Journal of Biomolecular Structure & Dynamics最新文献_第7页

Enhanced sensing of bacteria biomarkers by ZnO and graphene oxide decorated PEDOT film. 氧化锌和氧化石墨烯装饰的 PEDOT 薄膜增强了对细菌生物标记物的感应。

IF 2.4 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-08-01 Epub Date: 2024-03-18 DOI: 10.1080/07391102.2024.2328740

Victor Malachy Udowo, Tomsmith O Unimuke, Hitler Louis, Inime Ime Udoh, Henry O Edet, Peter C Okafor

{"title":"Enhanced sensing of bacteria biomarkers by ZnO and graphene oxide decorated PEDOT film.","authors":"Victor Malachy Udowo, Tomsmith O Unimuke, Hitler Louis, Inime Ime Udoh, Henry O Edet, Peter C Okafor","doi":"10.1080/07391102.2024.2328740","DOIUrl":"10.1080/07391102.2024.2328740","url":null,"abstract":"Developing a biofilm biomarker detector and inhibitor will immensely benefit efforts geared at curbing infectious diseases and microbiologically induced corrosion of medical implants, marine vessels and buried steel pipelines. N-Acyl homoserine lactones (AHLs) are important biomarkers gram-negative bacteria use for communication. In this work, we investigated the interactions between three AHL molecules and graphene oxide (GO) and ZnO nanomaterials embedded in conjugated poly(3,4-ethylenedioxythiophene) (PEDOT) film. The results show that PEDOT/GO/ZnO detected AHLs to a considerable extent with adsorption enthalpies of -4.02, -4.87 and -4.97 KJ/mol, respectively, for N-(2-oxotetrahydrofuran-3-yl)heptanamide (AHL1), 2-hydroxy-N-(2-oxotetrahydrofuran-3-yl)nonanamide (AHL2) and (E)-3-(3-hydroxyphenyl)-N-(2-oxotetrahydrofuran-3-yl)acrylamide (AHL3) molecules. The ZnO nanoparticles facilitated charge redistribution and transfer, thereby enhancing the conductivity and overall sensitivity of the substrate toward the AHLs. The adsorption distance and sites of interactions further tuned the charge migration and signal generation by the substrate, thus affirming the suitability of the modeled thin film as a sensor material. Excellent stability and conductivity were maintained before and after the adsorption of each AHL molecule. Moreover, the desorption time for each AHL molecule was calculated, and the result affirmed that the modeled film materials are promising for developing highly sensitive biosensors.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"6188-6201"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140158257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Correction. 更正。

IF 2.4 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-08-01 Epub Date: 2024-06-22 DOI: 10.1080/07391102.2024.2369383

引用次数: 0

Unveiling fructose and glucose binding to human serum albumin: fluorescence measurements and docking, molecular dynamics and quantum biochemistry computations. 揭示果糖和葡萄糖与人类血清白蛋白的结合：荧光测量和对接、分子动力学和量子生物化学计算。

IF 2.4 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-08-01 Epub Date: 2024-01-30 DOI: 10.1080/07391102.2024.2310211

André Hadad, Victor L B França, Marcos William Crisostomo, Kellen Brunaldi, Hernandes F Carvalho, Valder N Freire

{"title":"Unveiling fructose and glucose binding to human serum albumin: fluorescence measurements and docking, molecular dynamics and quantum biochemistry computations.","authors":"André Hadad, Victor L B França, Marcos William Crisostomo, Kellen Brunaldi, Hernandes F Carvalho, Valder N Freire","doi":"10.1080/07391102.2024.2310211","DOIUrl":"10.1080/07391102.2024.2310211","url":null,"abstract":"This research examines the interaction between human serum albumin (HSA) and various sugar forms (β-D-fructofuranose (FRC), α-D-glucopyranose (GLC), Keto-D-fructose (FRO), Aldehydo-D-glucose (GLO), and modified Aldehydo-D-glucose (GLOm)) using fluorescent spectroscopy, molecular docking simulations, molecular dynamics, protein conformational clusters (EnGens), molecular fractionation with conjugate caps (MFCC) and quantum biochemistry analysis. We analyze molecular and quantum aspects, uncovering interaction energies between sugar atoms and amino acids. Total interaction energy considers protein fragmentation, energetic decomposition, and interaction energy from a bottom-up perspective. Molecular dynamics reveal that unmodified Aldehydo-D-glucose (GLO) escapes HSA binding sites, explaining gradual glycation. We pioneer studying HSA's binding mechanism with glucose and fructose in a 1:1 ratio using long molecular dynamics simulations. Results suggest the transitional GLOm form has a higher Sudlow I site propensity than unmodified glucose, crucial for K195 glycation. FRO and GLOm interaction tendencies move toward a deeper FA7 cavity, near its center. This approach effectively elucidates small molecule binding mechanisms, consistent with previous experimental results.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"6770-6790"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139575895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

CDH1 gene as biomarker towards breast cancer prediction. 将 CDH1 基因作为预测乳腺癌的生物标志物。

IF 2.4 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-08-01 Epub Date: 2024-02-19 DOI: 10.1080/07391102.2024.2316770

Srijan Banerjee, Antara Sengupta, Shankar Kumar Ghosh, Raja Banerjee

{"title":"CDH1 gene as biomarker towards breast cancer prediction.","authors":"Srijan Banerjee, Antara Sengupta, Shankar Kumar Ghosh, Raja Banerjee","doi":"10.1080/07391102.2024.2316770","DOIUrl":"10.1080/07391102.2024.2316770","url":null,"abstract":"Breast cancer is considered to be happened due to genetic aberration. Out of several genes expressed, it is found that cadherin 1, type 1 (CDH1) is responsible in several ways to control the metabolic order in human. Deregulation of the function of protein E-cadherin, expressed from CDH1 plays an important role in lobular breast cancer. In order to understand the root cause of this recent claim, we focus on CDH1 gene: whether the genetic information translated due to any deviation/alteration/modification in its sequence is related to the occurrence of the different types breast cancer. Towards this end, quantitative analysis of different biophysical and bio-chemical properties of CDH1 gene in genomic and proteomic levels from the available genomic (cDNA) sequences of CDH1 gene (obtained from the COSMIC Database for 78 patients, suffering from various types of breast cancer) clearly emphasizes that alternation/modification in the sequence of the CDH1 gene can be detrimental. Furthermore, Random forest, K-nearest neighbour and stochastic gradient descent (SGD) algorithms are applied on the derived dataset to classify the types of breast cancer, and to validate our hypothesis regarding the acute role of CDH1 as potential bio marker for breast cancer. Analysis of the mutated CDH1 gene sequences, and their related parameters using aforesaid machine learning techniques clearly establish that CDH1 gene can take the deterministic role in predicting the chances of occurrences of different types of breast cancer with an accuracy of <math><mrow><mo>></mo><mn>90</mn><mi>%</mi></mrow><mo>.</mo></math> Such an observation opens a new paradigm in diagnostic approach of breast cancer.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"6474-6487"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139905723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Discovery of novel inhibitor via molecular dynamics simulations against D-alanyl-D-alanine carboxypeptidase of Enterobacter cloacae. 通过分子动力学模拟发现针对丁香杆菌 D-丙氨酰-D-丙氨酸羧肽酶的新型抑制剂

IF 2.4 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-08-01 Epub Date: 2024-02-20 DOI: 10.1080/07391102.2024.2316790

Faisal Ahmad, Saba Ismail, Syed Sikander Azam

{"title":"Discovery of novel inhibitor via molecular dynamics simulations against D-alanyl-D-alanine carboxypeptidase of Enterobacter cloacae.","authors":"Faisal Ahmad, Saba Ismail, Syed Sikander Azam","doi":"10.1080/07391102.2024.2316790","DOIUrl":"10.1080/07391102.2024.2316790","url":null,"abstract":"Antibiotics resistance by bacterial pathogens is a major concern to public health worldwide resulting in high health care costs and rising mortality. Subtractive proteomics prioritized D-alanyl-D-alanine carboxypeptidas (DacB) enzyme from Enterobacter cloacae ATCC 13047 as a potential candidate for drugs designing to block pathogen cell wall biosynthesis. Virtual screening of an antibacterial library against the target unraveled a hit compound (2-[(1-methylsulfonylpiperidin-3-yl)methyl]-6-(1H-pyrazol-4-yl) pyrazine) showing high affinity and stability with the target. The N-methyl-N-propyl-methanesulfonamide of the compound is seen as a closed affinity towards domain involving strong hydrogen bonds with Ser41, Lys44, Ser285, and Asn287. The 4-methyl-1H-pyrazole is posed towards the open cavity of domain I and II and formed hydrophobic and hydrophilic contacts. The system is highly stable with average carbon-alpha deviations of 1.69 Å over trajectories of 400-ns. Three vital residues projected: Arg437, Arg438 and Leu400 from enzyme pocket via Radial distribution function (RDF) assay, which actively engaged the inhibitor. Further confirmation is done by estimating binding free energies, which confirms the very low delta energy of -7.24 kcal/mol in Generalized Born (GB) method and -7.4363 kcal/mol in Poisson-Boltzmann (PB) method. WaterSwap calculations were performed that revealed the energies highly converged, an agreement on good system stability. Lastly, three DacB mutants were created to investigate the role of functional active residues and a decline in binding affinity of the residues was noticed. These computational results provide a gateway for experimentalists to further confirm their efficacy both in-vitro and in-vivo.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"6816-6831"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139905724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

MMV method: a new approach to compare protein sequences under binary representation. MMV 方法：一种在二进制表示下比较蛋白质序列的新方法。

IF 2.4 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-08-01 Epub Date: 2024-02-20 DOI: 10.1080/07391102.2024.2317982

Jayanta Pal, Soumen Ghosh, Bansibadan Maji, Dilip Kumar Bhattacharya

{"title":"MMV method: a new approach to compare protein sequences under binary representation.","authors":"Jayanta Pal, Soumen Ghosh, Bansibadan Maji, Dilip Kumar Bhattacharya","doi":"10.1080/07391102.2024.2317982","DOIUrl":"10.1080/07391102.2024.2317982","url":null,"abstract":"In the present work, a new form of descriptor using minimal moment vector (MMV) is introduced to compare protein sequences in the frequency domain under their component wise binary representations. From every sequence, 20 different binary component sequences are formed, each corresponding to 20 amino acids. Each such vector is now shifted from the time domain to the frequency domain by applying the Fast Fourier Transform (FFT). Next, the power spectrum calculated from the FFT values for each component sequence is so normalized that the sum of the components equals 1. The descriptor is defined as a 20-component vector composed of the 20 second-order minimal moments calculated from the normalized spectrum of the 20 component sequences. Once the descriptor is known, the distance matrix is created by applying the Euclidean Distance measure. The phylogenetic tree is generated by applying the unweighted pair group method with the arithmetic mean (UPGMA) algorithm using Molecular Evolutionary Genetics Analysis11 (MEGA11) software. In this work, the datasets used for similarity studies are 9 NADH dehydrogenase 5 (ND5), 12 Baculoviruses, 24 Transferrins (TF) proteins, and 50 Spike Protein of coronavirus. A qualitative measure using rationalized perception is used to compare the effectiveness of the proposed method. Quantitative measure based on symmetric distance (SD) is used to compare the phylogenetic trees of the present method with those obtained by other methods. It is observed that the phylogenetic trees generated by the proposed technique are at par with their known biological references, and they produce results better than those of the earlier methods.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"6563-6569"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139905725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Identification of phytocompounds as potent inhibitors of sodium/glucose cotransporter-2 leading to diabetes treatment. 鉴定植物化合物作为钠/葡萄糖共转运体-2 的强效抑制剂，以治疗糖尿病。

IF 2.4 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-08-01 Epub Date: 2024-02-20 DOI: 10.1080/07391102.2024.2319674

Ananta Swargiary, Manita Daimari, Arup Swargiary, Arup Biswas, Dulur Brahma, Hiloljyoti Singha

{"title":"Identification of phytocompounds as potent inhibitors of sodium/glucose cotransporter-2 leading to diabetes treatment.","authors":"Ananta Swargiary, Manita Daimari, Arup Swargiary, Arup Biswas, Dulur Brahma, Hiloljyoti Singha","doi":"10.1080/07391102.2024.2319674","DOIUrl":"10.1080/07391102.2024.2319674","url":null,"abstract":"Type-II diabetes, a major metabolic disorder has threatened the very existence of a healthy life since long ago. Commercially available antidiabetic drugs are known for several adverse effects. The present study attempted to identify potential phytocompounds as inhibitors of sodium/glucose cotransporter-2 (SGLT2), a major protein that helps in glucose re-absorption from renal tubules. A total of 28 phytocompounds were collected based on the literature survey. 3D co-ordinates of phytocompounds were collected from PubChem database. Molecular docking was carried out with SGLT2 protein and the best 3 docking complexes were subjected to molecular dynamics simulation for 100 ns. Free energy changes were also analyzed using MM/PBSA analysis. Phytocompounds were also analyzed for their drug-likeness and ADMET properties. Docking study observed a strong binding affinity of phytocompounds (> -7.0 kcal/mol). More than 10 phytocompounds showed better binding affinity compared to reference drugs. Further analysis of three best docking complexes when analyzed by MD simulation showed better stability and compactness of the complexes compared to reference drug, empagliflozin. MM/PBSA analysis also revealed that van der Waals force and electrostatic energy are the major binding energy involved in the complex formation. Like docking energy, free energy analysis also observed stronger binding energies (ΔGGAS) in SGLT2-phytocompound complexes compared to empagliflozin complex. All the phytocompounds showed drug-likeness and considerable ADMET properties. The study, therefore, suggests that Trifolirhizin-6'-monoacetate, Aspalathin, and Quercetin-3-glucoside could be a possible inhibitor of SGLT2 protein. However, further studies need to be carried out to reveal the exact mode of activity.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"6667-6680"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139912697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Identification of the odorant binding proteins of Western Flower Thrips (Frankliniella occidentalis), characterization and binding analysis of FoccOBP3 with molecular modelling, molecular dynamics simulations and a confirmatory field trial. 鉴定西花蓟马（Frankliniella occidentalis）的气味结合蛋白，通过分子建模、分子动力学模拟和田间试验确认 FoccOBP3 的特征和结合分析。

IF 2.4 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-08-01 Epub Date: 2024-02-28 DOI: 10.1080/07391102.2024.2317990

Zeeshan Zafar, Martyn J Wood, Sidra Fatima, Muhammad Faraz Bhatti, Farooq A Shah, Zack Saud, E Joel Loveridge, Ismail Karaca, Tariq M Butt

{"title":"Identification of the odorant binding proteins of Western Flower Thrips (Frankliniella occidentalis), characterization and binding analysis of FoccOBP3 with molecular modelling, molecular dynamics simulations and a confirmatory field trial.","authors":"Zeeshan Zafar, Martyn J Wood, Sidra Fatima, Muhammad Faraz Bhatti, Farooq A Shah, Zack Saud, E Joel Loveridge, Ismail Karaca, Tariq M Butt","doi":"10.1080/07391102.2024.2317990","DOIUrl":"10.1080/07391102.2024.2317990","url":null,"abstract":"Olfactory systems are indispensable for insects as they, including Western Flower Thrips (Frankliniella occidentalis), use olfactory cues for ovipositing and feeding. F. occidentalis use odorant binding proteins (OBPs) to transport semiochemicals to odorant receptors to induce a behavioural response from the sensillum lymph of the insect's antennae. This study identifies four OBPs of F. occidentalis and analyses their expression at three stages of growth: larvae, adult males and adult females. Further, it investigates the presence of conserved motifs and their phylogenetic relationship to other insect species. Moreover, FoccOBP3 was in silico characterized to analyse its structure along with molecular docking and molecular dynamics simulations to understand its binding with semiochemicals of F. occidentalis. Molecular docking revealed the interactions of methyl isonicotinate, p-anisaldehyde and (S)-(-)-verbenone with FoccOBP3. Moreover, molecular dynamics simulations showed bonding stability of these ligands with FoccOBP3, and field trials validated that Lurem TR (commercial product) and p-anisaldehyde had greater attraction as compared to (S)-(-)-verbenone, given the compound's binding with FoccOBP3. The current study helps in understanding the tertiary structure and interaction of FoccOBP3 with lures using computational and field data and will help in the identification of novel lures of insects in the future, given the importance of binding with OBPs.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"6853-6868"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139982965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Insights into the inhibitory potential of novel hydrazinyl thiazole-linked indenoquinoxaline against alpha-amylase: a comprehensive QSAR, pharmacokinetic, and molecular modeling study. 新型肼基噻唑连环茚喹喔啉对α-淀粉酶抑制潜力的见解：一项全面的 QSAR、药物动力学和分子建模研究。

IF 2.4 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-08-01 Epub Date: 2024-02-02 DOI: 10.1080/07391102.2024.2310778

Oussama Abchir, Imane Yamari, Amneh Mohammad Shtaiwi, Hassan Nour, Mhammed El Kouali, Mohammed Talbi, Abdelkbir Errougui, Samir Chtita

{"title":"Insights into the inhibitory potential of novel hydrazinyl thiazole-linked indenoquinoxaline against alpha-amylase: a comprehensive QSAR, pharmacokinetic, and molecular modeling study.","authors":"Oussama Abchir, Imane Yamari, Amneh Mohammad Shtaiwi, Hassan Nour, Mhammed El Kouali, Mohammed Talbi, Abdelkbir Errougui, Samir Chtita","doi":"10.1080/07391102.2024.2310778","DOIUrl":"10.1080/07391102.2024.2310778","url":null,"abstract":"The rising prevalence of diabetes necessitates the development of novel drugs, especially given the side effects associated with current medications like Acarbose and Voglibose. A series of 36 Hydrazinyl thiazole-linked indenoquinoxaline derivatives with notable activity against alpha-amylase were studied. To create a molecular model predicting alpha-amylase activity, a QSAR study was performed on these compounds. Molecular descriptors were calculated using Chem3D and Gaussian software and then correlated with their IC50 biological activities to form a dataset. This model data was refined using PCA and modeled with MLR. The model's performance was statistically verified (R2 =0.800; <math><mrow><msubsup><mrow><mi>R</mi></mrow><mrow><mtext>adj</mtext></mrow><mrow><mn>2</mn></mrow></msubsup></mrow></math> = 0.767; <math><mrow><msubsup><mrow><mi>R</mi></mrow><mrow><mtext>cv</mtext></mrow><mrow><mn>2</mn></mrow></msubsup></mrow></math> = 0.651) and its applicability domain was defined. It was predicted to possess high predictive power (<math><mrow><msubsup><mrow><mi>R</mi></mrow><mrow><mtext>test</mtext></mrow><mrow><mn>2</mn></mrow></msubsup></mrow><mi> </mi></math> = 0.872). Based on this, new compounds were proposed, and their activities were predicted using the developed model. Additionally, their binding ability to the biological target was studied through molecular docking and dynamics. Their pharmacokinetics were also evaluated using ADMET predictions. Two designed compounds named AE and AB emerged as particularly promising, displaying properties that suggest substantial therapeutic potential and they can form stable complexes into the binding pocket of alpha-amylase enzyme.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5701-5718"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139671901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

In silico molecular characterization of TGF-β gene family in Bufo bufo: genome-wide analysis. 蟾蜍 TGF-β 基因家族的硅学分子特征：全基因组分析。

IF 2.4 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-08-01 Epub Date: 2024-02-12 DOI: 10.1080/07391102.2024.2313168

Mehwish Sultana, Muhammad Tayyab, Sunil, Shakeela Parveen, Muhammad Hussain, Saba Saeed, Zainab Riaz, Saman Shabbir

{"title":"In silico molecular characterization of TGF-β gene family in Bufo bufo: genome-wide analysis.","authors":"Mehwish Sultana, Muhammad Tayyab, Sunil, Shakeela Parveen, Muhammad Hussain, Saba Saeed, Zainab Riaz, Saman Shabbir","doi":"10.1080/07391102.2024.2313168","DOIUrl":"10.1080/07391102.2024.2313168","url":null,"abstract":"Bufo bufo is a living example of evolutionary processes due to its numerous physiological and ecological adaptations. This is the first study to genetically characterize the TGF-β gene family in B. bufo at the genome-wide level, and a total of 28 TGF-β gene family homologs are identified. Physicochemical characteristics of TGF-β homologs exhibit a basic nature except for BMP1, BMP4, BMP10, BMP15, AMH, INHA, NODAL Modulator and TGFB1. Phylogenetic analysis divided the TGF-β gene family homologs into 2 major clades along with other vertebrate species. In domain and motif composition analysis, the gene structure for all TGF-β homologs exhibited homogeneity except BMP1. We have identified the TGF-β propeptide domain together with the TGF-β in all family homologs of TGF-β superfamily. Gene structure comparisons indicated that the TGF-β gene family have arisen by gene duplications. We also identified 10 duplicated gene pairs, all of which were detected to be segmental duplications. The Ka/Ks test ratio findings for every pair of genes revealed that none of the ratios surpassed 1 except for one gene pair (INHA/BMP1), indicating that these proteins are under positive selection. Circos analysis showed that TGF-β gene family homologs are arranged in 11 dispersed clusters and all were segmentally arrayed in the genome. This study provides a molecular basis for TGF-β ligand protein functional analysis and may serve as a reference for in-depth phylogenomics and may promote the development of novel strategies.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5834-5848"},"PeriodicalIF":2.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139722727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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