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Dual Antimicrobial and Anticancer Activity of Membrane-Active Peptide BP52 膜活性肽 BP52 的双重抗菌和抗癌活性
IF 1.9 4区 生物学
The Protein Journal Pub Date : 2024-08-27 DOI: 10.1007/s10930-024-10231-y
Hai Bui Thi Phuong, Hoa Doan Ngan, Hue Pham Thi, Binh Nguyen Thi Thanh, Tien T. Dang, Thao N.T. Ho, Tung Truong Thanh, Minh Nguyen Hong, Huy Luong Xuan
{"title":"Dual Antimicrobial and Anticancer Activity of Membrane-Active Peptide BP52","authors":"Hai Bui Thi Phuong,&nbsp;Hoa Doan Ngan,&nbsp;Hue Pham Thi,&nbsp;Binh Nguyen Thi Thanh,&nbsp;Tien T. Dang,&nbsp;Thao N.T. Ho,&nbsp;Tung Truong Thanh,&nbsp;Minh Nguyen Hong,&nbsp;Huy Luong Xuan","doi":"10.1007/s10930-024-10231-y","DOIUrl":"10.1007/s10930-024-10231-y","url":null,"abstract":"<div><p>The linear undecapeptide <b>BP52</b> was previously reported to have antibacterial activity against phytopathogenic bacteria species. Due to the structural similarities to naturally occurring cationic helical antimicrobial peptides, it was speculated that this peptide could potentially target microbial pathogens and cancer cells found in mammals. Consequently, this study aims to further investigate the structural and biological properties of this peptide. Our findings indicate that <b>BP52</b> exhibits strong antimicrobial and anticancer activity while displaying relatively low levels of hemolytic activity. Hence, this study suggests that <b>BP52 could</b> be a potential lead compound for drug discovery against infectious diseases and cancer. Besides, new insights into the relationships between the structure and the multifunctional properties of antimicrobial peptides were also explored.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 5","pages":"1025 - 1034"},"PeriodicalIF":1.9,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074915","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
Characterization of the Three DHFRs and K65P Variant: Enhanced Substrate Affinity and Molecular Dynamics Analysis 三种 DHFR 和 K65P 变体的特征:增强的底物亲和力和分子动力学分析。
IF 1.9 4区 生物学
The Protein Journal Pub Date : 2024-08-23 DOI: 10.1007/s10930-024-10228-7
Ruirui Feng, Shuanghao Yang, Xingchu Zhao, Bo Sun, Shengkai Zhang, Qirong Shen, Qun Wan
{"title":"Characterization of the Three DHFRs and K65P Variant: Enhanced Substrate Affinity and Molecular Dynamics Analysis","authors":"Ruirui Feng,&nbsp;Shuanghao Yang,&nbsp;Xingchu Zhao,&nbsp;Bo Sun,&nbsp;Shengkai Zhang,&nbsp;Qirong Shen,&nbsp;Qun Wan","doi":"10.1007/s10930-024-10228-7","DOIUrl":"10.1007/s10930-024-10228-7","url":null,"abstract":"<div><p>Dihydrofolate reductase (DHFR) is ubiquitously present in all living organisms and plays a crucial role in the growth of the fungal pathogen <i>R.solani</i>. Sequence alignment confirmed the evolutionary conservation of the essential lid domain, with the amino acid ‘P’ within the PEKN lid domain appearing with a frequency of 89.5% in higher organisms and 11.8% in lower organisms. Consequently, a K65P variant was introduced into <i>R.solani</i> DHFR (<i>r</i>DHFR). Subsequent enzymatic kinetics assays were conducted for human DHFR (hDHFR), <i>r</i>DHFR, <i>E. coli</i> DHFR (<i>e</i>DHFR), and the K65P variant. hDHFR exhibited the highest <i>k</i><sub><i>cat</i></sub> of 0.95 s<sup>−1</sup>, followed by <i>r</i>DHFR with 0.14 s<sup>−1</sup>, while <i>e</i>DHFR displayed the lowest <i>k</i><sub><i>cat</i></sub> of 0.09 s<sup>−1</sup>. Remarkably, the K65P variant induced a significant reduction in <i>K</i><sub><i>m</i></sub>, resulting in a 1.8-fold enhancement in catalytic efficiency (<i>k</i><sub><i>cat</i></sub>/<i>K</i><sub><i>m</i></sub>) relative to the wild type. Differential scanning fluorimetry and binding free energy calculations confirmed the enhanced substrate affinity for both folate and NADPH in the K65P variant. These results suggest that the K65P mutation enhances substrate affinity and catalytic efficiency in DHFR, highlighting the evolutionary and functional importance of the K65 residue.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 5","pages":"935 - 948"},"PeriodicalIF":1.9,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047693","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
Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen 瘤胃中细菌和真菌碳水化合物酯酶家族 15 葡萄糖醛酸酯酶的结构、生化和系统发育分析
IF 1.9 4区 生物学
The Protein Journal Pub Date : 2024-08-17 DOI: 10.1007/s10930-024-10221-0
Robert J. Gruninger, Maya Kevorkova, Kristin E. Low, Darryl R. Jones, Liam Worrall, Tim A. McAllister, D. Wade Abbott
{"title":"Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen","authors":"Robert J. Gruninger,&nbsp;Maya Kevorkova,&nbsp;Kristin E. Low,&nbsp;Darryl R. Jones,&nbsp;Liam Worrall,&nbsp;Tim A. McAllister,&nbsp;D. Wade Abbott","doi":"10.1007/s10930-024-10221-0","DOIUrl":"10.1007/s10930-024-10221-0","url":null,"abstract":"<div><p>Glucuronoyl esterases (GEs) are carbohydrate active enzymes in carbohydrate esterase family 15 which are involved in the hydrolysis of lignin-carbohydrate complexes. They are encoded by a wide range of aerobic and anaerobic fungi and bacteria inhabiting diverse environments. The rumen microbiome is a complex microbial community with a wide array of enzymes that specialize in deconstructing plant cell wall carbohydrates. Enzymes from the rumen tend to show low similarity to homologues found in other environments, making the rumen microbiome a promising source for the discovery of novel enzymes. Using a combination of phylogenetic and structural analysis, we investigated the structure-function relationship of GEs from the rumen bacteria <i>Fibrobacter succinogenes</i> and <i>Ruminococcus flavefaciens</i>, and from the rumen fungus, <i>Piromyces rhizinflata</i>. All adopt a canonical α/β hydrolase fold and possess a structurally conserved Ser-His-Glu/Asp catalytic triad. Structural variations in the enzymes are localized to loops surrounding the active site. Analysis of the active site structures in these enzymes emphasized the importance of structural plasticity in GEs with non-canonical active site conformations. We hypothesize that interkingdom HGT events may have contributed to the diversity of GEs in the rumen, and this is demonstrated by the phylogenetic and structural similarity observed between rumen bacterial and fungal GEs. This study advances our understanding of the structure-function relationship in glucuronoyl esterases and illuminates the evolutionary dynamics that contribute to enzyme diversity in the rumen microbiome.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 4","pages":"910 - 922"},"PeriodicalIF":1.9,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11345330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141997163","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: 0
Rational Design, Synthesis, and Computational Investigation of Dihydropyridine [2,3-d] Pyrimidines as Polyphenol Oxidase Inhibitors with Improved Potency 二氢吡啶[2,3-d]嘧啶作为多酚氧化酶抑制剂的合理设计、合成和计算研究,提高了其效力。
IF 1.9 4区 生物学
The Protein Journal Pub Date : 2024-08-04 DOI: 10.1007/s10930-024-10220-1
Mustafa Oğuzhan Kaya, Mine Nazan Kerimak-Öner, Tuna Demirci, Ahmad Badreddin Musatat, Oğuzhan Özdemir, Yeşim Kaya, Mustafa Arslan
{"title":"Rational Design, Synthesis, and Computational Investigation of Dihydropyridine [2,3-d] Pyrimidines as Polyphenol Oxidase Inhibitors with Improved Potency","authors":"Mustafa Oğuzhan Kaya,&nbsp;Mine Nazan Kerimak-Öner,&nbsp;Tuna Demirci,&nbsp;Ahmad Badreddin Musatat,&nbsp;Oğuzhan Özdemir,&nbsp;Yeşim Kaya,&nbsp;Mustafa Arslan","doi":"10.1007/s10930-024-10220-1","DOIUrl":"10.1007/s10930-024-10220-1","url":null,"abstract":"<div><p>Polyphenol oxidase (PPO) is an industrially important enzyme associated with browning reactions. In the present study, a set of ten new dihydropyridine [2,3-d] pyrimidines (TD-Hid-1-10) were synthesized and was found to be proven characteristically by <sup>1</sup>H NMR, <sup>13</sup>C NMR, IR, elemental analysis, and assessed as possible PPO inhibitors. PPO was purified from banana using three-phase partitioning, achieving an 18.65-fold purification and 136.47% activity recovery. Enzyme kinetics revealed that the compounds TD-Hid-6 and TD-Hid-7 are to be the most potent inhibitors, exhibiting mixed-type inhibition profile with <i>IC</i><sub><i>50</i></sub> values of 1.14 µM, 5.29 µM respectively against purified PPO enzyme. Electronic structure calculations at the B3LYP/PBE0 level of theories using def-2 SVP, def2-TZVP basis sets with various molecular descriptors characterized the electronic behavior of studied derivatives TD-Hid-1-10. Molecular electrostatic potential (MEP) and reduced density gradient analyses of RDG-NCI provided insights into charge distributions and weak intermolecular interactions. Docking study simulations predicted binding poses within crucial amino acid sequence in the 2y9x enzyme’s active site, which is typically similar in sequence to the PPO form is not allowed. Ligands were analysed in terms of binding energies, inhibitor concentrations (mM) and various molecular interactions such as H-bonds, H-carbon, π-carbon, π-sigma, π-sigma, π-π T-shaped, π-π stacked, π-alkyl, Van der Waals and Cu interactions. The lowest binding energy (-7.83 kcal/mol) and the highest inhibitory effect (1.83 mM) were shown by the ligand Td-Hid-6, which forms H-bonds with Met280 and Asn260, exhibits π-sigma interactions with His61 and π-alkyl interactions with Val283. Other ligands also showed different interactions with various amino acids; for example, the Td-Hid-1 ligand formed H-bonds with His244 and showed π-sigma interactions with His244 and Val283.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 4","pages":"869 - 887"},"PeriodicalIF":1.9,"publicationDate":"2024-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141891419","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
Structural, Biochemical Characterization and Molecular Mechanism of Cerastokunin: A New Kunitz-Type Peptide with Potential Inhibition of Thrombin, Factor Xa and Platelets Cerastokunin 的结构、生化特征和分子机制:一种具有潜在凝血酶、Xa 因子和血小板抑制作用的新型 Kunitz 型多肽。
IF 1.9 4区 生物学
The Protein Journal Pub Date : 2024-08-02 DOI: 10.1007/s10930-024-10226-9
Noussaiba Saghour, Fatah Chérifi, Samah Saoud, Younes Zebbiche, Amel Meribai, Nadjia Bekkari, Taright-Mahi Samya, Fatima Laraba-Djebari
{"title":"Structural, Biochemical Characterization and Molecular Mechanism of Cerastokunin: A New Kunitz-Type Peptide with Potential Inhibition of Thrombin, Factor Xa and Platelets","authors":"Noussaiba Saghour,&nbsp;Fatah Chérifi,&nbsp;Samah Saoud,&nbsp;Younes Zebbiche,&nbsp;Amel Meribai,&nbsp;Nadjia Bekkari,&nbsp;Taright-Mahi Samya,&nbsp;Fatima Laraba-Djebari","doi":"10.1007/s10930-024-10226-9","DOIUrl":"10.1007/s10930-024-10226-9","url":null,"abstract":"<div><p>The current investigation focused on separating <i>Cerastes cerastes</i> venom to produce the first Kunitz-type peptide. Based on its anti-trypsin effect, Cerastokunin, a 7.75 kDa peptide, was purified until homogenity by three steps of chromatography. Cerastokunin was found to include 67 amino acid residues that were obtained by de novo sequencing using LC-MALDI-MSMS. Upon alignment with Kunitz-type peptides, there was a high degree of similarity. Cerastokunin’s 3D structure had 12% α-helices and 21% β-strands with pI 8.48. Cerastokunin showed a potent anticoagulant effect by inhibiting the protease activity of thrombin and trypsin as well as blocking the intrinsic and extrinsic coagulation pathways. In both PT and aPPT, Cerastokunin increased the blood clotting time in a dose-dependent way. Using Lys48 and Gln192 for direct binding, Cerastokunin inhibited thrombin, Factor Xa and trypsin as shown by molecular docking. Cerastokunin exhibited a dose–response blockade of PARs-dependent pathway platelet once stimulated by thrombin. An increased concentration of Cerastokunin resulted in a larger decrease of tail thrombus in the mice-carrageenan model in an in vivo investigation when compared to the effects of antithrombotic medications. At all Cerastokunin doses up to 6 mg/kg, no in vivo toxicity was seen in challenged mice over the trial’s duration.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 4","pages":"888 - 909"},"PeriodicalIF":1.9,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141879961","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
Structural Phylogenetics with Protein Mass Spectrometry: A Proof-of-Concept 利用蛋白质质谱进行结构系统学研究:概念验证。
IF 1.9 4区 生物学
The Protein Journal Pub Date : 2024-07-29 DOI: 10.1007/s10930-024-10227-8
Benjamin P. Todd, Kevin M. Downard
{"title":"Structural Phylogenetics with Protein Mass Spectrometry: A Proof-of-Concept","authors":"Benjamin P. Todd,&nbsp;Kevin M. Downard","doi":"10.1007/s10930-024-10227-8","DOIUrl":"10.1007/s10930-024-10227-8","url":null,"abstract":"<div><p>It is demonstrated, for the first time, that a mass spectrometry approach (known as <i>phylonumerics</i>) can be successfully implemented for structural phylogenetics investigations to chart the evolution of a protein’s structure and function. Illustrated for the compact globular protein myoglobin, peptide masses produced from the proteolytic digestion of the protein across animal species generate trees congruent to the sequence tree counterparts. Single point mutations calculated during the same mass tree building step can be followed along interconnected branches of the tree and represent a viable structural metric. A mass tree built for 15 diverse animal species, easily resolve the birds from mammal species, and the ruminant mammals from the remainder of the animals. Mutations within helix-spanning peptide segments alter both the mass and structure of the protein in these segments. Greater evolution is found in the B-helix over the A, E, F, G and H helices. A further mass tree study, of six more closely related primate species, resolves gorilla from the other primates based on a P22S mutation within the B-helix. The remaining five primates are resolved into two groups based on whether they contain a glycine or serine at position 23 in the same helix. The orangutan is resolved from the gibbon and siamang by its G-helix C110S mutation, while homo sapiens are resolved from chimpanzee based on the Q116H mutation. All are associated with structural perturbations in such helices. These structure altering mutations can be tracked along interconnecting branches of a mass tree, to follow the protein’s structure and evolution, and ultimately the evolution of the species in which the proteins are expressed. Those that have the greatest impact on a protein’s structure, its function, and ultimately the evolution of the species, can be selectively tracked or monitored.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 5","pages":"997 - 1008"},"PeriodicalIF":1.9,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141794471","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
Protein S-Nitrosylation: A Chemical Modification with Ubiquitous Biological Activities 蛋白质 S-亚硝基化:具有普遍生物活性的化学修饰
IF 1.9 4区 生物学
The Protein Journal Pub Date : 2024-07-28 DOI: 10.1007/s10930-024-10223-y
Adam A. Aboalroub, Khaldun M. Al Azzam
{"title":"Protein S-Nitrosylation: A Chemical Modification with Ubiquitous Biological Activities","authors":"Adam A. Aboalroub,&nbsp;Khaldun M. Al Azzam","doi":"10.1007/s10930-024-10223-y","DOIUrl":"10.1007/s10930-024-10223-y","url":null,"abstract":"<div><p>Nitric oxide (NO) induces protein posttranslational modification (PTM), known as S-nitrosylation, which has started to gain attention as a critical regulator of thousands of substrate proteins. However, our understanding of the biological consequences of this emerging PTM is incomplete because of the limited number of identified S-nitrosylated proteins (S–NO proteins). Recent advances in detection methods have effectively contributed to broadening the spectrum of discovered S–NO proteins. This article briefly reviews the progress in S–NO protein detection methods and discusses how these methods are involved in characterizing the biological consequences of this PTM. Additionally, we provide insight into S–NO protein-related diseases, focusing on the role of these proteins in mitigating the severity of infectious diseases.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 4","pages":"639 - 655"},"PeriodicalIF":1.9,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141775100","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 Insights into How the Single Point Mutation Change the Autoantibody Repertoire 单点突变如何改变自身抗体汇集的机制启示
IF 1.9 4区 生物学
The Protein Journal Pub Date : 2024-07-28 DOI: 10.1007/s10930-024-10225-w
Zhong Ni, Fangyuan Song, Huimin Zhou, Ying Xu, Zhiguo Wang, Dongfeng Chen
{"title":"Mechanistic Insights into How the Single Point Mutation Change the Autoantibody Repertoire","authors":"Zhong Ni,&nbsp;Fangyuan Song,&nbsp;Huimin Zhou,&nbsp;Ying Xu,&nbsp;Zhiguo Wang,&nbsp;Dongfeng Chen","doi":"10.1007/s10930-024-10225-w","DOIUrl":"10.1007/s10930-024-10225-w","url":null,"abstract":"<div><p>A recent study showed that just one point mutation F33 to Y in the complementarity-determining region 1 of heavy chain (H-CDR1) could lead to the auto-antibody losing its DNA binding ability. However, the potential molecular mechanisms have not been well elucidated. In this study, we investigated how the antibody lost the DNA binding ability caused by mutation F33 to Y in the H-CDR1. We found that the electrostatic force was not the primary driving force for the interaction between anti-DNA antibodies and the antigen single strand DNA (ssDNA), and that the H-CDR2 largely contributed to the binding of antigen ssDNA, even larger than H-CDR1. The H-F33Y mutation could increase the hydrogen-bond interaction but impair the pi-pi stacking interaction between the antibody and ssDNA. We further found that F33<sub>H</sub>, W98<sub>H</sub> and Y95<sub>L</sub> in the wiletype antibody could form the stable pi-pi stacking interaction with the nucleotide bases of ssDNA. However, the Y33 in mutant could not form the parallel sandwich pi-pi stacking interaction with the ssDNA. To further confirm the importance of pi-pi stacking, the wildtype antibody and the mutants (F33Y<sub>H</sub>, F33A<sub>H</sub>, W98A<sub>H</sub> and Y95A<sub>L</sub>) were experimentally expressed in CHO cells and purified, and the results from ELISA clearly showed that all the mutants lost the ssDNA binding ability. Taken together, our findings may not only deepen the understanding of the underlying interaction mechanism between autoantibody and antigen, but also broad implications in the field of antibody engineer.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 4","pages":"683 - 696"},"PeriodicalIF":1.9,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141786192","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
A Machine Learning Approach to Identify C Type Lectin Domain (CTLD) Containing Proteins 识别含 C 型连接蛋白域 (CTLD) 蛋白质的机器学习方法
IF 1.9 4区 生物学
The Protein Journal Pub Date : 2024-07-28 DOI: 10.1007/s10930-024-10224-x
Lovepreet Singh, Sukhwinder Singh, Desh Deepak Singh
{"title":"A Machine Learning Approach to Identify C Type Lectin Domain (CTLD) Containing Proteins","authors":"Lovepreet Singh,&nbsp;Sukhwinder Singh,&nbsp;Desh Deepak Singh","doi":"10.1007/s10930-024-10224-x","DOIUrl":"10.1007/s10930-024-10224-x","url":null,"abstract":"<div><p>Lectins are sugar interacting proteins which bind specific glycans reversibly and have ubiquitous presence in all forms of life. They have diverse biological functions such as cell signaling, molecular recognition, etc. C-type lectins (CTL) are a group of proteins from the lectin family which have been studied extensively in animals and are reported to be involved in immune functions, carcinogenesis, cell signaling, etc. The carbohydrate recognition domain (CRD) in CTL has a highly variable protein sequence and proteins carrying this domain are also referred to as C-type lectin domain containing proteins (CTLD). Because of this low sequence homology, identification of CTLD from hypothetical proteins in the sequenced genomes using homology based programs has limitations. Machine learning (ML) tools use characteristic features to identify homologous sequences and it has been used to develop a tool for identification of CTLD. Initially 500 sequences of well annotated CTLD and 500 sequences of non CTLD were used in developing the machine learning model. The classifier program Linear SVC from sci kit library of python was used and characteristic features in CTLD sequences like dipeptide and tripeptide composition were used as training attributes in various classifiers. A precision, recall and multiple correlation coefficient (MCC) value of 0.92, 0.91 and 0.82 respectively were obtained when tested on external test set. On fine tuning of the parameters like kernel, C value, gamma, degree and increasing number of non CTLD sequences there was improvement in precision, recall and MCC and the corresponding values were 0.99, 0.99 and 0.96. New CTLD have also been identified in the hypothetical segment of human genome using the trained model. The tool is available on our local server for interested users.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 4","pages":"718 - 725"},"PeriodicalIF":1.9,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141775104","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
A Protease from Moringa oleifera Lam. Exhibits In-vitro Blood Clot Solubilization and Fibrin Hydrolysis 从油辣木中提取的一种蛋白酶具有体外溶解血凝块和水解纤维蛋白的作用
IF 1.9 4区 生物学
The Protein Journal Pub Date : 2024-07-28 DOI: 10.1007/s10930-024-10222-z
Sawetaji, Kamal Krishan Aggarwal
{"title":"A Protease from Moringa oleifera Lam. Exhibits In-vitro Blood Clot Solubilization and Fibrin Hydrolysis","authors":"Sawetaji,&nbsp;Kamal Krishan Aggarwal","doi":"10.1007/s10930-024-10222-z","DOIUrl":"10.1007/s10930-024-10222-z","url":null,"abstract":"<div><p>Thrombosis is the formation of abnormal blood clots in the blood vessels that obstruct blood flow and lead to thrombosis. Current treatments for thrombosis are associated with serious side effects. Therefore there is a need for alternative natural therapy. A fibrinolytic protease was isolated from fresh leaves of <i>Moringa oleifera</i> Lam. and characterized for its potential to solubilize blood clots and hydrolyse fibrin under in-vitro conditions. The isolated protease showed a single protein band on native-PAGE. It showed optimum fibrinolytic activity at pH 8.0, 37 <sup>o</sup>C with 50 µg protein. The fibrinolytic activity of isolated protease was also confirmed by fibrin zymography. K<sub>m</sub> and V<sub>max</sub> of isolated protease were determined by the Lineweaver Burk plot. The isolated protease could solubilize 96.41% of blood clots by 96 h under in-vitro conditions. In-vitro fibrin hydrolysis and blood clot solubilization activities shown by an isolated protease from leaves of <i>Moringa oleifera</i> Lam. suggest its fibrinolytic potential to dissolve blood clots. Being a natural molecule and from a dietary plant it can be explored as an alternative natural therapy against thrombosis.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 4","pages":"923 - 934"},"PeriodicalIF":1.9,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141775102","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
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