scholarly journals Phosphorylation regulates the secondary structure and function of dentin phosphoprotein peptides

Bone ◽  
2017 ◽  
Vol 95 ◽  
pp. 65-75 ◽  
Author(s):  
Eduardo Villarreal-Ramirez ◽  
David Eliezer ◽  
Ramon Garduño-Juarez ◽  
Arne Gericke ◽  
Jose Manuel Perez-Aguilar ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Structure And Function ◽  
Dentin Phosphoprotein ◽  
And Function

scholarly journals Bifunctional Chloroplastic DJ-1B from Arabidopsis thaliana is an Oxidation-Robust Holdase and a Glyoxalase Sensitive to H2O2

Antioxidants ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 8 ◽  
Author(s):  
Aleksandra Lewandowska ◽  
Trung Nghia Vo ◽  
Thuy-Dung Ho Nguyen ◽  
Khadija Wahni ◽  
Didier Vertommen ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Arabidopsis Thaliana ◽  
Secondary Structure ◽  
Structure And Function ◽  
Transcript Levels ◽  
Chaperone Function ◽  
Multifunctional Enzymes ◽  
And Function ◽  
Discrete Functions

Members of the DJ-1 protein family are multifunctional enzymes whose loss increases the susceptibility of the cell to oxidative stress. However, little is known about the function of the plant DJ-1 homologs. Therefore, we analyzed the effect of oxidation on the structure and function of chloroplastic AtDJ-1B and studied the phenotype of T-DNA lines lacking the protein. In vitro oxidation of AtDJ-1B with H2O2 lowers its glyoxalase activity, but has no effect on its holdase chaperone function. Remarkably, upon oxidation, the thermostability of AtDJ-1B increases with no significant alteration of the overall secondary structure. Moreover, we found that AtDJ-1B transcript levels are invariable, and loss of AtDJ-1B does not affect plant viability, growth and stress response. All in all, two discrete functions of AtDJ-1B respond differently to H2O2, and AtDJ-1B is not essential for plant development under stress.

scholarly journals Significance of arginine radicals for sturgeon gonadotropin secondary structure and function

2010 ◽  
Vol 64 (3-4) ◽  
pp. 144-148
Author(s):  
Henriks Zenkevičs ◽  
Ilze Vosekalna ◽  
Vija Vose
Keyword(s):  
Secondary Structure ◽  
Active Sites ◽  
Positive Charge ◽  
Cd Spectroscopy ◽  
Structure And Function ◽  
Dimeric Molecule ◽  
Gonadotropic Hormone ◽  
Chemically Modified ◽  
Individual Subunit ◽  
And Function

Significance of arginine radicals for sturgeon gonadotropin secondary structure and function Guanidine groups of arginine side chains were selectively chemically modified with 1,2-cyclohexanedione (CHD) in sturgeon (Acipenser güldenstädti Br.) gonadotropic hormone (GTH) and in its subunits. It was found that only two of the six guanidines were accessible for the reagent and each of the two modified groups was bound to an individual subunit. The results showed that both modified groups were located on the surface of the hormone dimeric molecule. CD-spectroscopy of the modified hormonal preparations did not indicate any considerable changes in their secondary structure. On the basis of the data obtained, a conclusion was made that the free guanidine groups are of exclusive importance for the hormone function at the receptor level as the bearers of the positive charge in the functionally important active sites or effector zones located on the surface of the hormone molecule. Also, it was shown that the guanidine groups played a certain role in sustaining the functionally effective spatial structure of the subunits and GTH.

EFFECTS OF HEAT SHOCK PROTEIN CLPC’S ɑ4-β2 LOOP DELETION FROM AN ALKALIPHILIC BACILLUS LEHENSIS G1 ON ITS STABILITY AND ACTIVITY

2017 ◽  
Vol 79 (5) ◽  
Author(s):  
Siti Aishah Rashid ◽  
Farah Diba Abu Bakar ◽  
Abdul Munir Abdul Murad ◽  
Rosli Md. Illias
Keyword(s):  
Heat Shock ◽  
Secondary Structure ◽  
Heat Shock Protein ◽  
Atpase Activity ◽  
Deep Understanding ◽  
Structure And Function ◽  
Optimum Temperature ◽  
Structural Perturbations ◽  
Alkaliphilic Bacillus ◽  
And Function

Protein loops are frequently considered as critical determinants that influence not only the function but also the structure of a protein. Bacillus lehensis G1 ClpC (WT) has a four-residue insertion at the ɑ4-β2 loop, which is absent in Bacillus subtillis ClpC. To foster a deep understanding of the significance of additional residues in the structure and function of ClpC, a deletion mutation involving residues 76-79 (∆76-79) was constructed. Circular dichroism spectroscopy was used to evaluate the structural perturbations associated with the deletion. The results demonstrated that, the precise configuration of the ɑ4-β2 loop is important for maintaining the structure and function of WT. ∆76-79 leads to severe global destabilisation and unfolding of the secondary structure of the protein, which decreases ATPase activity. The optimum temperature for ∆76-79 is 25 °C, down from 45 °C for WT. The results suggest that the additional four residues at the ɑ4-β2 loop are critical for WT’s structure and function.

scholarly journals The amphipathic helix in the exchangeable apolipoproteins: a review of secondary structure and function.

1992 ◽  
Vol 33 (2) ◽  
pp. 141-166 ◽  
Author(s):  
JP Segrest ◽  
MK Jones ◽  
H De Loof ◽  
CG Brouillette ◽  
YV Venkatachalapathi ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Structure And Function ◽  
Amphipathic Helix ◽  
And Function

scholarly journals An alternative D. melanogaster 7SK snRNP

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Duy Nguyen ◽  
Nicolas Buisine ◽  
Olivier Fayol ◽  
Annemieke A. Michels ◽  
Olivier Bensaude ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Polymerase Ii ◽  
Biological Function ◽  
Expression Profiles ◽  
Structure And Function ◽  
Small Nuclear Rna ◽  
Primary Sequence ◽  
Nuclear Rna ◽  
And Function

Abstract Background The 7SK small nuclear RNA (snRNA) found in most metazoans is a key regulator of P-TEFb which in turn regulates RNA polymerase II elongation. Although its primary sequence varies in protostomes, its secondary structure and function are conserved across evolutionary distant taxa. Results Here, we describe a novel ncRNA sharing many features characteristic of 7SK RNAs, in D. melanogaster. We examined the structure of the corresponding gene and determined the expression profiles of the encoded RNA, called snRNA:7SK:94F, during development. It is probably produced from the transcription of a lncRNA which is processed into a mature snRNA. We also addressed its biological function and we show that, like dm7SK, this alternative 7SK interacts in vivo with the different partners of the P-TEFb complex, i.e. HEXIM, LARP7 and Cyclin T. This novel RNA is widely expressed across tissues. Conclusion We propose that two distinct 7SK genes might contribute to the formation of the 7SK snRNP complex in D. melanogaster.

scholarly journals Role of Carboxyl Groups in the Secondary Structure and Function of Sturgeon Gonadotropin

2008 ◽  
Vol 62 (3) ◽  
pp. 110-114
Author(s):  
Henriks Zenkevičs ◽  
Ilze Vosekalna ◽  
Vija Vose
Keyword(s):  
Secondary Structure ◽  
Cd Spectroscopy ◽  
Structure And Function ◽  
Membrane Receptors ◽  
Carboxyl Groups ◽  
Gonadotropic Hormone ◽  
Glycine Ethyl Ester ◽  
And Function ◽  
Specific Membrane

Role of Carboxyl Groups in the Secondary Structure and Function of Sturgeon Gonadotropin Free negatively charged carboxyl groups were selectively modified (neutralised) in sturgeon (Acipenser güldenstädti Br.) gonadotropic hormone (GTH) α and β subunits. Eleven free carboxyl groups, three in the α and eight in the β subunit, were neutralised by reaction with glycine ethyl ester. Investigation of reassociated α-β dimers (recombinants) comprising one or both modified subunits showed that specific hormonal activity was completely lost while immunoreactivity was lowered in comparison with that of the standard α-β dimer. CD-spectroscopy of the modified subunits did not indicate any considerable changes in their spatial structure. A conclusion was made that free COOH groups of GTH were important as bearers of the negative charge necessary for the hormone activity on the level of the hormone-specific membrane receptors.

scholarly journals End-to-end multitask learning, from protein language to protein features without alignments

2019 ◽  
Author(s):  
Ahmed Elnaggar ◽  
Michael Heinzinger ◽  
Christian Dallago ◽  
Burkhard Rost
Keyword(s):  
Protein Structure ◽  
Secondary Structure ◽  
Structure And Function ◽  
Water Soluble ◽  
Language Models ◽  
Quality Data ◽  
Evolutionary Information ◽  
End To End ◽  
Sequence Databases ◽  
And Function

AbstractCorrectly predicting features of protein structure and function from amino acid sequence alone remains a supreme challenge for computational biology. For almost three decades, state-of-the-art approaches combined machine learning and evolutionary information from multiple sequence alignments. Exponentially growing sequence databases make it infeasible to gather evolutionary information for entire microbiomes or meta-proteomics. On top, for many important proteins (e.g. dark proteome and intrinsically disordered proteins) evolutionary information remains limited. Here, we introduced a novel approach combining recent advances of Language Models (LMs) with multi-task learning to successfully predict aspects of protein structure (secondary structure) and function (cellular component or subcellular localization) without using any evolutionary information from alignments. Our approach fused self-supervised pre-training LMs on an unlabeled big dataset (UniRef50, corresponding to 9.6 billion words) with supervised training on labelled high-quality data in one single end-to-end network. We provided a proof-of-principle for the novel concept through the semi-successful per-residue prediction of protein secondary structure and through per-protein predictions of localization (Q10=69%) and the distinction between integral membrane and water-soluble proteins (Q2=89%). Although these results did not reach the levels obtained by the best available methods using evolutionary information from alignments, these less accurate multi-task predictions have the advantage of speed: they are 300-3000 times faster (where HHblits needs 30-300 seconds on average, our method needed 0.045 seconds). These new results push the boundaries of predictability towards grayer and darker areas of the protein space, allowing to make reliable predictions for proteins which were not accessible by previous methods. On top, our method remains scalable as it removes the necessity to search sequence databases for evolutionary related proteins.

scholarly journals Emergence of Unique SARS-CoV-2 ORF10 Variants and Their Impact on Protein Structure and Function

2021 ◽  
Author(s):  
Sk. Sarif Hassan ◽  
Kenneth Lundstrom ◽  
Ángel Serrano-Aroca ◽  
Parise Adadi ◽  
Alaa Aljabali ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Structure And Function ◽  
Open Reading Frame ◽  
Host Protein ◽  
Protein Disorder ◽  
Reading Frame ◽  
Pharmaceutical Development ◽  
Intrinsic Protein Disorder ◽  
Human Proteins ◽  
And Function

The devastating impact of the ongoing coronavirus disease 2019 (COVID-19) on public health, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has made fighting of the COVID-19 pandemic is a top priority in medical research and pharmaceutical development. Surveillance of SARS-CoV-2 mutations is essential for the comprehension of SARS-CoV-2 variant diversity and their impact on virulence and pathogenicity. The SARS-CoV-2 open reading frame 10 (ORF10) protein interacts with multiple human proteins CUL2, ELOB, ELOC, MAP7D1, PPT1, RBX1, THTPA, TIMM8B, and ZYG11B expressed in the lung tissues. Mutations and co-mutations in the emerging SARS-CoV-2 ORF10 variants are expected to impact the severity of the virus and its associated consequences. In this article, We highlight 128 single mutations and 35 co-mutations in the unique SARS-CoV-2 ORF10 variants in this article. The possible predicted effects of these mutations and co-mutations on the secondary structure of ORF10 variants and host protein interactomes are presented. The findings highlight the possible effects of mutations and co-mutations on the emerging 140 ORF10 unique variants from secondary structure and intrinsic protein disorder perspectives.

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