new protein
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2021 ◽  
Author(s):  
Tae-Eun Kim ◽  
Kotaro Tsuboyama ◽  
Scott Houliston ◽  
Cydney M. Martell ◽  
Claire M. Phoumyvong ◽  
...  

Designing entirely new protein structures remains challenging because we do not fully understand the biophysical determinants of folding stability. Yet some protein folds are easier to design than others. Previous work identified the 43-residue αββ&#945 fold as especially challenging: the best designs had only a 2% success rate, compared to 39-87% success for other simple folds (1). This suggested the αββ&#945 fold would be a useful model system for gaining a deeper understanding of folding stability determinants and for testing new protein design methods. Here, we designed over ten thousand new αββ&#945 proteins and found over three thousand of them to fold into stable structures using a high-throughput protease-based assay. Nuclear magnetic resonance, hydrogen-deuterium exchange, circular dichroism, deep mutational scanning, and scrambled sequence control experiments indicated that our stable designs fold into their designed αββ&#945 structures with exceptional stability for their small size. Our large dataset enabled us to quantify the influence of universal stability determinants including nonpolar burial, helix capping, and buried unsatisfied polar atoms, as well as stability determinants unique to the αββ&#945 topology. Our work demonstrates how large-scale design and test cycles can solve challenging design problems while illuminating the biophysical determinants of folding.


2021 ◽  
Vol 2086 (1) ◽  
pp. 012123
Author(s):  
A A Vronskaia ◽  
A D Mikushina ◽  
I E Eliseev

Abstract Tandem repeat proteins have composite structure and unique properties, which allow them to be used in multiple fields, such as soft photonics, drug delivery and textile industry. The recent discovery of squid ring teeth (SRT) proteins have expanded the existing repertoire of repetitive polypeptides. We chose previously unexplored squid B. magister for our research, isolated and analyzed a new protein forming its ring teeth and hooks, and amplified the corresponding gene. Finally, we used this new isolated SRT protein to fabricate transparent thin films and microspheres.


2021 ◽  
Vol 2114 (1) ◽  
pp. 012069
Author(s):  
Ghaith AlMasraf ◽  
Safanah Albayati

Abstract This research aims to find a new approach to deal with cancer, by targeting a protein that controls the growth and increases the size of the tumour. The approach uses computer-aid drug designed to find the best drug for inhibiting f Methionine Aminopeptidase (Metap2) which is an enzyme that is responsible for starting the synthesis of new protein. The inhibition of the enzyme was found to be crucial in stopping the growth of the tumour and its development. In this research, an in-silico approach was conducted to obtain compounds that are capable of inhibiting the enzyme with non-toxic features. This is done by using Ligand-Based. The Zinc15 and National Institute of Cancer Data (NCI) Databases were screened to attain a variety of manufactured Compounds. Then, molecular docking filtration process was carried out using PyRx, and Autodock4. Finally, SwissADME protocol was used to show the ADMET properties and that compounds can permit the blood barriers and validate better pharmacokinetic properties than the Fumagillin.


2021 ◽  
Author(s):  
Aleksander Giwercman ◽  
Barbara Sahlin ◽  
Indira Pla Parada ◽  
Krzysztof Pawlowski ◽  
Carl Fehninger ◽  
...  

Background: Reliable biomarkers of androgen activity in humans are lacking. The aim of this study was, therefore, to identify new protein markers of biological androgen activity and test their predictive value in relation to low vs. normal testosterone values and some androgen deficiency linked pathologies.<br />Methods: Blood samples from 30 healthy GnRH-antagonist treated males were collected at three time points: a) before GnRH antagonist administration; b) 3 weeks later, just before testosterone undecanoate injection, and c) after additional 2 weeks. Subsequently they were analysed by mass spectrometry to identify potential protein biomarkers of testosterone activity. Levels of proteins most significantly associated with testosterone fluctuations were further tested in a cohort of 75 hypo- and eugonadal males suffering from infertility. Associations between levels of those markers and cardio-metabolic parameters, bone mineral density as well as androgen receptor CAG repeat lengths, were explored.<br />Results: Using ROC analysis, 4-hydroxyphenylpyruvate dioxygenase (4HPPD), insulin-like growth factor-binding protein 6 (IGFBP6) and fructose-bisphosphate aldolase (ALDOB), as well as a Multi Marker Algorithm, based on levels of 4HPPD and IGFBP6, were shown to be best predictors of low (< 8 nmol/L) vs. normal (> 12 nmol/L) testosterone. They were also more strongly associated with metabolic syndrome and diabetes than testosterone levels. Levels of ALDOB and 4HPPD levels also showed association with AR CAG-repeat lengths.<br />Conclusions: We identified potential new protein biomarkers of testosterone action. Further investigations to eluciadate their clinical potential are warranted.<br />Funding: The work was supported by ReproUnion 2.0 (grant no 20201846), which is funded by the Interreg V EU program.


eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Yoanna Ariosa-Morejon ◽  
Alberto Santos ◽  
Roman Fischer ◽  
Simon Davis ◽  
Philip Charles ◽  
...  

Collagen-rich tissues have poor reparative capacity that predisposes to common age-related disorders such as osteoporosis and osteoarthritis. We used in vivo pulsed SILAC labelling to quantify new protein incorporation into cartilage, bone, and skin of mice across the healthy life course. We report dynamic turnover of the matrisome, the proteins of the extracellular matrix, in bone and cartilage during skeletal maturation, which was markedly reduced after skeletal maturity. Comparing young adult with older adult mice, new protein incorporation was reduced in all tissues. STRING clustering revealed changes in epigenetic modulators across all tissues, a decline in chondroprotective growth factors such as FGF2 and TGFβ in cartilage, and clusters indicating mitochondrial dysregulation and reduced collagen synthesis in bone. Several pathways were implicated in age-related disease. Fewer changes were observed for skin. This methodology provides dynamic protein data at a tissue level, uncovering age-related molecular changes that may predispose to disease.


2021 ◽  
Author(s):  
Yiyu Hong ◽  
Junsu Ko ◽  
Juyong Lee

In this study, we propose a new protein 3D structure modeling method, A-Prot, using MSA Transformer, one of the state-of-the-art protein lan-guage models. For a given MSA, an MSA feature tensor and row attention maps are extracted and converted into 2D residue-residue distance and dihedral angle predictions. We demonstrated that A-Prot predicts long-range contacts better than the existing methods. Additionally, we modeled the 3D structures of the free modeling and hard template-based modeling targets of CASP14. The assessment shows that the A-Prot models are more accurate than most top server groups of CASP14. These results imply that A-Prot captures evolutionary and structural infor-mation of proteins accurately with relatively low computational cost. Thus, A-Prot can provide a clue for the development of other protein prop-erty prediction methods.


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