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Biophysical and Biochemical Characterization of the Receptor Binding Domain of SARS-CoV-2 Variants SARS-CoV-2变异体受体结合域的生物物理生化特征
IF 3 4区 生物学
The Protein Journal Pub Date : 2022-09-01 DOI: 10.1007/s10930-022-10073-6
Ritika Khatri, Hilal Ahmad Parray, Gazala Siddiqui, Adarsh Kumar Chiranjivi, Sneha Raj, Rachel Kaul, Vikas Maithil, Sweety Samal, Shubbir Ahmed
{"title":"Biophysical and Biochemical Characterization of the Receptor Binding Domain of SARS-CoV-2 Variants","authors":"Ritika Khatri,&nbsp;Hilal Ahmad Parray,&nbsp;Gazala Siddiqui,&nbsp;Adarsh Kumar Chiranjivi,&nbsp;Sneha Raj,&nbsp;Rachel Kaul,&nbsp;Vikas Maithil,&nbsp;Sweety Samal,&nbsp;Shubbir Ahmed","doi":"10.1007/s10930-022-10073-6","DOIUrl":"10.1007/s10930-022-10073-6","url":null,"abstract":"<div><p>The newly emerging SARS-CoV-2 variants are potential threat and posing new challenges for medical intervention due to high transmissibility and escaping neutralizing antibody (NAb) responses. Many of these variants have mutations in the receptor binding domain (RBD) of SARS-CoV-2 spike protein that interacts with the host cell receptor. Rapid mutation in the RBD through natural selection to improve affinity for host receptor and antibody pressure from vaccinated or infected individual will greatly impact the presently adopted strategies for developing interventions. Understanding the nature of mutations and how they impact the biophysical, biochemical and immunological properties of the RBD will help immensely to improve the intervention strategies. To understand the impact of mutation on the protease sensitivity, thermal stability, affinity for the receptor and immune response, we prepared several mutants of soluble RBD that belong to the variants of concern (VoCs) and interest (VoIs) and characterize them. Our results show that the mutations do not impact the overall structure of the RBD. However, the mutants showed increase in the thermal melting point, few mutants were more sensitive to protease degradation, most of them have enhanced affinity for ACE2 and some of them induced better immune response compared to the parental RBD.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"41 4-5","pages":"457 - 467"},"PeriodicalIF":3.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10930-022-10073-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4063732","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
Improved Protein Real-Valued Distance Prediction Using Deep Residual Dense Network (DRDN) 基于深度残差密集网络(DRDN)的改进蛋白质实值距离预测
IF 3 4区 生物学
The Protein Journal Pub Date : 2022-08-25 DOI: 10.1007/s10930-022-10067-4
S. Geethu, E. R. Vimina
{"title":"Improved Protein Real-Valued Distance Prediction Using Deep Residual Dense Network (DRDN)","authors":"S. Geethu,&nbsp;E. R. Vimina","doi":"10.1007/s10930-022-10067-4","DOIUrl":"10.1007/s10930-022-10067-4","url":null,"abstract":"<div><p>Three-dimensional protein structure prediction is one of the major challenges in bioinformatics. According to recent research findings, real-valued distance prediction plays a vital role in determining the unique three-dimensional protein structure. This paper proposes a novel methodology involving a deep residual dense network (DRDN) for predicting protein real-valued distance. The features extracted from the given query protein sequence and its corresponding homologous sequences are used for training the model. Multi-aligned homologous sequences for each query protein sequence are retrieved from five different databases using DeepMSA, HHblits, and HITS_PR_HHblits methods. The proposed method yielded outcomes of 3.89, 0.23, 0.45, and 0.63, respectively, corresponding to the evaluation metrics such as Absolute Error, Relative Error, High-accuracy Pairwise Distance Test (PDA), and Pairwise Distance Test (PDT). Further, the contact map is computed based on CASP criteria by converting the predicted real-valued distance, and it is evaluated using the precision metric. It is observed that precision of long-range top L/5 contact prediction on the CASP13 dataset by the proposed method, RaptorX, Zhang, trRosetta, JinboXu &amp; JinLu, and Deepdist are 0.834, 0.657, 0.70, 0.785, 0.786, and 0.812, respectively. Also, Top-L/5 contact prediction on the CASP14 dataset evaluated using average precision resulted in 0.847, 0.707, 0.752, 0.783, 0.792, 0.817, and 0.825 respectively, corresponding to the proposed method, Zhang, RaptorX, trRosetta, Deepdist, JinboXu &amp; JinLu, and Alphafold2.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"41 4-5","pages":"468 - 476"},"PeriodicalIF":3.0,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10930-022-10067-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4963867","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
A New Combination: Anti Glypican-3 scFv and Diphtheria Toxin with the Best Flexible Linker 抗Glypican-3 scFv与白喉毒素最佳柔性连接的新组合
IF 3 4区 生物学
The Protein Journal Pub Date : 2022-08-24 DOI: 10.1007/s10930-022-10074-5
Hamid Hashemi Yeganeh, Mohammad Heiat, Seyed Moayed Alavian, Ehsan Rezaei
{"title":"A New Combination: Anti Glypican-3 scFv and Diphtheria Toxin with the Best Flexible Linker","authors":"Hamid Hashemi Yeganeh,&nbsp;Mohammad Heiat,&nbsp;Seyed Moayed Alavian,&nbsp;Ehsan Rezaei","doi":"10.1007/s10930-022-10074-5","DOIUrl":"10.1007/s10930-022-10074-5","url":null,"abstract":"<div><p>Along with all cancer treatments, including chemotherapy, radiotherapy, and surgery, targeting therapy is a new treatment manner. Immunotoxins are new recombinant structures that kill cancer cells by targeting specific antigens. Immunotoxins are composed of two parts: toxin moiety, which disrupts protein synthesis process, and antigen binding moiety that bind to antigens on the surface of cancer cells. Glypican 3 (GPC3) is an oncofetal antigen on the surface of Hepatocellular carcinoma (HCC) cells. In this study, truncated <i>Diphtheria</i> toxin (DT389) was fused to humanized scFv YP7 by one, two and three repeats of GGGGS linkers (DT389-(GGGGS)<sub>1-3</sub>YP7). In-silico and experimental investigation were performed to find out how many repeats of linker between toxin and scFv moieties are sufficient. Results of in-silico investigations revealed that the difference in the number of linkers does not have a significant effect on the main structures of the immunotoxin; however, the three-dimensional structure of two repeats of linker had a more appropriate structure compared to others with one and three linker replications. In addition, with enhancing the number of linkers, the probability of protein solubility has increased. Generally, the bioinformatics results of DT389-(GGGGS)<sub>2</sub>-YP7 structure showed that expression and folding is suitable; and YP7 scFv has appropriate orientation to bind GPC3. The experimental investigations indicated that the fusion protein was expressed as near to 50% soluble. Due to the high binding affinity of YP7 scFv and the proven potency of diphtheria in inhibiting protein synthesis, the proposed DT389-(GGGGS)<sub>2</sub>-YP7 immunotoxin is expected to function well in inhibiting HCC.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"41 4-5","pages":"527 - 542"},"PeriodicalIF":3.0,"publicationDate":"2022-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4919690","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 Influence of Heparan Sulfate on Breast Amyloidosis and the Toxicity of the Pre-fibrils Formed by β-casein 硫酸肝素对乳腺淀粉样变性的影响及β-酪蛋白形成的前原纤维的毒性
IF 3 4区 生物学
The Protein Journal Pub Date : 2022-08-13 DOI: 10.1007/s10930-022-10071-8
Jia Wang, Jiayin Liu, Qinghai Dong, Yang An, Jun Su, Hongliu Xie, Bo Sun, Jihua Liu
{"title":"The Influence of Heparan Sulfate on Breast Amyloidosis and the Toxicity of the Pre-fibrils Formed by β-casein","authors":"Jia Wang,&nbsp;Jiayin Liu,&nbsp;Qinghai Dong,&nbsp;Yang An,&nbsp;Jun Su,&nbsp;Hongliu Xie,&nbsp;Bo Sun,&nbsp;Jihua Liu","doi":"10.1007/s10930-022-10071-8","DOIUrl":"10.1007/s10930-022-10071-8","url":null,"abstract":"<div><p>Heparan sulfate (HS) as a mediator is usually involved in both inflammation and fibrosis. Besides, pre-fibrils are the intermediates of amyloid fibrils that usually cause cell death and tissue damage, like the amyloid-β in Alzheimer’s disease, α-synuclein in Parkinson disease and islet amyloid polypeptide in type II diabetes mellitus. However, the related study was involved rarely in breast. Therefore, the combing technologies including hematoxylin-eosin staining and thioflavin S staining were used to investigate the influence of HS on breast amyloidosis. To further study the toxicity of the pre-fibrils formed by β-casein on the HC11 cells and the breast mammary gland, the combing technologies including pentamer formyl thiophene acetic acid fluorescence analysis, MTT assay, Annexin V/PI staining and hematoxylin-eosin staining were performed. The results demonstrated that HS, acted as an endogenous molecule, induced the inflammation and amyloid fibril formation at the same time, and there was a close relationship between inflammation and fibrosis of breast. In addition, the pre-fibrils formed by β-casein were toxic because they induced the death and apoptosis of HC11 cells, as well as the inflammation of mammary gland of rats. Therefore, the early examination and identify of the pre-fibrils in the breast were worth considering to prevent the disease development, and it was interesting to explore the HS mimetics to impair the breast amyloidosis and attenuate the inflammatory response in the future.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"41 4-5","pages":"543 - 549"},"PeriodicalIF":3.0,"publicationDate":"2022-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10930-022-10071-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4527755","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
Molecular and Enzymatic Characterization of 9-Cis-epoxycarotenoid Dioxygenases from Mulberry 桑树9-顺式环氧类胡萝卜素双加氧酶的分子和酶学表征
IF 3 4区 生物学
The Protein Journal Pub Date : 2022-08-13 DOI: 10.1007/s10930-022-10072-7
Dan Liu, Changyu Qiu, Yanrong Zeng, Qiang Lin
{"title":"Molecular and Enzymatic Characterization of 9-Cis-epoxycarotenoid Dioxygenases from Mulberry","authors":"Dan Liu,&nbsp;Changyu Qiu,&nbsp;Yanrong Zeng,&nbsp;Qiang Lin","doi":"10.1007/s10930-022-10072-7","DOIUrl":"10.1007/s10930-022-10072-7","url":null,"abstract":"<div><p>Abscisic acid (ABA) is involved in many physiological regulatory processes in plants, such as leaf shedding, stomatal closure, inhibition of cell elongation, as well as responses to multi-abiotic stress, and 9-cis epoxy carotenoid dioxygenase (NCED) is related to the indirect synthesis of ABA. However, <i>NCED</i> genes involved in multi-abiotic stress and ABA synthesis pathway in mulberry (<i>Morus alba</i> L.) are still unknown. Here, two <i>NCED</i> genes cloned from mulberry (<i>MaNCED</i>) and their function were preliminarily identified. Interestingly, <i>MaNCED2</i> responded strongly to drought stress while <i>MaNCED1</i> responded strongly to pathogen stress. Then, two MaNCED proteins were successfully obtained by prokaryotic expression, and the degradation products of MaNCED1 and MaNCED2 were analyzed using UPLC-MS. The results show that recombinant MaNCED1 and MaNCED2 both cleave 9-<i>cis</i>-violaxanthin to form C<sub>15</sub> xanthoxin, involved in the formation of the precursor of ABA.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"41 4-5","pages":"504 - 514"},"PeriodicalIF":3.0,"publicationDate":"2022-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10930-022-10072-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4529132","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
Biochemical and Biophysical Characterization of Carbonic Anhydrase VI from Human Milk and Saliva 人乳和唾液中碳酸酐酶VI的生化和生物物理特性
IF 3 4区 生物学
The Protein Journal Pub Date : 2022-08-10 DOI: 10.1007/s10930-022-10070-9
Alma Yrjänäinen, Maarit S. Patrikainen, Latifeh Azizi, Martti E. E. Tolvanen, Mikko Laitaoja, Janne Jänis, Vesa P. Hytönen, Alessio Nocentini, Claudiu T. Supuran, Seppo Parkkila
{"title":"Biochemical and Biophysical Characterization of Carbonic Anhydrase VI from Human Milk and Saliva","authors":"Alma Yrjänäinen,&nbsp;Maarit S. Patrikainen,&nbsp;Latifeh Azizi,&nbsp;Martti E. E. Tolvanen,&nbsp;Mikko Laitaoja,&nbsp;Janne Jänis,&nbsp;Vesa P. Hytönen,&nbsp;Alessio Nocentini,&nbsp;Claudiu T. Supuran,&nbsp;Seppo Parkkila","doi":"10.1007/s10930-022-10070-9","DOIUrl":"10.1007/s10930-022-10070-9","url":null,"abstract":"<div><p>Carbonic anhydrases (CA, EC 4.2.1.1) catalyze the hydration of carbon dioxide and take part in many essential physiological processes. In humans, 15 CAs are characterized, including the only secreted isoenzyme CA VI. CA VI has been linked to specific processes in the mouth, namely bitter taste perception, dental caries, and maintenance of enamel pellicle, and implicated in several immunity-related phenomena. However, little is known of the mechanisms of the above. In this study, we characterized human CA VI purified from saliva and milk with biophysical methods and measured their enzyme activities and acetazolamide inhibition. Size-exclusion chromatography showed peaks of salivary and milk CA VI corresponding to hexameric state or larger at pH 7.5. At pH 5.0 the hexamer peaks dominated. SDS- PAGE of milk CA VI protein treated with a bifunctional crosslinker further confirmed that a majority of CA VI is oligomers of similar sizes in solution. Mass spectrometry experiments confirmed that both of the two putative N-glycosylation sites, Asn67 and Asn256, are heterogeneously glycosylated. The attached glycans in milk CA VI were di- and triantennary complex-type glycans, carrying both a core fucose and 1 to 2 additional fucose units, whereas the glycans in salivary CA VI were smaller, seemingly degraded forms of core fucosylated complex- or hybrid-type glycans. Mass spectrometry also verified the predicted signal peptide cleavage site and the terminal residue, Gln 18, being in pyroglutamate form. Thorough characterization of CA VI paves way to better understanding of the biological function of the protein.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"41 4-5","pages":"489 - 503"},"PeriodicalIF":3.0,"publicationDate":"2022-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10930-022-10070-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4409190","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
Functional Characterization of Recombinant Endo-Levanase (LevBk) from Bacillus koreensis HL12 on Short-Chain Levan-Type Fructooligosaccharides Production 韩国芽孢杆菌HL12重组内切利末酸酶(levane - enase, LevBk)在短链利末型低聚果糖生产中的功能研究
IF 3 4区 生物学
The Protein Journal Pub Date : 2022-08-06 DOI: 10.1007/s10930-022-10069-2
Hataikarn Lekakarn, Benjarat Bunterngsook, Phuphiphat Jaikaew, Thanyanun Kuantum, Rungtiva Wansuksri, Verawat Champreda
{"title":"Functional Characterization of Recombinant Endo-Levanase (LevBk) from Bacillus koreensis HL12 on Short-Chain Levan-Type Fructooligosaccharides Production","authors":"Hataikarn Lekakarn,&nbsp;Benjarat Bunterngsook,&nbsp;Phuphiphat Jaikaew,&nbsp;Thanyanun Kuantum,&nbsp;Rungtiva Wansuksri,&nbsp;Verawat Champreda","doi":"10.1007/s10930-022-10069-2","DOIUrl":"10.1007/s10930-022-10069-2","url":null,"abstract":"<div><p>Levan-type fructooligosaccharides (L-FOSs) are a prominent class of non-digestible oligosaccharides with potential as nutritional prebiotics. Endo-levanase, which randomly hydrolyzes β-(2,6)-linkages in fructans, is a promising enzyme for short-chain FOS production. In this work, a recombinant levanase (LevBk) from <i>Bacillus koreensis</i> strain HL12 was characterized. Soluble LevBk protein was produced in <i>Escherichia coli</i> BL21(DE3) system at 40 mg/L of culture medium. Based on sequence and structural analysis, LevBk was classified as a member of endo-levanase in GH32 family containing N-terminal substrate binding pocket and C-terminal β-sandwich domains. LevBk optimally worked at 45 °C, pH 6.0 with the specific activity of 2.43 U/mg. Based on enzymatic hydrolysis, short-chain L-FOSs with degree of polymerization (DP) of 2–4 were produced from hydrolysis of timothy grass levan under optimal conditions for 9–24 h. With its ability to produce L-FOSs with specific chain lengths, LevBk could be attractively applied for converting of levan containing material to high value-added sweetener in the biorefinery industry.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"41 4-5","pages":"477 - 488"},"PeriodicalIF":3.0,"publicationDate":"2022-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4241227","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: 1
Expression of Codon-Optimized Gene Encoding Murine Moloney Leukemia Virus Reverse Transcriptase in Escherichia coli 小鼠白血病病毒逆转录酶密码子优化基因在大肠杆菌中的表达
IF 3 4区 生物学
The Protein Journal Pub Date : 2022-08-06 DOI: 10.1007/s10930-022-10066-5
Isa Nuryana, Fina Amreta Laksmi, Eva Agustriana, Kartika Sari Dewi, Ade Andriani, Ahmad Thontowi, Wien Kusharyoto, Puspita Lisdiyanti
{"title":"Expression of Codon-Optimized Gene Encoding Murine Moloney Leukemia Virus Reverse Transcriptase in Escherichia coli","authors":"Isa Nuryana,&nbsp;Fina Amreta Laksmi,&nbsp;Eva Agustriana,&nbsp;Kartika Sari Dewi,&nbsp;Ade Andriani,&nbsp;Ahmad Thontowi,&nbsp;Wien Kusharyoto,&nbsp;Puspita Lisdiyanti","doi":"10.1007/s10930-022-10066-5","DOIUrl":"10.1007/s10930-022-10066-5","url":null,"abstract":"<div><p>Moloney murine leukemia virus reverse transcriptase (MMLV-RT) is the most frequently used enzyme in molecular biology for cDNA synthesis. To date, reverse transcription coupled with Polymerase Chain Reaction, known as RT-PCR, has been popular as an excellent approach for the detection of SARS-CoV-2 during the COVID-19 pandemic. In this study, we aimed to improve the enzymatic production and performance of MMLV-RT by optimizing both codon and culture conditions in <i>E. coli</i> expression system. By applying the optimized codon and culture conditions, the enzyme was successfully overexpressed and increased at high level based on the result of SDS-PAGE and Western blotting. The total amount of MMLV-RT has improved 85-fold from 0.002 g L<sup>−1</sup> to 0.175 g L<sup>−1</sup> of culture. One-step purification by nickel affinity chromatography has been performed to generate the purified enzyme for further analysis of qualitative and quantitative RT activity. Overall, our investigation provides useful strategies to enhance the recombinant enzyme of MMLV-RT in both production and performance. More importantly, the enzyme has shown promising activity to be used for RT-PCR assay.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"41 4-5","pages":"515 - 526"},"PeriodicalIF":3.0,"publicationDate":"2022-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10930-022-10066-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4242228","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
Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations 通过分子动力学模拟揭示更强的SARS-CoV-2变体的进化
IF 3 4区 生物学
The Protein Journal Pub Date : 2022-08-01 DOI: 10.1007/s10930-022-10065-6
Alec J. Wozney, Macey A. Smith, Mobeen Abdrabbo, Cole M. Birch, Kelsey A. Cicigoi, Connor C. Dolan, Audrey E. L. Gerzema, Abby Hansen, Ethan J. Henseler, Ben LaBerge, Caterra M. Leavens, Christine N. Le, Allison C. Lindquist, Rikaela K. Ludwig, Maggie G. O’Reilly, Jacob H. Reynolds, Brandon A. Sherman, Hunter W. Sillman, Michael A. Smith, Marissa J. Snortheim, Levi M. Svaren, Emily C. Vanderpas, Aidan Voon, Miles J. Wackett, Moriah M. Weiss, Sanchita Hati, Sudeep Bhattacharyya
{"title":"Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations","authors":"Alec J. Wozney,&nbsp;Macey A. Smith,&nbsp;Mobeen Abdrabbo,&nbsp;Cole M. Birch,&nbsp;Kelsey A. Cicigoi,&nbsp;Connor C. Dolan,&nbsp;Audrey E. L. Gerzema,&nbsp;Abby Hansen,&nbsp;Ethan J. Henseler,&nbsp;Ben LaBerge,&nbsp;Caterra M. Leavens,&nbsp;Christine N. Le,&nbsp;Allison C. Lindquist,&nbsp;Rikaela K. Ludwig,&nbsp;Maggie G. O’Reilly,&nbsp;Jacob H. Reynolds,&nbsp;Brandon A. Sherman,&nbsp;Hunter W. Sillman,&nbsp;Michael A. Smith,&nbsp;Marissa J. Snortheim,&nbsp;Levi M. Svaren,&nbsp;Emily C. Vanderpas,&nbsp;Aidan Voon,&nbsp;Miles J. Wackett,&nbsp;Moriah M. Weiss,&nbsp;Sanchita Hati,&nbsp;Sudeep Bhattacharyya","doi":"10.1007/s10930-022-10065-6","DOIUrl":"10.1007/s10930-022-10065-6","url":null,"abstract":"<div><p>Using molecular dynamics simulations, the protein–protein interactions of the receptor-binding domain of the wild-type and seven variants of the severe acute respiratory syndrome coronavirus 2 spike protein and the peptidase domain of human angiotensin-converting enzyme 2 were investigated. These variants are alpha, beta, gamma, delta, eta, kappa, and omicron. Using 100 ns simulation data, the residue interaction networks at the protein–protein interface were identified. Also, the impact of mutations on essential protein dynamics, backbone flexibility, and interaction energy of the simulated protein–protein complexes were studied. The protein–protein interface for the wild-type, delta, and omicron variants contained several stronger interactions, while the alpha, beta, gamma, eta, and kappa variants exhibited an opposite scenario as evident from the analysis of the inter-residue interaction distances and pair-wise interaction energies. The study reveals that two distinct residue networks at the central and right contact regions forge stronger binding affinity between the protein partners. The study provides a molecular-level insight into how enhanced transmissibility and infectivity by delta and omicron variants are most likely tied to a handful of interacting residues at the binding interface, which could potentially be utilized for future antibody constructs and structure-based antiviral drug design.\u0000</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"41 4-5","pages":"444 - 456"},"PeriodicalIF":3.0,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10930-022-10065-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4008546","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
Photopolymerization with EDTA and Riboflavin for Proteins Analysis in Polyacrylamide Gel Electrophoresis EDTA和核黄素光聚合用于聚丙烯酰胺凝胶电泳分析
IF 3 4区 生物学
The Protein Journal Pub Date : 2022-07-27 DOI: 10.1007/s10930-022-10068-3
Volodymyr Shlyakhovenko, Olena Samoylenko
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引用次数: 1
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