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Proton conductance and regulation of proton/potassium fluxes in Escherichia coli FhlA-lacking cells during fermentation of mixed carbon sources
In this study contribution of formate hydrogen lyase (FHL) complexes in the proton/potassium fluxes and the formation of proton conductance (CMH+) were investigated using fhlA mutant strain. The proton flux rate (JH+) decreased in fhlA by ∼ 25 % and ∼70 % during the utilization of glucose and glycerol, respectively, at 20 h suggesting H+ transport via or through FHL complexes. The decrease in JK+ in fhlA by ∼40 % proposed the interaction between FHL and Trk secondary transport system during mixed carbon fermentation. Moreover, the usage of N,N'-dicyclohexylcarbodiimide (DCCD) demonstrated the mediation of FOF1-ATPase...
Source: Archives of Biochemistry and Biophysics - April 15, 2024 Category: Biochemistry Authors: Heghine Gevorgyan Anna Poladyan Karen Trchounian Anait Vassilian Source Type: research

Thermodynamics of a Hyperthermostable Carboxylesterase from Anoxybacillus geothermalis D9
In this study, we attempted to probe the conformational adaptability of EstD9 under extreme conditions via in silico approaches. Circular dichroism revealed that EstD9 generated new β-sheets at 80 °C that make up the core of the hydrolase fold. Interestingly, the profiles of molecular dynamics simulation showed the lowest scores of radius of gyration and solvent accessible surface area (SASA) at 80 °C. Three loops were responsible for protecting the catalytic site, residing at the interface between the two domains. To further investigate molecular adaptation in extreme conditions, the intramolecular interactions of nati...
Source: Archives of Biochemistry and Biophysics - April 15, 2024 Category: Biochemistry Authors: Ummie Umaiera Mohd Johan Raja Noor Zaliha Raja Abd Rahman Nor Hafizah Ahmad Kamarudin Mohd Shukuri Mohamad Ali Source Type: research

Advances in molecular function of UPF1 in Cancer
This article provides an overview of the aberrant expression of UPF1, its functional properties, and molecular processes during cancer for clinical applications in cancer. We also discussed the interactions of lncRNA with UPF1 for cell growth during tumorigenesis.PMID:38621446 | DOI:10.1016/j.abb.2024.109989 (Source: Archives of Biochemistry and Biophysics)
Source: Archives of Biochemistry and Biophysics - April 15, 2024 Category: Biochemistry Authors: Gazmend Temaj Silvia Chichiarelli Pelin Telkoparan-Akillilar Sarmistha Saha Nexhibe Nuhii Rifat Hadziselimovic Luciano Saso Source Type: research

DTYMK is an essential gene in mice and heterozygosity does not cause neural tube defects
Arch Biochem Biophys. 2024 Apr 15;755:109991. doi: 10.1016/j.abb.2024.109991. Online ahead of print.ABSTRACTRegulation of nucleotide biosynthesis is necessary for maintaining cellular processes including DNA replication and repair. A key enzyme in this process is deoxythymidylate kinase (dTYMK), which catalyzes the initial step in the production of dTTP from dTMP. This gene constitutes the first merged step of dTTP synthesis from the de novo and salvage pathways which regulate dTMP biosynthesis. Decreased de novo dTMP biosynthesis causes dysregulated dTTP:dUTP pools, and leads to increased uracil in DNA and neural tube clo...
Source: Archives of Biochemistry and Biophysics - April 15, 2024 Category: Biochemistry Authors: Kendra A Tiani Patrick J Stover Source Type: research

Kinetic Analysis of T4 Polynucleotide Kinase via Isothermal Titration Calorimetry
This study demonstrates that quantitative analysis of kinase activity can be amenable to the ITC single injection approach.PMID:38621448 | DOI:10.1016/j.abb.2024.109995 (Source: Archives of Biochemistry and Biophysics)
Source: Archives of Biochemistry and Biophysics - April 15, 2024 Category: Biochemistry Authors: Rebecca C Lim Ronald K Gary Source Type: research

Architectonic principles of polyproline II helix bundle protein domains
Arch Biochem Biophys. 2024 Apr 7:109981. doi: 10.1016/j.abb.2024.109981. Online ahead of print.ABSTRACTGlycine rich polyproline II helix assemblies are an emerging class of natural domains found in several proteins with different functions and diverse origins. The distinct properties of these domains relative to those composed of α-helices and β-sheets could make glycine-rich polyproline II helix assemblies a useful building block for protein design. Whereas the high population of polyproline II conformers in disordered state ensembles could facilitate glycine-rich polyproline II helix folding, the architectonic bases of...
Source: Archives of Biochemistry and Biophysics - April 9, 2024 Category: Biochemistry Authors: Cristian Segura Rodr íguez Douglas V Laurents Source Type: research

Allergen specific immunotherapy regulates macrophage property in the airways
CONCLUSIONS: The nAIT has a much better therapeutic effect on suppressing the airway allergic response, in which macrophages play a critical role.PMID:38588908 | DOI:10.1016/j.abb.2024.109984 (Source: Archives of Biochemistry and Biophysics)
Source: Archives of Biochemistry and Biophysics - April 8, 2024 Category: Biochemistry Authors: Jiangqi Liu Xiaojun Xiao Yun Liao Xuejie Xu Yu Liu Aifa Tang Xianhai Zeng Pingchang Yang Source Type: research

Associating protein sequence positions with the modulation of quantitative phenotypes
Arch Biochem Biophys. 2024 Apr 5;755:109979. doi: 10.1016/j.abb.2024.109979. Online ahead of print.ABSTRACTAlthough protein sequences encode the information for folding and function, understanding their link is not an easy task. Unluckily, the prediction of how specific amino acids contribute to these features is still considerably impaired. Here, we developed a simple algorithm that finds positions in a protein sequence with potential to modulate the studied quantitative phenotypes. From a few hundred protein sequences, we perform multiple sequence alignments, obtain the per-position pairwise differences for both the sequ...
Source: Archives of Biochemistry and Biophysics - April 7, 2024 Category: Biochemistry Authors: Ayel én S Hernández Berthet Ariel A Aptekmann Jes ús Tejero Ignacio E S ánchez Mart ín E Noguera Ernesto A Roman Source Type: research

Associating protein sequence positions with the modulation of quantitative phenotypes
Arch Biochem Biophys. 2024 Apr 5:109979. doi: 10.1016/j.abb.2024.109979. Online ahead of print.ABSTRACTAlthough protein sequences encode the information for folding and function, understanding their link is not an easy task. Unluckily, the prediction of how specific amino acids contribute to these features is still considerably impaired. Here, we developed a simple algorithm that finds positions in a protein sequence with potential to modulate the studied quantitative phenotypes. From a few hundred protein sequences, we perform multiple sequence alignments, obtain the per-position pairwise differences for both the sequence...
Source: Archives of Biochemistry and Biophysics - April 7, 2024 Category: Biochemistry Authors: Ayel én S Hernández Berthet Ariel A Aptekmann Jes ús Tejero Ignacio E S ánchez Mart ín E Noguera Ernesto A Roman Source Type: research

Oleuropein attenuates the nephrotoxic effect of sunitinib in rats: Unraveling the potential role of SIRT6/Notch-1/NLRP-3/IL-1 β axis
Arch Biochem Biophys. 2024 Apr 4;755:109986. doi: 10.1016/j.abb.2024.109986. Online ahead of print.ABSTRACTSunitinib (SUN) is a chemotherapeutic agent clinically approved for treatment of metastatic renal carcinoma. Despite its remarkable benefits, various renal toxicities have been reported that limit its clinical uses. Oleuropein (OLE) is the main polyphenolic constituent of olive tree and mediates the majority of its valuable pharmacological activities. The current study examined the probable renoprotective effects of OLE against SUN-induced nephrotoxicity. Adult male albino rats were co-treated by SUN (25 mg/kg, 3 time...
Source: Archives of Biochemistry and Biophysics - April 6, 2024 Category: Biochemistry Authors: Rania A Elrashidy Hoda E Mohamed Sara M Abdel Aal Samar R Mohamed Sara M Tolba Yasmin K Mahmoud Source Type: research

Oleuropein attenuates the nephrotoxic effect of sunitinib in rats: Unraveling the potential role of SIRT6/Notch-1/NLRP-3/IL-1 β axis
Arch Biochem Biophys. 2024 Apr 4:109986. doi: 10.1016/j.abb.2024.109986. Online ahead of print.ABSTRACTSunitinib (SUN) is a chemotherapeutic agent clinically approved for treatment of metastatic renal carcinoma. Despite its remarkable benefits, various renal toxicities have been reported that limit its clinical uses. Oleuropein (OLE) is the main polyphenolic constituent of olive tree and mediates the majority of its valuable pharmacological activities. The current study examined the probable renoprotective effects of OLE against SUN-induced nephrotoxicity. Adult male albino rats were co-treated by SUN (25mg/kg, 3 times/wee...
Source: Archives of Biochemistry and Biophysics - April 6, 2024 Category: Biochemistry Authors: Rania A Elrashidy Hoda E Mohamed Sara M Abdel Aal Samar R Mohamed Sara M Tolba Yasmin K Mahmoud Source Type: research