{"title":"A Comprehensive Review on Machine Learning Techniques for Protein Family Prediction","authors":"T. Idhaya, A. Suruliandi, S. P. Raja","doi":"10.1007/s10930-024-10181-5","DOIUrl":"10.1007/s10930-024-10181-5","url":null,"abstract":"<div><p>Proteomics is a field dedicated to the analysis of proteins in cells, tissues, and organisms, aiming to gain insights into their structures, functions, and interactions. A crucial aspect within proteomics is protein family prediction, which involves identifying evolutionary relationships between proteins by examining similarities in their sequences or structures. This approach holds great potential for applications such as drug discovery and functional annotation of genomes. However, current methods for protein family prediction have certain limitations, including limited accuracy, high false positive rates, and challenges in handling large datasets. Some methods also rely on homologous sequences or protein structures, which introduce biases and restrict their applicability to specific protein families or structures. To overcome these limitations, researchers have turned to machine learning (ML) approaches that can identify connections between protein features and simplify complex high-dimensional datasets. This paper presents a comprehensive survey of articles that employ various ML techniques for predicting protein families. The primary objective is to explore and improve ML techniques specifically for protein family prediction, thus advancing future research in the field. Through qualitative and quantitative analyses of ML techniques, it is evident that multiple methods utilizing a range of classifiers have been applied for protein family prediction. However, there has been limited focus on developing novel classifiers for protein family classification, highlighting the urgent need for improved approaches in this area. By addressing these challenges, this research aims to enhance the accuracy and effectiveness of protein family prediction, ultimately facilitating advancements in proteomics and its diverse applications.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 2","pages":"171 - 186"},"PeriodicalIF":1.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139998771","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}
Erika Maria Gomes Ferreira Teixeira, Dario Eluam Kalume, Patrícia Fernandes Ferreira, Thayane Aparecida Alves, Ana Paula G. A. Fontão, André Luís Franco Sampaio, Danilo Ribeiro de Oliveira, José Andrés Morgado-Díaz, Raquel Elisa Silva-López
{"title":"A Novel Trypsin Kunitz-Type Inhibitor from Cajanus cajan Leaves and Its Inhibitory Activity on New Cancer Serine Proteases and Its Effect on Tumor Cell Growth","authors":"Erika Maria Gomes Ferreira Teixeira, Dario Eluam Kalume, Patrícia Fernandes Ferreira, Thayane Aparecida Alves, Ana Paula G. A. Fontão, André Luís Franco Sampaio, Danilo Ribeiro de Oliveira, José Andrés Morgado-Díaz, Raquel Elisa Silva-López","doi":"10.1007/s10930-023-10175-9","DOIUrl":"10.1007/s10930-023-10175-9","url":null,"abstract":"<div><p>A novel trypsin inhibitor from <i>Cajanus cajan</i> (TIC) fresh leaves was partially purified by affinity chromatography. SDS-PAGE revealed one band with about 15 kDa with expressive trypsin inhibitor activity by zymography. TIC showed high affinity for trypsin (Ki = 1.617 μM) and was a competitive inhibitor for this serine protease. TIC activity was maintained after 24 h of treatment at 70 °C, after 1 h treatments with different pH values, and β-mercaptoethanol increasing concentrations, and demonstrated expressive structural stability. However, the activity of TIC was affected in the presence of oxidizing agents. In order to study the effect of TIC on secreted serine proteases, as well as on the cell culture growth curve, SK-MEL-28 metastatic human melanoma cell line and CaCo-2 colon adenocarcinoma was grown in supplemented DMEM, and the extracellular fractions were submitted salting out and affinity chromatography to obtain new secreted serine proteases. TIC inhibited almost completely, 96 to 89%, the activity of these serine proteases and reduced the melanoma and colon adenocarcinoma cells growth of 48 and 77% respectively. Besides, it is the first time that a trypsin inhibitor was isolated and characterized from <i>C. cajan</i> leaves and cancer serine proteases were isolated and partial characterized from SK-MEL-28 and CaCo-2 cancer cell lines. Furthermore, TIC shown to be potent inhibitor of tumor protease affecting cell growth, and can be one potential drug candidate to be employed in chemotherapy of melanoma and colon adenocarcinoma.</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 2","pages":"333 - 350"},"PeriodicalIF":1.9,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725527","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}
{"title":"The Structural Features of MlaD Illuminate its Unique Ligand-Transporting Mechanism and Ancestry","authors":"Angshu Dutta, Shankar Prasad Kanaujia","doi":"10.1007/s10930-023-10179-5","DOIUrl":"10.1007/s10930-023-10179-5","url":null,"abstract":"<div><p>The membrane-associated solute-binding protein (SBP) MlaD of the maintenance of lipid asymmetry (Mla) system has been reported to help the transport of phospholipids (PLs) between the outer and inner membranes of Gram-negative bacteria. Despite the availability of structural information, the molecular mechanism underlying the transport of PLs and the ancestry of the protein MlaD remain unclear. In this study, we report the crystal structures of the periplasmic region of MlaD from <i>Escherichia coli</i> (<i>Ec</i>MlaD) at a resolution range of 2.3–3.2 Å. The <i>Ec</i>MlaD protomer consists of two distinct regions, viz. N-terminal β-barrel fold consisting of seven strands (referred to as MlaD domain) and C-terminal α-helical domain (HD). The protein <i>Ec</i>MlaD oligomerizes to give rise to a homo-hexameric ring with a central channel that is hydrophobic and continuous with a variable diameter. Interestingly, the structural analysis revealed that the HD, instead of the MlaD domain, plays a critical role in determining the oligomeric state of the protein. Based on the analysis of available structural information, we propose a working mechanism of PL transport, viz. “asymmetric protomer movement (APM)”. Wherein half of the <i>Ec</i>MlaD hexamer would rise in the periplasmic side along with an outward movement of pore loops, resulting in the change of the central channel geometry. Furthermore, this study highlights that, unlike typical SBPs, <i>Ec</i>MlaD possesses a fold similar to EF/AMT-type beta(6)-barrel and a unique ancestry. Altogether, the findings firmly establish <i>Ec</i>MlaD to be a non-canonical SBP with a unique ligand-transport mechanism.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 2","pages":"298 - 315"},"PeriodicalIF":1.9,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725528","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}
Libo Yuan, Ke Wang, Yuan Fang, Xiujuan Xu, Yingcun Chen, Dongxin Zhao, Kui Lu
{"title":"Interaction of Cecropin A (1–7) Analogs with DNA Analyzed by Multi-spectroscopic Methods","authors":"Libo Yuan, Ke Wang, Yuan Fang, Xiujuan Xu, Yingcun Chen, Dongxin Zhao, Kui Lu","doi":"10.1007/s10930-023-10177-7","DOIUrl":"10.1007/s10930-023-10177-7","url":null,"abstract":"<div><p>Cecropin A (1–7) is a cationic antimicrobial peptide which contain lots of basic amino acids. To understand the effect of basic amino acids on cecropin A (1–7), analogues CA2, CA3 and CA4 which have more arginine or lysine at the N-terminal or C-terminal were designed and synthesized. The interaction of cecropin A (1–7) and its analogs with DNA was studied using ultraviolet–visible spectroscopy, fluorescence spectroscopy and circular dichroism spectroscopy. Multispectral analysis showed that basic amino acids improved the interaction between the analogues and DNA. The interaction between CA4 and DNA is most pronounced. Fluorescence spectrum indicated that Ksv value of CA4 is 1.19 × 10<sup>5</sup> L mol<sup>−1</sup> compared to original peptide cecropin A (1–7) of 3.73 × 10<sup>4</sup> L mol<sup>−1</sup>. The results of antimicrobial experiments with cecropin A (1–7) and its analogues showed that basic amino acids enhanced the antimicrobial effect of the analogues. The antimicrobial activity of CA4 against <i>E. coli</i> was eightfold higher than that of cecropin A (1–7). The importance of basic amino acid in peptides is revealed and provides useful information for subsequent studies of antimicrobial peptides.</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 2","pages":"274 - 282"},"PeriodicalIF":1.9,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139543117","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}
{"title":"Refolding, Crystallization, and Crystal Structure Analysis of a Scavenger Receptor Cysteine-Rich Domain of Human Salivary Agglutinin Expressed in Escherichia coli","authors":"Changyu Zhang, Peng Lu, Sibo Wei, Chaoyue Hu, Mitsuko Miyoshi, Ken Okamoto, Hideaki Itoh, Suguru Okuda, Michio Suzuki, Hiroshi Kawakami, Koji Nagata","doi":"10.1007/s10930-023-10173-x","DOIUrl":"10.1007/s10930-023-10173-x","url":null,"abstract":"<div><p>Scavenger receptors are a protein superfamily that typically consists of one or more repeats of the scavenger receptor cysteine-rich structural domain (SRCRD), which is an ancient and highly conserved protein module. The expression and purification of eukaryotic proteins containing multiple disulfide bonds has always been challenging. The expression systems that are commonly used to express SRCRD proteins mainly consist of eukaryotic protein expression systems. Herein, we established a high-level expression strategy of a Type B SRCRD unit from human salivary agglutinin using the <i>Escherichia coli</i> expression system, followed by a refolding and purification process. The untagged recombinant SRCRD was expressed in <i>E. coli</i> using the pET-32a vector, which was followed by a refolding process using the GSH/GSSG redox system. The SRCRD expressed in <i>E. coli</i> SHuffle T7 showed better solubility after refolding than that expressed in <i>E. coli</i> BL21(DE3), suggesting the importance of the disulfide bond content prior to refolding. The quality of the refolded protein was finally assessed using crystallization and crystal structure analysis. As proteins refolded from inclusion bodies exhibit a high crystal quality and reproducibility, this method is considered a reliable strategy for SRCRD protein expression and purification. To further confirm the structural integrity of the refolded SRCRD protein, the purified protein was subjected to crystallization using sitting-drop vapor diffusion method. The obtained crystals of SRCRD diffracted X-rays to a resolution of 1.47 Å. The solved crystal structure appeared to be highly conserved, with four disulfide bonds appropriately formed. The surface charge distribution of homologous SRCRD proteins indicates that the negatively charged region at the surface is associated with their calcium-dependent ligand recognition. These results suggest that a high-quality SRCRD protein expressed by <i>E. coli</i> SHuffle T7 can be successfully folded and purified, providing new options for the expression of members of the scavenger receptor superfamily.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 2","pages":"283 - 297"},"PeriodicalIF":1.9,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11058800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139543118","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}
{"title":"Heterologous Production of Antimicrobial Peptides: Notes to Consider","authors":"Masoumeh Kordi, Parnian Ghaedi Talkhounche, Helia Vahedi, Naser Farrokhi, Maryam Tabarzad","doi":"10.1007/s10930-023-10174-w","DOIUrl":"10.1007/s10930-023-10174-w","url":null,"abstract":"<div><p>Heavy and irresponsible use of antibiotics in the last century has put selection pressure on the microbes to evolve even faster and develop more resilient strains. In the confrontation with such sometimes called “superbugs”, the search for new sources of biochemical antibiotics seems to have reached the limit. In the last two decades, bioactive antimicrobial peptides (AMPs), which are polypeptide chains with less than 100 amino acids, have attracted the attention of many in the control of microbial pathogens, more than the other types of antibiotics. AMPs are groups of components involved in the immune response of many living organisms, and have come to light as new frontiers in fighting with microbes. AMPs are generally produced in minute amounts within organisms; therefore, to address the market, they have to be either produced on a large scale through recombinant DNA technology or to be synthesized via chemical methods. Here, heterologous expression of AMPs within bacterial, fungal, yeast, plants, and insect cells, and points that need to be considered towards their industrialization will be reviewed.</p><h3>Graphical Abstract</h3><p>Sources of peptide production and their applications. Some AMPs directly extracted from natural sources, some of them are chemically synthesized either using liquid or solid phase peptides synthesis, and for large scale production, recombinant expression using heterologous expression systems have been used.</p>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 2","pages":"129 - 158"},"PeriodicalIF":1.9,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139099450","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}
{"title":"Engineering Human Pancreatic RNase 1 as an Immunotherapeutic Agent for Cancer Therapy Through Computational and Experimental Studies","authors":"Mohammadreza Nassiri, Shahrokh Ghovvati, Marzieh Gharouni, Mojtaba Tahmoorespur, Ahmad Reza Bahrami, Hesam Dehghani","doi":"10.1007/s10930-023-10171-z","DOIUrl":"10.1007/s10930-023-10171-z","url":null,"abstract":"<div><p>Most plant and bacterial toxins are highly immunogenic with non-specific toxic effects. Human ribonucleases are thought to provide a promising basis for reducing the toxic agent’s immunogenic properties, which are candidates for cancer therapy. In the cell, the ribonuclease inhibitor (RI) protein binds to the ribonuclease enzyme and forms a tight complex. This study aimed to engineer and provide a gene construct encoding an improved version of Human Pancreatic RNase 1 (HP-RNase 1) to reduce connection to RI and modulate the immunogenic effects of immunotoxins. To further characterize the interaction complex of HP-RNase 1 and RI, we established various in silico and in vitro approaches. These methods allowed us to specifically monitor interactions within native and engineered HP-RNase 1/RI complexes. In silico research involved molecular dynamics (MD) simulations of native and mutant HP-RNase 1 in their free form and when bound to RI. For HP-RNase 1 engineering, we designed five mutations (K8A/N72A/N89A/R92D/E112/A) based on literature studies, as this combination proved effective for the intended investigation. Then, the cDNA encoding HP-RNase 1 was generated by RT-PCR from blood and cloned into the pSYN2 expression vector. Consequently, wild-type and the engineered HP-RNase 1 were over-expressed in <i>E. coli</i> TG1 and purified using an IMAC column directed against a poly-his tag. The protein products were detected by SDS–PAGE and Western blot analysis. HP-RNase 1 catalytic activity, in the presence of various concentrations of RI, demonstrated that the mutated version of the protein is able to escape the ribonuclease inhibitor and target the RNA substrate 2.5 folds more than that of the wild type. From these data, we tend to suggest the engineered recombinant HP-RNase 1 potentially as a new immunotherapeutic agent for application in human cancer therapy.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 2","pages":"316 - 332"},"PeriodicalIF":1.9,"publicationDate":"2023-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139033143","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}
Manali Chandnani, Disha Patel, Twinkle Patel, Aditi Buch
{"title":"Tartrate Dehydrogenase in Bacillus Species: Deciphering Unique Catalytic Diversity Through Kinetic, Structural and Molecular Docking Analysis","authors":"Manali Chandnani, Disha Patel, Twinkle Patel, Aditi Buch","doi":"10.1007/s10930-023-10170-0","DOIUrl":"10.1007/s10930-023-10170-0","url":null,"abstract":"<div><p>Divergently evolved Tartrate dehydrogenase (TDH) exhibits multiple catalytic activities at a single active site; the enzyme from <i>P. putida</i> (pTDH) being structurally and biochemically well-characterized. Occurrence of TDH-associated ability to aerobically metabolize L-tartrate in <i>Bacillus</i> isolates and limited resemblance of <i>ycsA</i>-encoded protein sequences with pTDH rendered <i>Bacillus</i> TDH as an intriguing enzyme with possible catalytic diversity as well as evolutionary significance. The present study explores substrate interactions of TDHs from <i>B. subtilis</i> 168 (168bTDH) and <i>B. licheniformis</i> DSM-13 (429bTDH) through kinetic, structural and molecular docking-based analysis. Heterologously expressed bTDHs, purified from insoluble fractions of <i>E. coli</i> BL21(DE3) cells, could significantly catalyze L-tartrate and <i>meso</i>-tartrate as substrates in forward reaction. Unlike pTDH, bTDHs distinctly and more efficiently catalyzed the reverse reaction using dihydroxyfumarate substrate following sigmoidal kinetics; the ability being ~ 4 fold higher in 168bTDH. Their binding energies predicted from molecular docking, further substantiated the relative substrate specificities, while revealing major residues involved in protein-ligand interactions at active site. The kinetic analysis and homology modelling validated using Ramachandran Plot analysis predicted a dimeric nature for bTDH. Collectively, the results highlight unique catalytic potential of phylogenetically recent bTDHs, offering an important protein engineering target to mediate efficient enantioselective enzymatic biotransformations.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 1","pages":"96 - 114"},"PeriodicalIF":1.9,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138833856","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}
{"title":"Biochemical Characterization of Laccase from Spirulina CPCC-695 and Their Role in Estrone Degradation","authors":"Neha Sami, Bushra Afzal, Durdana Yasin, Tasneem Fatma","doi":"10.1007/s10930-023-10169-7","DOIUrl":"10.1007/s10930-023-10169-7","url":null,"abstract":"<div><p>The addition of exogenous endocrine disrupting compounds (EDCs) like estrone, in the food chain through the aquatic system, disrupts steroid biosynthesis and metabolism by altering either the genomic or non-genomic pathway that eventually results in various diseases. Thus, bioremediation of these compounds is urgently required to prevent their addition and persistence in the environment. Enzymatic degradation has proven to be a knight in shining armour as it is safe and generates no toxic products. The multicopper oxidases (E.C. 1.10.3.2 benzenediol: oxygen oxidoreductase), laccase with the potential to degrade both phenolic and non-phenolic substrates has recently gained attention. In this study, the laccase was purified, characterized, and used to study estrone degradation. The culture filtrate (crude laccase) was concentrated and precipitated using cold-acetone and dialyzed against tris buffer (50 mM) giving a four-fold partially purified form, with 45.56% yield and 204.14 U/mg as specific activity and a single peak at 250–300 nm. The partially purified laccase was approximately 80 kDa as estimated by SDS-PAGE preferred ABTS as substrate. Both crude and partially purified laccase showed maximum activity at pH 3.0, 40 °C, and 4 mM ABTS. Kinetic constants (Km, Vmax) of crude and partially purified laccase were found to be 0.83 mM; 494.31 mM/min, and 0.58 mM; 480.54 mM/min respectively. Iron sulphate and sodium azide inhibited laccase maximally. Crude and partially purified laccase degradation efficiency was 87.55 and 91.35% respectively. <i>Spirulina</i> CPCC-695 laccase with efficient estrone degradation ability renders them promising candidates for EDCs bioremediation.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 1","pages":"115 - 128"},"PeriodicalIF":1.9,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138833810","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}