Increased drug resistance to anti-malarials highlights the need for the development of new therapeutics for the treatment of malaria. To this end, the lactate dehydrogenase (LDH) gene was cloned and sequenced from genomic DNA of Plasmodium vivax ( PvLDH) Belem strain. The 316 amino acid protein-coding region of the PvLDH gene was inserted into the prokaryotic expression vector pKK223-3 and a 34 kDa protein with LDH activity was expressed in E. coli. Structural differences between human LDHs and PfLDH make the latter an attractive target for inhibitors leading to novel anti-malarial drugs. The sequence similarity between PvLDH and PfLDH (90% residue identity and no insertions or deletions) indicate that the same approach could be applied to Plasmodium vivax, the most common human malaria parasite in the world.

<b><i>Introduction:</i></b> Hereditary cholestasis is a heterogeneous group of liver diseases that mostly show autosomal recessive inheritance. The phenotype of cholestasis is highly variable. Molecular genetic testing offers an useful approach to differentiate different types of cholestasis because some symptoms and findings overlap. Biallelic variants in <i>USP53</i> have recently been reported in cholestasis phenotype. <b><i>Methods:</i></b> In this study, we aimed to characterize clinical findings and biological insights on a novel <i>USP53</i> splice variant causing cholestasis phenotype and provided a review of the literature. We performed whole-exome sequencing and then confirmed it with Sanger sequencing. In addition, as a result of in silico analyses and cDNA analysis, we showed that the USP53 protein in our patient was shortened. <b><i>Results:</i></b> We report a novel splice variant (NM_019050.2:c.238–1G&#x3e;C) in the <i>USP53</i> gene via whole-exome sequencing in a patient with cholestasis phenotype. This variant was confirmed by Sanger sequencing and was a result of family segregation analysis; it was found to be in a heterozygous state in the parents and the other healthy elder brother of our patient. According to in silico analyses, the change in the splice region resulted in an increase in the length of exon 2, whereas the stop codon after the additional 3 amino acids (VTF) caused the protein to terminate prematurely. Thus, the mature USP53 protein, consisting of 1,073 amino acids, has been reduced to a small protein of 82 amino acids. <b><i>Conclusion:</i></b> We propose a model for the tertiary structure of USP53 for the first time, and together with all these data, we support the association of biallelic variants of the <i>USP53</i> gene with cholestasis phenotype. We also present a comparison of previously reported patients with <i>USP53</i>-associated cholestasis phenotype to contribute to the literature.

Objectives This study aimed to model the changes resulting from mutations in surface (spike/S) glycoproteins, which play a key role in the entry of the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) into host cells, in a protein quaternary structure and to evaluate their possible effects on the functional structure. Methods Genome sequence information of SARS CoV-2-infected patients located in Turkey was obtained from the GISAID EpiCoV database. Structural analysis of spike proteins was done using bioinformatics tools (MAFFT, PSIPRED, ProMod3, PyMoL and DynOmics). Results We identified 76 Thr>Ile mutations in the N-terminal domain; 468 Ile>Val mutations in the receptor binding site and 614 Asp>Gly, 679 Asn>Lys, 771 Ala>Val and 772 Val>Ile mutations in the S1 subunit. It has been observed that the mutations, except those of residues 771 and 772, may cause significant conformational, topological and electrostatic changes in a protein quaternary structure. It has been determined that the mutations in the receptor binding site transform the protein structure into a formation that can mask the binding site and affect receptor affinity. Conclusions It has been considered that SARS CoV-2 S glycoprotein mutations may cause changes in a protein functional structure that can affect the severity of disease.

Severe Acute Respiratory Syndrome Corona Virus-2 (SARS CoV-2) is a single-stranded positive polarity RNA virus with a high virulence effect. Spike (S) glycoprotein is the outermost component of the SARS CoV-2 virion and is important in the entry of the virus into the cell via the angiotensin converting enzyme 2 (ACE2) receptor. ACE2 plays an important role in the regulation of human blood pressure by converting the vasoconstrictor angiotensin 2 to the vasodilator angiotensin 1-7. In this study, the changes that mutations in Asian isolates may cause in S glycoprotein structure were analyzed and modeled to contribute to drug and vaccine targeting studies. Genome, proteome and mutation analyses were done using bioinformatics tools (MAFFT, MegaX, PSIPRED, MolProbity, PyMoL). Protein modelling was performed using ProMod3. We detected 26 mutations in the S glycoprotein. The changes that these mutations reveal in the general topological and conformational structure of the S glycoprotein may affect the virulence features of SARS CoV-2. It was determined that mutations converted the receptor binding domain (RBD) from down-formation to like-up formation. It is thought that conformational change occurring after mutation in RBD may cause an increase in receptor affinity. These findings could be beneficial for disease prevention of and drug/vaccine development for SARS CoV-2. Özet: Şiddetli akut solunum yolu sendromu koronavirüsü-2 (SARS CoV-2) yüksek virülans etkiye sahip tek zincirli pozitif polariteli RNA virüsüdür. Spike (S) glikoprotein SARS CoV-2 virionunun en dıştaki bileşenidir ve anjiyotensin dönüştürücü enzim 2 (ACE2) reseptörü aracılığı ile virüsün hücreye girişinde önemlidir. ACE2, vazokonstriktör anjiyotensin 2'yi vazodilatör anjiyotensin 1-7'ye dönüştürerek insanda kan basıncının düzenlenmesinde önemli roller üstlenir. Bu çalışmada, Asya izolatlarındaki mutasyonların S glikoprotein yapısında neden olabileceği değişiklikler analiz edilmiş ve ilaç ve aşı hedefleme çalışmalarına katkıda bulunmak üzere modellenmiştir. Genom, proteom ve mutasyon analizleri biyoinformatik araçları (MAFFT, MegaX, PSIPRED, MolProbity, PyMoL) kullanılarak yapıldı. Protein modellemesi ProMod3 kullanılarak yapıldı. S glikoproteinde 26 mutasyon tespit edilmiştir. Bu mutasyonların S glikoproteininin genel topolojik ve konformasyonel yapısında ortaya çıkardığı değişiklikler, SARS CoV-2'nin virülans özelliklerini etkileyebilir. Mutasyonların reseptör bağlanma bölgesini (RBB) kapalı formasyondan açık formasyon benzeri bir yapıya dönüştürdüğü belirlenmiştir. RBB'de mutasyondan sonra meydana gelen konformasyonel değişimin reseptör afinitesinde bir artışa neden olabileceği düşünülmektedir. Bu bulgular hastalığın önlenmesi ve SARS CoV-2 ilaç ve aşı geliştirme çalışmaları için faydalı olabilir.

No abstract