii belong to clade Viride of Trichoderma, the largest and most diverse group of this genus. They produce a wide range of bioactive secondary metabolites, including peptaibols with antibacterial, antifungal, and antiviral properties. The unusual amino acid residues of peptaibols, i.e., α-aminoisobutyric acid (Aib), isovaline (Iva), and the C-terminal 1,2-amino alcohol make them unique among peptides. In this study, the peptaibiomes of T. koningiopsis and T. gamsii were investigated by HPLC-ESI-MS. The examined strains appeared to produce 19-residue peptaibols, most of which are unknown from literature, but their amino acid sequences are similar to those of trikoningins, tricholongins, trichostrigocins, trichorzianins, and trichorzins. A new group of peptaibols detected in T. koningiopsis are described here under the name “Koningiopsin”. Trikoningin KA V, the closest peptaibol compound to the peptaibols produced by these two strains, was selected for structural investigation by short MD simulation, which revealed that many residues show high preference for left handed helix formation. The bioactivity of the peptaibol mixtures produced by T. koningiopsis and T. gamsii was tested on agar plates against bacteria, yeasts, and filamentous fungi. The results revealed characteristic differences in bioactivities towards the different groups of target microorganisms, which can be explained with the differences in their cell wall structures.

scholarly journals Structural Insights into the Subclass B3 Metallo-β-Lactamase SMB-1 and the Mode of Inhibition by the Common Metallo-β-Lactamase Inhibitor Mercaptoacetate

2012 ◽  
Vol 57 (1) ◽  
pp. 101-109 ◽  
Author(s):  
Jun-ichi Wachino ◽  
Yoshihiro Yamaguchi ◽  
Shigetarou Mori ◽  
Hiromasa Kurosaki ◽  
Yoshichika Arakawa ◽  
...  
Keyword(s):  
Amino Acid ◽  
Active Site ◽  
Hydrolytic Activity ◽  
The Other ◽  
Amino Acid Residues ◽  
Hydrogen Bond Interaction ◽  
Content Type ◽  
Carboxylate Oxygen ◽  
Wide Range ◽  
Environmental Bacteria

ABSTRACTA novel subclass B3 metallo-β-lactamase (MBL), SMB-1, recently identified from aSerratia marcescensclinical isolate, showed a higher hydrolytic activity against a wide range of β-lactams than did the other subclass B3 MBLs, i.e., BJP-1 and FEZ-1, from environmental bacteria. To identify the mechanism underlying the differences in substrate specificity among the subclass B3 MBLs, we determined the structure of SMB-1, using 1.6-Å diffraction data. Consequently, we found that SMB-1 reserves a space in the active site to accommodate β-lactam, even with a bulky R1 side chain, due to a loss of amino acid residues corresponding to F31 and L226 of BJP-1, which protrude into the active site to prevent β-lactam from binding. The protein also possesses a unique amino acid residue, Q157, which probably plays a role in recognition of β-lactams via the hydrogen bond interaction, which is missing in BJP-1 and FEZ-1, whoseKmvalues for β-lactams are particularly high. In addition, we determined the mercaptoacetate (MCR)-complexed SMB-1 structure and revealed the mode of its inhibition by MCR: the thiolate group bridges to two zinc ions (Zn1 and Zn2). One of the carboxylate oxygen atoms of MCR makes contact with Zn2 and Ser221, and the other makes contact with T223 and a water molecule. Our results demonstrate the possibility that MCR could be a potent inhibitor for subclass B3 MBLs and that the screening technique using MCR as an inhibitor would be effective for detecting subclass B3 MBL producers.

scholarly journals Molecular Characterization and Functional Analysis of a Necrosis- and Ethylene-Inducing, Protein-Encoding Gene Family from Verticillium dahliae

2012 ◽  
Vol 25 (7) ◽  
pp. 964-975 ◽  
Author(s):  
Bang-Jun Zhou ◽  
Pei-Song Jia ◽  
Feng Gao ◽  
Hui-Shan Guo
Keyword(s):  
Functional Analysis ◽  
Amino Acid ◽  
Verticillium Dahliae ◽  
Defense Responses ◽  
Phytopathogenic Fungus ◽  
Amino Acid Residues ◽  
Wide Range ◽  
Protein Encoding ◽  
Necrotrophic Stage ◽  
Verticillium Dahliae Kleb

Verticillium dahliae Kleb. is a hemibiotrophic, phytopathogenic fungus that causes wilt disease in a wide range of crops, including cotton. Successful host colonization by hemibiotrophic pathogens requires the induction of plant cell death to provide the saprophytic nutrition for the transition from the biotrophic to the necrotrophic stage. In this study, we identified a necrosis-inducing Phytophthora protein (NPP1) domain–containing protein family containing nine genes in a virulent, defoliating isolate of V. dahliae (V592), named the VdNLP genes. Functional analysis demonstrated that only two of these VdNLP genes, VdNLP1 and VdNLP2, encoded proteins that were capable of inducing necrotic lesions and triggering defense responses in Nicotiana benthamiana, Arabidopsis, and cotton plants. Both VdNLP1 and VdNLP2 induced the wilting of cotton seedling cotyledons. However, gene-deletion mutants targeted by VdNLP1, VdNLP2, or both did not affect the pathogenicity of V. dahliae V592 in cotton infection. Similar expression and induction patterns were found for seven of the nine VdNLP transcripts. Through a comparison of the conserved amino acid residues of VdNLP with different necrosis-inducing activities, combined with mutagenesis-based analyses, we identified several novel conserved amino acid residues, in addition to the known conserved heptapeptide GHRHDWE motif and the cysteine residues of the NPP domain–containing protein, that are indispensable for the necrosis-inducing activity of the VdNLP2 protein.

scholarly journals Identification of betacellulin as a major peptide growth factor in milk: purification, characterization and molecular cloning of bovine betacellulin

1999 ◽  
Vol 344 (3) ◽  
pp. 713-721 ◽  
Author(s):  
Andrew J. DUNBAR ◽  
Ilka K. PRIEBE ◽  
David A. BELFORD ◽  
Chris GODDARD
Keyword(s):  
Amino Acid ◽  
Growth Factor ◽  
Transmembrane Domain ◽  
Signal Sequence ◽  
Bovine Milk ◽  
Gel Filtration ◽  
Exchange Chromatography ◽  
Amino Acid Residues ◽  
Wide Range ◽  
Rapid Amplification

Betacellulin (BTC), a member of the epidermal growth factor (EGF) family of peptide growth factors, was purified from a growth-factor-enriched whey fraction of bovine milk by a combination of ion-exchange chromatography, gel-filtration chromatography, affinity chromatography and reverse-phase HPLC. Bovine BTC (bBTC) had an apparent molecular mass of 21-22 kDa on SDS/PAGE and exists in a glycosylated form. The cDNA encoding bBTC was obtained by a combination of 5ʹ and 3ʹ rapid amplification of cDNA ends (‘RACE’). The primary translation product consists of 178 amino acid residues containing a putative signal sequence, a transmembrane domain, the mature BTC domain and a cytoplasmic domain containing a highly hydrophilic Arg-Lys-rich region similar to that of mouse BTC and human BTC. The amino acid sequence of the bBTC precursor was 88% identical with human BTC and 79% identical with mouse BTC. The bBTC gene was found to be expressed in a wide range of tissues, including the mammary gland. The identification of BTC in milk raises the possibility that it has a major role in the growth and development of the neonatal gastrointestinal tract.

Influence of specific amino acid side-chains on the antimicrobial activity and structure of bovine lactoferrampin1This article is part of Special Issue entitled Lactoferrin and has undergone the Journal’s usual peer review process.

2012 ◽  
Vol 90 (3) ◽  
pp. 362-377 ◽  
Author(s):  
Evan F. Haney ◽  
Kamran Nazmi ◽  
Jan G.M. Bolscher ◽  
Hans J. Vogel
Keyword(s):  
Antimicrobial Activity ◽  
Amino Acid ◽  
Peer Review Process ◽  
Titration Calorimetry ◽  
Resonance Spectroscopy ◽  
Bovine Lactoferrin ◽  
Amino Acid Residues ◽  
Scanning Calorimetry ◽  
Specific Amino Acid ◽  
Wide Range

Lactoferrin is an 80 kDa iron binding protein found in the secretory fluids of mammals and it plays a major role in host defence. An antimicrobial peptide, lactoferrampin, was identified through sequence analysis of bovine lactoferrin and its antimicrobial activity against a wide range of bacteria and yeast species is well documented. In the present work, the contribution of specific amino acid residues of lactoferrampin was examined to evaluate the role that they play in membrane binding and bilayer disruption. The structures of all the bovine lactoferrampin derivatives were examined with circular dichroism and nuclear magnetic resonance spectroscopy, and their interactions with phospholipids were evaluated with differential scanning calorimetry and isothermal titration calorimetry techniques. From our results it is apparent that the amphipathic N-terminal helix anchors the peptide to membranes with Trp 268 and Phe 278 playing important roles in determining the strength of the interaction and for inducing peptide folding. In addition, the N-terminal helix capping residues (DLI) increase the affinity for negatively charged vesicles and they mediate the depth of membrane insertion. Finally, the unique flexibility in the cationic C-terminal region of bovine lactoferrampin does not appear to be essential for the antimicrobial activity of the peptide.

scholarly journals Recombinant Sickle Hemoglobin Containing a Lysine Substitution at Asp-85(α): Expression in Yeast, Functional Properties, and Participation in Gel Formation

Blood ◽  
1997 ◽  
Vol 89 (11) ◽  
pp. 4196-4203 ◽  
Author(s):  
Juha-Pekka Himanen ◽  
Anthony M. Popowicz ◽  
James M. Manning
Keyword(s):  
Amino Acid ◽  
Double Mutant ◽  
Oxygen Affinity ◽  
Quantitative Information ◽  
Inhibitory Effect ◽  
Chloride Ions ◽  
Fiber Formation ◽  
Amino Acid Residues ◽  
Calculated Molecular Weight ◽  
Wide Range

Abstract Clinical modalities based on inhibition of gelation of HbS are hindered by the lack of quantitative information on the extent of participation of different amino acid residues in the aggregation process. One such site is Asp-85(α), which is involved in a parallel interdouble strand ionic interaction with Lys-144(β) according to the crystal structure of HbS, but electron microscopy does not specifically show Asp-85(α) as a contact site for fiber formation. Using a yeast recombinant system, we have substituted this site by Lys to abolish ion pairing and to make a quantitative determination of its participation in aggregation. The purified double mutant was shown to have the expected pI, the calculated molecular weight, correct amino acid composition, and peptide map. The recombinant double mutant has an oxygen affinity of 10 mm Hg, which is identical to that for HbA and HbS under the same conditions; it also has high cooperativity with an average n value of 2.7. The change in P50 in response to chloride ions was about 25% less than that for HbA or HbS and is ascribed to the introduction of a new positive charge near one of the major oxygen-linked chloride binding sites of hemoglobin. The gelation concentration of the double mutant was measured by a new procedure (Bookchin et al, 1994); the maximal amount of soluble hemoglobin (Csat ) in the presence of dextran indicated a decreased tendency for gelation with a Csat of 53 mg/mL compared with 34 mg/mL for HbS. This inhibitory effect is smaller than that of the E6V(β)/L88A(β) (Csat , 67 mg/mL) and the E6V(β)/K95I(β) (Csat , 90 mg/mL) recombinant hemoglobins. Thus, we would classify Asp-85(α) as a moderate contributor to the strength of the HbS aggregate. This wide range of gelation values demonstrates that some sites are more important than others in promoting HbS aggregation.

scholarly journals An Activity-based Probe Targeting Non-catalytic, Highly Conserved Amino Acid Residues Within Bromodomains

2018 ◽  
Author(s):  
Melissa D’Ascenzio ◽  
Kathryn Pugh ◽  
Rebecca Konietzny ◽  
Georgina Berridge ◽  
Cynthia Tallant ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factors ◽  
Amino Acid ◽  
Cancer Development ◽  
Tyrosine Residue ◽  
Amino Acid Residues ◽  
Entire Family ◽  
Cellular Processes ◽  
Wide Range ◽  
Endogenous Proteins

<b>Bromodomain-containing proteins are epigenetic modulators involved in a wide range of cellular processes, from physiological recruitment of transcription factors to pathological disruption of gene regulation and cancer development. Since the druggability of these acetyl-lysine reader domains was established, efforts were made to develop potent and selective inhibitors across the entire family. Here we report the development of a small molecule based approach to covalently modify recombinant and endogenous bromodomain-containing proteins by targeting a conserved lysine and a tyrosine residue in the variable ZA or BC loops. Moreover, the addition of a reporter tag, via copper-catalyzed alkyne azide coupling, to an alkyne handle on the probe allowed in-gel visualization and selective pull-down of the desired bromodomains using both recombinant and endogenous proteins.</b>

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