Biochimica et biophysica acta. Proteins and proteomics最新文献

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Elucidating the inhibitory effects of rationally designed novel hexapeptide against hen egg white lysozyme fibrillation at acidic and physiological pH 阐明合理设计的新型六肽在酸性和生理pH下对蛋清溶菌酶纤颤的抑制作用
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2023-05-01 DOI: 10.1016/j.bbapap.2023.140899
Amit Mitra, Nandini Sarkar
{"title":"Elucidating the inhibitory effects of rationally designed novel hexapeptide against hen egg white lysozyme fibrillation at acidic and physiological pH","authors":"Amit Mitra,&nbsp;Nandini Sarkar","doi":"10.1016/j.bbapap.2023.140899","DOIUrl":"10.1016/j.bbapap.2023.140899","url":null,"abstract":"<div><p><span><span><span>Inhibition of highly ordered cross-β-sheet-rich aggregates of misfolded amyloid proteins using rationally designed sequence-based short peptides is a promising therapeutic strategy for the treatment of neurodegenerative diseases. Here, we have explored the anti-amyloidogenic potency of a rationally designed hexapeptide (Tyr-Pro-Gln-Ile-Pro-Asn) on in vitro hen egg white </span>lysozyme (HEWL) </span>amyloid fibril<span> formation at acidic pH and physiological pH using computational docking as well as various biophysical techniques such as fluorescence spectroscopy, UV–vis spectroscopy, </span></span>FTIR spectroscopy<span><span>, confocal microscopy and </span>TEM. The peptide was designed based on the aggregation-prone region (APR) of HEWL and thus referred to as SqP1 (Sequence-based Peptide 1). SqP1 showed over 70% inhibition of HEWL amyloid formation at pH 2.2 and approximately 50% inhibition at pH 7.5. We propose that SqP1 binds to the APR of HEWL and interacts strongly with the Trp62/Trp63, ultimately stabilizing monomeric HEWL at both the pH conditions and preventing conformation changes in the structure of HEWL, leading to the formation of amyloidogenic fibrillar structures. A sequence-based peptide inhibitor of HEWL amyloid formation was not reported previously, making this a critical study that will further emphasize the importance of short synthetic peptides as amyloid inhibitors.</span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9118050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The oxidative nuclease activity of human cytochrome c with mutations in Ω-loop C/D Ω-loop c /D突变的人细胞色素c的氧化核酸酶活性
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2023-05-01 DOI: 10.1016/j.bbapap.2023.140897
Yu Feng , Yao Dong , Ke-Jie Du , Xi-Chun Liu , Shu-Qin Gao , Ying-Wu Lin
{"title":"The oxidative nuclease activity of human cytochrome c with mutations in Ω-loop C/D","authors":"Yu Feng ,&nbsp;Yao Dong ,&nbsp;Ke-Jie Du ,&nbsp;Xi-Chun Liu ,&nbsp;Shu-Qin Gao ,&nbsp;Ying-Wu Lin","doi":"10.1016/j.bbapap.2023.140897","DOIUrl":"10.1016/j.bbapap.2023.140897","url":null,"abstract":"<div><p><span><span><span>Natural and artificial nucleases have extensive applications in biotechnology and </span>biomedicine. The exploration of protein with potential </span>DNA<span> cleavage activity also inspires the design of artificial nuclease and helps to understand the physiological process<span> of DNA damage. In this study, we engineered four human cytochrome </span></span></span><em>c</em> (Cyt <em>c</em>) mutants (N52S, N52A, I81N, and I81D Cyt <em>c</em>), which showed enhanced DNA cleavage activity and degradation in comparison with WT Cyt <em>c</em>, especially under acidic conditions. The mechanism assays revealed that the superoxide (O<sub>2</sub><sup>•−</sup><span>) plays an important role in the nuclease reaction. The kinetic assays showed that the peroxidase activity of the I81D Cyt </span><em>c</em> mutant enhanced up to 9-fold at pH 5. This study suggests that the mutations of Ile81 and Asn52 in Ω-loop C/D are critical for the nuclease activity of Cyt <em>c</em>, which may have physiological significance in DNA damage and potential applications in biomedicine.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9112769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The structural basis of conserved residue variant effect on enzyme activity of UGT2B15 保守残基变异对UGT2B15酶活性影响的结构基础
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2023-05-01 DOI: 10.1016/j.bbapap.2023.140888
Lin Zhang , Xuerong Zhang , Yibing Yang , Jiangyong Gu , Zhongqiu Liu , Caiyan Wang
{"title":"The structural basis of conserved residue variant effect on enzyme activity of UGT2B15","authors":"Lin Zhang ,&nbsp;Xuerong Zhang ,&nbsp;Yibing Yang ,&nbsp;Jiangyong Gu ,&nbsp;Zhongqiu Liu ,&nbsp;Caiyan Wang","doi":"10.1016/j.bbapap.2023.140888","DOIUrl":"10.1016/j.bbapap.2023.140888","url":null,"abstract":"<div><p><span><span>UDP-glucuronosyltransferase 2B15 (UGT2B15) is a crucial phase II drug-metabolizing enzyme, which glucuronidates various compounds, including clinical drugs and hormones. Mutants might affect </span>glucuronidation, leading to a disruption of drug metabolism </span><em>in vivo</em><span><span><span> and decrease of therapeutic effect. Here, we mainly analyzed two representative mutants, H401P and L446S, on UGT2B15 activity using glucuronidation assays, molecular dynamic (MD) simulation and X-ray diffraction methods. The enzyme activity<span> of L446S obviously increased six-fold than the wild type, although the enzyme activities of P191L, T374A, and H401P were lost apparently. Furthermore, we used MD simulations to calculate the energy change in the catalytic process of H401P and L446S, and the results indicated the free binding energies of H401P mutant to </span></span>oxazepam and </span>UDPGA<span><span> were −30.98 ± 1.00 kcal/mol and −36.42 ± 1.04 kcal/mol, respectively, increased obviously compared to wild type, suggesting the mutation on position 401 had a crucial effect on the catalysis. Moreover, the three-dimensional structure of UGT2B15 C-terminal domain L446S was determined through protein crystallography and X-ray diffraction technology and the results suggested that one more </span>hydrogen bonding<span> between S446 and K410 was formed in the S446 crystal structure, compared to the wild type. Isothermal titration calorimetry assay further revealed the </span></span></span><em>K</em><sub>d</sub><span> values of C-terminal domain of UGT2B15 harbored L446S towards the cofactor UDPGA was similar to the value of wild type. Above all, our results pointed out that H401P and L446S affected the enzyme activity by different mechanism. Our work provided a helpful mechanism for variance explained in the UGTs catalyzation process.</span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9118647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cd-induced cytosolic proteome changes in the cyanobacterium Anabaena sp. PCC7120 are mediated by LexA as one of the regulatory proteins cd诱导的蓝藻Anabaena sp. PCC7120胞质蛋白质组变化是由LexA作为调控蛋白之一介导的
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2023-05-01 DOI: 10.1016/j.bbapap.2023.140902
Akanksha Srivastava , Arvind Kumar , Subhankar Biswas , Vaibhav Srivastava , Hema Rajaram , Yogesh Mishra
{"title":"Cd-induced cytosolic proteome changes in the cyanobacterium Anabaena sp. PCC7120 are mediated by LexA as one of the regulatory proteins","authors":"Akanksha Srivastava ,&nbsp;Arvind Kumar ,&nbsp;Subhankar Biswas ,&nbsp;Vaibhav Srivastava ,&nbsp;Hema Rajaram ,&nbsp;Yogesh Mishra","doi":"10.1016/j.bbapap.2023.140902","DOIUrl":"10.1016/j.bbapap.2023.140902","url":null,"abstract":"<div><p><span><span>LexA, a well-characterized transcriptional repressor of SOS genes in heterotrophic bacteria, has been shown to regulate diverse genes in </span>cyanobacteria. An earlier study showed that LexA overexpression in a cyanobacterium, </span><span><em>Anabaena</em></span><span> sp. PCC7120 reduces its tolerance to Cd stress. This was later shown to be due to modulation of photosynthetic redox poising by LexA under Cd stress. However, due to the global regulatory nature of LexA and the prior prediction of AnLexA-box in a few heavy metal-responsive genes, we speculated that LexA has a broad role in Cd tolerance, with regulation over a variety of Cd stress-responsive genes in addition to photosynthetic genes. Thus, to further expand the knowledge on the regulatory role of LexA in Cd stress tolerance, a cytosolic proteome profiling of </span><em>Anabaena</em><span><span><span> constitutively overexpressing LexA upon Cd stress was performed. The proteomic study revealed 25 differentially accumulated proteins (DAPs) in response to the combined effect of LexA overexpression and Cd stress, and the other 11 DAPs exclusively in response to either LexA overexpression or Cd stress. The 36 identified proteins were related with a variety of functions, including </span>photosynthesis, C-metabolism, </span>antioxidants<span>, protein turnover, post-transcriptional modifications, and a few unknown and hypothetical proteins. The regulation of LexA on corresponding genes, and six previously reported Cd efflux transporters, was further validated by the presence of AnLexA-boxes, transcript, and/or promoter analyses. In a nutshell, this study identifies the regulation of </span></span><em>Anabaena</em> LexA on several Cd stress-responsive genes of various functions, hence expanding the regulatory role of LexA under Cd stress.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9113619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Peptide from NSP7 is able to form amyloid-like fibrils: Artifact or challenge to drug design? 来自NSP7的肽能够形成淀粉样蛋白样原纤维:人工产物还是对药物设计的挑战?
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2023-02-01 DOI: 10.1016/j.bbapap.2022.140884
Yuri Garmay , Aleksandr Rubel , Vladimir Egorov
{"title":"Peptide from NSP7 is able to form amyloid-like fibrils: Artifact or challenge to drug design?","authors":"Yuri Garmay ,&nbsp;Aleksandr Rubel ,&nbsp;Vladimir Egorov","doi":"10.1016/j.bbapap.2022.140884","DOIUrl":"10.1016/j.bbapap.2022.140884","url":null,"abstract":"<div><p></p><ul><li><span>•</span><span><p>We found potential amyloidogenic fragment in NSP7 SARS-CoV2 protein <em>in silico</em></p></span></li><li><span>•</span><span><p>NSP7 (52–62) fragment is able to form amyloid-like fibrils</p></span></li><li><span>•</span><span><p>The possibility of using such a peptide as the basis for an antiviral drug is discussed</p></span></li></ul></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9711895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9470502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Effect of tubulin self-association on GTP hydrolysis and nucleotide exchange reactions 微管蛋白自结合对GTP水解和核苷酸交换反应的影响
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2023-02-01 DOI: 10.1016/j.bbapap.2022.140869
Asaf Shemesh , Hiba Ghareeb , Raviv Dharan , Yael Levi-Kalisman , Norman Metanis , Israel Ringel , Uri Raviv
{"title":"Effect of tubulin self-association on GTP hydrolysis and nucleotide exchange reactions","authors":"Asaf Shemesh ,&nbsp;Hiba Ghareeb ,&nbsp;Raviv Dharan ,&nbsp;Yael Levi-Kalisman ,&nbsp;Norman Metanis ,&nbsp;Israel Ringel ,&nbsp;Uri Raviv","doi":"10.1016/j.bbapap.2022.140869","DOIUrl":"10.1016/j.bbapap.2022.140869","url":null,"abstract":"<div><p>We investigated how the self-association of isolated tubulin dimers affects the rate of GTP hydrolysis and the equilibrium of nucleotide exchange. Both reactions are relevant for microtubule (MT) dynamics. We used HPLC to determine the concentrations of GDP and GTP and thereby the GTPase activity of SEC-eluted tubulin dimers in assembly buffer solution, free of glycerol and tubulin aggregates. When GTP hydrolysis was negligible, the nucleotide exchange mechanism was studied by determining the concentrations of tubulin-free and tubulin-bound GTP and GDP. We observed no GTP hydrolysis below the critical conditions for MT assembly (either below the critical tubulin concentration and/or at low temperature), despite the assembly of tubulin 1D curved oligomers and single-rings, showing that their assembly did not involve GTP hydrolysis. Under conditions enabling spontaneous slow MT assembly, a slow pseudo-first-order GTP hydrolysis kinetics was detected, limited by the rate of MT assembly. Cryo-TEM images showed that GTP-tubulin 1D oligomers were curved also at 36 °C. Nucleotide exchange depended on the total tubulin concentration and the molar ratio between tubulin-free GDP and GTP. We used a thermodynamic model of isodesmic tubulin self-association, terminated by the formation of tubulin single-rings to determine the molar fractions of dimers with exposed and buried nucleotide exchangeable sites (E-sites). Our analysis shows that the GDP to GTP exchange reaction equilibrium constant was an order-of-magnitude larger for tubulin dimers with exposed E-sites than for assembled dimers with buried E-sites. This conclusion may have implications on the dynamics at the tip of the MT plus end.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9486332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mechanistic aspects of the transamination reactions catalyzed by D-amino acid transaminase from Haliscomenobacter hydrossis 水解哈利氏杆菌d -氨基酸转氨酶催化转氨化反应的机理
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2023-02-01 DOI: 10.1016/j.bbapap.2022.140886
Alina K. Bakunova , Alexey A. Kostyukov , Vladimir A. Kuzmin , Vladimir O. Popov , Ekaterina Yu. Bezsudnova
{"title":"Mechanistic aspects of the transamination reactions catalyzed by D-amino acid transaminase from Haliscomenobacter hydrossis","authors":"Alina K. Bakunova ,&nbsp;Alexey A. Kostyukov ,&nbsp;Vladimir A. Kuzmin ,&nbsp;Vladimir O. Popov ,&nbsp;Ekaterina Yu. Bezsudnova","doi":"10.1016/j.bbapap.2022.140886","DOIUrl":"10.1016/j.bbapap.2022.140886","url":null,"abstract":"<div><p><span><span>Pyridoxal-5′-phosphate-(PLP-) dependent D-amino acid transaminases<span> (DAATs) catalyze stereoselective reversible transfer of the amino group between D-amino acids and keto acids. In vivo DAATs are commonly known to synthesize D-glutamate for cell wall </span></span>peptidoglycans. Today DAATs meet increasing attention for application in the synthesis of D-amino acids, whereas little is known about the mechanism of substrate recognition and catalytic steps of the D-amino acids conversion by DAATs. In this work, the pre-steady-state kinetics of the half-reactions of DAAT from </span><em>Haliscomenobacter hydrossis</em><span><span><span> with D-glutamate, D-alanine, D-leucine, and D-phenylalanine was examined at two wavelengths, 416 and 330 nm, using a stopped-flow technique. Monophasic kinetics was observed with specific substrates D-glutamate and D-alanine, whereas half-reactions with D-leucine and D-phenylalanine exhibited biphasic kinetics. All half-reactions proceeded until the complete conversion of PLP due to the release of the pyridoxamine-5′-phosphate form of cofactor from the holoenzyme . Comparison of </span>kinetic parameters of half-reactions and the overall </span>transamination<span> reactions for D-leucine, D-phenylalanine revealed the increase in the rates of deamination of these substrates in the overall reaction with α-ketoglutarate. In the overall transamination reaction, the catalytic turnover rates for D-leucine and D-phenylalanine increased by 260 and 60 times, correspondingly, comparing with the slowest step rate constants in the half-reactions. We suggested the activating effect by a specific substrate α-ketoglutarate in the overall transamination reaction. The study of half-reactions helped to quantify the specificity of DAAT from </span></span><em>H. hydrossis</em> for D-amino acids with different properties. The results obtained are the first detailed analysis of half-reactions catalyzed by DAAT.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9115706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modulation of α-synuclein phase separation by biomolecules 生物分子对α-突触核蛋白相分离的调节
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2023-02-01 DOI: 10.1016/j.bbapap.2022.140885
Leandro Cruz Rodríguez, Nahuel N. Foressi, M. Soledad Celej
{"title":"Modulation of α-synuclein phase separation by biomolecules","authors":"Leandro Cruz Rodríguez,&nbsp;Nahuel N. Foressi,&nbsp;M. Soledad Celej","doi":"10.1016/j.bbapap.2022.140885","DOIUrl":"10.1016/j.bbapap.2022.140885","url":null,"abstract":"<div><p><span>Liquid-liquid phase separation (LLPS) is currently recognized as a common mechanism involved in the regulation of a number of cellular functions. On the other hand, aberrant phase separation has been linked to the biogenesis of several neurodegenerative disorders since many proteins that undergo LLPS are also found in pathological aggregates. The formation of mixed protein coacervates may constitute a risk factor in overlapping neuropathologies, such as Parkinson's (PD) and Alzheimer's (AD) diseases. In this work, we evaluated the homotypic and heterotypic phase behaviour of the PD-related protein α-synuclein (AS) in the presence of the biologically relevant molecules ATP, </span>polyamines, and the AD-related protein Tau. We found that AS exhibits a low propensity to form homotypic liquid droplets, yet phase separates into liquid-like or solid-like phases depending on the interacting biomolecule. We further demonstrated the synergistic droplet formation of AS and Tau providing support for a mechanism in which mixed condensates might contribute to the biogenesis of AS/Tau pathologies.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9118176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
AP lyase activity of the human ribosomal protein uS3: The DNA cleavage sequence specificity and the location of the enzyme active center 人核糖体蛋白uS3的AP裂解酶活性:DNA裂解序列特异性和酶活性中心的位置
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2023-02-01 DOI: 10.1016/j.bbapap.2022.140880
Anastasia Ochkasova , Grigory Arbuzov , Marsel Kabilov, Alexey Tupikin, Galina Karpova, Dmitri Graifer
{"title":"AP lyase activity of the human ribosomal protein uS3: The DNA cleavage sequence specificity and the location of the enzyme active center","authors":"Anastasia Ochkasova ,&nbsp;Grigory Arbuzov ,&nbsp;Marsel Kabilov,&nbsp;Alexey Tupikin,&nbsp;Galina Karpova,&nbsp;Dmitri Graifer","doi":"10.1016/j.bbapap.2022.140880","DOIUrl":"10.1016/j.bbapap.2022.140880","url":null,"abstract":"<div><p><span><span>The human protein uS3, a component of the small ribosomal subunit, has a long-known extra-ribosomal activity as an enzyme of base excision </span>DNA repair displayed in its ability to cleave DNA at abasic (AP) sites. It has been found that the efficacy of DNA cleavage by uS3 </span><em>in vitro</em><span><span> depends on the DNA sequence<span>. To clarify the issue on the sequence specificity of uS3 as an AP lyase in general, we applied a combinatorial approach based on the use of a model single-stranded circular DNA with an AP site flanked with random trinucleotides at both sides. The cleavage of this DNA by uS3 under conditions when only its minor portion undergoes the reaction resulted in the formation of the linear DNA with random triplets at the 5′ and 3′ termini. </span></span>NGS<span> sequencing of the DNA library derived from this DNA allowed identifying the contexts within which uS3 cleaves DNA the most and the least effectively. Given that the AP lyase reaction occurs via the formation of a covalent intermediate (Schiff base), we determined the region comprising the active center of the uS3 protein. By digesting of uS3 cross-linked to a radiolabeled AP site-containing model DNA with specific proteolytic agents followed by analysis of the resulting modified oligopeptides, the cross-link was mapped to the region 155–192 (likely, to R173/R178). Thus, our results clarified two previously unstudied features of the uS3 AP lyase activity, one related to the recognition of sequences in DNA surrounding the AP site, and the other to the protein region directly contacting this site.</span></span></p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9116737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The armadillo-repeat domain of Plakophilin 1 binds to human enzyme PADI4 Plakophilin 1的犰狳重复结构域与人类酶PADI4结合
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2023-02-01 DOI: 10.1016/j.bbapap.2022.140868
José L. Neira , Bruno Rizzuti , Salome Araujo-Abad , Olga Abian , María Esther Fárez-Vidal , Adrian Velazquez-Campoy , Camino de Juan Romero
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引用次数: 3
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