The Protein Journal最新文献

{"title":"Repurposing of Strychnine as the Potential Inhibitors of Aldo–keto Reductase Family 1 Members B1 and B10: Computational Modeling and Pharmacokinetic Analysis","authors":"Muhammad Sarfraz,&nbsp;Mubashir Aziz,&nbsp;Saira Afzal,&nbsp;Pervaiz Ali Channar,&nbsp;Bshra A. Alsfouk,&nbsp;Ghulam Abbas Kandhro,&nbsp;Sidra Hassan,&nbsp;Ahlam Sultan,&nbsp;Asad Hamad,&nbsp;Mosab Arafat,&nbsp;Muhammad Naeem Qaiser,&nbsp;Aftab Ahmed,&nbsp;Farhan Siddique,&nbsp;Syeda Abida Ejaz","doi":"10.1007/s10930-023-10163-z","DOIUrl":"10.1007/s10930-023-10163-z","url":null,"abstract":"<div><p>AKR1B1 and AKR1B10 are important members of aldo–keto reductase family which plays a significant role in cancer progression by modulating cellular metabolism. These enzymes are involved in various metabolic processes, including the synthesis and metabolism of hormones, detoxification of reactive aldehydes, and the reduction of various endogenous and exogenous compounds. This study aimed to explore the potential of strychnine as an anticancer agent by targeting AKR1B1 and AKR1B10 via drug repurposing approach. To assess the drug-like properties of strychnine, a physiologically based pharmacokinetic (PKPB) model and High Throughput Pharmacokinetics (HTPK) approach were employed. The obtained results fell within the expected range for drug molecules, confirming its suitability for further investigation. Additionally, density functional theory (DFT) studies were conducted to gain insight into the electronic properties contributing to the drug molecule’s reactivity. Building upon the promising DFT results, molecular docking analysis using the AutoDock tool was performed to examine the binding interactions between strychnine and the proposed targets, AKR1B1 and AKR1B10. Findings from the molecular docking studies suggested a higher probability of strychnine acting as an inhibitor of AKR1B1 and AKR1B10 with docking scores of − 30.84 and − 29.36 kJ/mol respectively. To validate the stability of the protein–ligand complex, Molecular Dynamic Simulation (MDS) studies were conducted, revealing the formation of a stable complex between the enzymes and strychnine. This comprehensive approach sheds light on the potential effectiveness of strychnine as a treatment for breast, lung, liver, and pancreatic cancers, as well as related malignancies. The novel insights gained from the physiologically based pharmacokinetic modeling, density functional theory, molecular docking, and molecular dynamics simulations collectively support the prospect of strychnine as a promising molecule for anticancer therapy. Further investigations are warranted to validate these findings and explore the therapeutic potential of strychnine in preclinical and clinical settings.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 2","pages":"207 - 224"},"PeriodicalIF":1.9,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71523980","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":"Targeting Aminoglycoside Acetyltransferase Activity of Mycobacterium tuberculosis (H37Rv) Derived Eis (Enhanced Intracellular Survival) Protein with Quercetin","authors":"Logesh Radhakrishnan,&nbsp;Rahul Dani,&nbsp;Irfan Navabshan,&nbsp;Shazia Jamal,&nbsp;Neesar Ahmed","doi":"10.1007/s10930-023-10165-x","DOIUrl":"10.1007/s10930-023-10165-x","url":null,"abstract":"<div><p>Eis (Enhanced intracellular survival) protein is an aminoglycoside acetyltransferase enzyme classified under the family – GNAT (GCN5-related family of N-acetyltransferases) secreted by <i>Mycobacterium tuberculosis (Mtb).</i> The enzymatic activity of Eis results in the acetylation of kanamycin, thereby impairing the drug’s action. In this study, we expressed and purified recombinant Eis (rEis) to determine the enzymatic activity of Eis and its potential inhibitor. Glide-enhanced precision docking was used to perform molecular docking with chosen ligands. Quercetin was found to interact Eis with a maximum binding affinity of -8.379 kcal/mol as compared to other ligands. Quercetin shows a specific interaction between the positively charged amino acid arginine in Eis and the aromatic ring of quercetin through π-cation interaction. Further, the effect of rEis was studied on the antibiotic activity of kanamycin A in the presence and absence of quercetin. It was observed that the activity of rEis aminoglycoside acetyltransferase decreased with increasing quercetin concentration. The results from the disk diffusion assay confirmed that increasing the concentration of quercetin inhibits the rEis protein activity. In conclusion, quercetin may act as a potential Eis inhibitor.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 1","pages":"12 - 23"},"PeriodicalIF":1.9,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71490831","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":"Improvement of α-amino Ester Hydrolase Stability via Computational Protein Design","authors":"Colton E. Lagerman,&nbsp;Emily A. Joe,&nbsp;Martha A. Grover,&nbsp;Ronald W. Rousseau,&nbsp;Andreas S. Bommarius","doi":"10.1007/s10930-023-10155-z","DOIUrl":"10.1007/s10930-023-10155-z","url":null,"abstract":"<div><p>Amino ester hydrolases (AEHs) are capable of rapid synthesis of cephalexin but suffer from rapid deactivation even at low temperatures. Previous efforts to engineer AEH have generated several improved variants but have been limited in scope in part due to limitations in activity assay throughput for β-lactam synthesis reactions. Rational design of ‘whole variants’ was explored to rapidly improve AEH thermostability by mutating between 3–15% of residues. Most variants were found to be inactive due to a mutated calcium binding site, the function of which has not previously been described. Four active variants, all with improved melting temperatures, were characterized in terms of synthesis and hydrolysis activity, melting temperature, and deactivation at 25°C. Two variants were found to have improved total turnover numbers relative to the initial AEH variant; however, a clear tradeoff exists between improved stability and overall activity of each variant.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"42 6","pages":"675 - 684"},"PeriodicalIF":3.0,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41224554","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":"Kennedy Epitope (KE)-dependent Retrograde Transport of Efficiently Cleaved HIV-1 Envelopes (Envs) and its Effect on Env Cell Surface Expression and Viral Particle Formation","authors":"Supratik Das,&nbsp;Hilal Ahmad Parray,&nbsp;Adarsh Kumar Chiranjivi,&nbsp;Prince Kumar,&nbsp;Abhishek Goswami,&nbsp;Manish Bansal,&nbsp;Deepak Kumar Rathore,&nbsp;Rajesh Kumar,&nbsp;Sweety Samal","doi":"10.1007/s10930-023-10161-1","DOIUrl":"10.1007/s10930-023-10161-1","url":null,"abstract":"<div><p>Efficiently cleaved HIV-1 Envs are the closest mimics of functional Envs as they specifically expose only bNAb (broadly neutralizing antibody) epitopes and not non-neutralizing ones, making them suitable for developing vaccine immunogens. We have previously identified several efficiently cleaved Envs from clades A, B, C and B/C. We also described that truncation of the CT (C-terminal tail) of a subset of these Envs, but not others, impairs their ectodomain conformation/antigenicity on the cell surface in a CT conserved hydrophilic domain (CHD) or Kennedy epitope (KE)-dependent manner. Here, we report that those Envs (4 − 2.J41 and JRCSF), whose native-like ectodomain conformation/antigenicity on the cell surface is disrupted upon CT truncation, but not other Envs like JRFL, whose CT truncation does not have an effect on ectodomain integrity on the cell surface, are also defective in retrograde transport from early to late endosomes. Restoration of the CHD/KE in the CT of these Envs restores wild-type levels of distribution between early and late endosomes. In the presence of retrograde transport inhibitor Retro 2, cell surface expression of 4 − 2.J41 and JRCSF Envs increases [as does in the presence of Rab7a DN and Rab7b DN (DN: dominant negative)] but particle formation decreases for 4 − 2.J41 and JRCSF Env pseudotyped viruses. Our results show for the first time a correlation between CT-dependent, CHD/KE regulated retrograde transport and cell surface expression/viral particle formation of these efficiently cleaved Envs. Based on our results we hypothesize that a subset of these efficiently cleaved Envs use a CT-dependent, CHD/KE-mediated mechanism for assembly and release from late endosomes.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"43 2","pages":"375 - 386"},"PeriodicalIF":1.9,"publicationDate":"2023-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41170262","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":"Biophysical Characterization of p51 and p66 Monomers of HIV-1 Reverse Transcriptase with Their Inhibitors","authors":"Supaphorn Seetaha,&nbsp;Nuntaporn Kamonsutthipaijit,&nbsp;Maho Yagi-Utsumi,&nbsp;Yanaka Seako,&nbsp;Takumi Yamaguchi,&nbsp;Supa Hannongbua,&nbsp;Koichi Kato,&nbsp;Kiattawee Choowongkomon","doi":"10.1007/s10930-023-10156-y","DOIUrl":"10.1007/s10930-023-10156-y","url":null,"abstract":"<div><p>Human immunodeficiency virus (HIV)-1 reverse transcriptase (HIV-1 RT) is responsible for the transcription of viral RNA genomes into DNA genomes and has become an important target for the treatment of acquired immune deficiency syndrome (AIDS). This study used biophysical techniques to characterize the HIV-1 RT structure, monomer forms, and the non-nucleoside reverse transcriptase inhibitors (NNRTIs) bound forms. Inactive p66_W401A and p51_W401A were selected as models to study the HIV-1 RT monomer structures. Nuclear magnetic resonance (NMR) spectroscopy revealed that the unliganded forms of p66_W401A protein and p51_W401A protein had similar conformation to each other in solution. The complexes of p66_W401A or p51_W401A with inhibitors showed similar conformations to p66 in the RT heterodimer bound to the NNRTIs. Furthermore, the results of paramagnetic relaxation enhancement (PRE)-assisted NMR revealed that the unliganded forms of the p66_W401A and p51_W401A conformations were different from the unliganded heterodimer, characterized by a greater distance between the fingers and thumb subdomains. Small-angle X-ray scattering (SAXS) experiments confirmed that p66_W401A and p51_W401A can bind with inhibitors, similar to the p66/p51 heterodimer. The findings of this study increase the structural knowledge base of HIV-1 RT monomers, which may be helpful in the future design of potent viral inhibitors.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"42 6","pages":"741 - 752"},"PeriodicalIF":3.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41171873","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":"Analysis of a Novel Peptide That Is Capable of Inhibiting the Enzymatic Activity of the Protein Kinase A Catalytic Subunit-Like Protein from Trypanosoma equiperdum","authors":"Nelson A. Araujo,&nbsp;José Bubis","doi":"10.1007/s10930-023-10153-1","DOIUrl":"10.1007/s10930-023-10153-1","url":null,"abstract":"<div><p>A 26-residue peptide possessing the αN-helix motif of the protein kinase A (PKA) regulatory subunit-like proteins from the <i>Trypanozoom</i> subgenera (VAP26, sequence = VAPYFEKSEDETALILKLLTYNVLFS), was shown to inhibit the enzymatic activity of the <i>Trypanosoma equiperdum</i> PKA catalytic subunit-like protein, in a similar manner that the mammalian heat-stable soluble PKA inhibitor known as PKI. However, VAP26 does not contain the PKI inhibitory sequence. Bioinformatics analyzes of the αN-helix motif from various <i>Trypanozoon</i> PKA regulatory subunit-like proteins suggested that the sequence could form favorable peptide-protein interactions of hydrophobic nature with the PKA catalytic subunit-like protein, which possibly may represent an alternative PKA inhibitory mechanism. The sequence of the αN-helix motif of the <i>Trypanozoon</i> proteins was shown to be highly homologous but significantly divergent from the corresponding αN-helix motifs of their <i>Leishmania</i> and mammalian counterparts. This sequence divergence contrasted with the proposed secondary structure of the αN-helix motif, which appeared conserved in every analyzed regulatory subunit-like protein. In silico mutation experiments at positions I234, L238 and F244 of the αN-helix motif from the <i>Trypanozoon</i> proteins destabilized both the specific motif and the protein. On the contrary, mutations at positions T239 and Y240 stabilized the motif and the protein. These results suggested that the αN-helix motif from the <i>Trypanozoon</i> proteins probably possessed a different evolutionary path than their <i>Leishmania</i> and mammalian counterparts. Moreover, finding stabilizing mutations indicated that new inhibitory peptides may be designed based on the αN-helix motif from the <i>Trypanozoon</i> PKA regulatory subunit-like proteins.</p><h3>Graphical Abstract</h3>\u0000 <div><figure><div><div><picture><source><img></source></picture></div></div></figure></div>\u0000 </div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"42 6","pages":"709 - 727"},"PeriodicalIF":3.0,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10235912","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":"Molecular Modeling and Optimization of Type II E.coli l-Asparginase Activity by in silico Design and in vitro Site-directed Mutagenesis","authors":"Mahdieh Mahboobi,&nbsp;Ali-Hatef Salmanian,&nbsp;Hamid Sedighian,&nbsp;Bijan Bambai","doi":"10.1007/s10930-023-10149-x","DOIUrl":"10.1007/s10930-023-10149-x","url":null,"abstract":"<div><h3>Introduction</h3><p>L-asparaginase (also known as L-ASNase) is a crucial therapeutic enzyme that is widely used in treatment of ALL (acute lymphoblastic leukemia) as a chemotherapeutic drug. Besides, this enzyme is used in the food industry as a food processing reagent to reduce the content of acrylamide in addition to the clinical industry. The improvement of activity and kinetic parameters of the L-ASNase enzyme may lead to higher efficiency resulting in practical achievement. In order to achieve this goal, we chosen glycine residue in position 88 as a potential mutation with advantageous outcomes.</p><h3>Method</h3><p>In this study, firstly to find the appropriate mutation on glycine 88, various <i>in silico</i> analyses, such as MD simulation and molecular docking, were carried out. Then, the rational design was adopted as the best strategy for molecular modifications of the enzyme to improve its enzymatic properties.</p><h3>Result</h3><p>Our <i>in silico</i> findings show that the four mutations G88Q, G88L, G88K, and G88A may be able to increase L-ASNase’s asparaginase activity. The catalytic efficiency of each enzyme (<i>k</i>_cat/<i>K</i>_m) is the most important feature for comparing the catalytic activity of the mutants with the wild type form. The laboratory experiments showed that the <i>k</i>_cat/<i>K</i>_m for the G88Q mutant is 36.32% higher than the <i>Escherichia coli</i> K12 ASNase II (wild type), which suggests that L-ASNase activity is improved at lower concentration of L-ASN. Kinetic characterization of the mutants L-ASNase activity confirmed the high turnover rate (<i>k</i>_cat) with ASN as substrate relative to the wild type enzyme.</p><h3>Conclusion</h3><p><i>In silico analyses</i> and laboratory experiments demonstrated that the G88Q mutation rather than other mutation (G88L, G88K, and G88A) could improve the kinetics of L-ASNase.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"42 6","pages":"664 - 674"},"PeriodicalIF":3.0,"publicationDate":"2023-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10083893","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 Effect of Ultrasonication on the Fibrillar/ Oligomeric Structures of Aβ1−42 at Different Concentrations","authors":"Nassim Faridi,&nbsp;Maryam Sanjari-Pour,&nbsp;Ping Wang,&nbsp;S. Zahra Bathaie","doi":"10.1007/s10930-023-10138-0","DOIUrl":"10.1007/s10930-023-10138-0","url":null,"abstract":"<div><p>The number of disease states linked the aberrant regular protein conformations to oligomers and amyloid fibrils. Amyloid beta 1–42 (Aβ₁₋₄₂) peptide is very hydrophobic and quickly forms the β-rich structure and fibrillar protein aggregates in some solutions and buffer conditions. Ultrasonication pulses can disrupt amyloid fibrils to smaller fragments and produce Aβ₁₋₄₂ peptides of different sizes and oligomers. Herein, we investigated the effects of buffer and ultrasonication on Aβ₁₋₄₂ structure at low and high concentrations. After ultrasonication, the Western blot results showed that Aβ₁₋₄₂ fibrils were disaggregated into different sizes. The transmission electron microscopy results indicated Aβ₁₋₄₂ at low concentration (25 µM) in Ham’s/F12 phenol red-free culture medium formed short-size fragments and oligomers. In comparison, Aβ₁₋₄₂ at higher concentration (100 µM) formed fibrils that break down into smaller fragments after ultrasonication. However, after regrowth, it formed mature fibrils again. Cell viability assay indicated that Aβ₁₋₄₂ oligomers formed at a low concentration (25 µM) were more toxic to PC12 cells than other forms. In conclusion, by applying ultrasonication pulses and controlling peptide concentration and buffer condition, we can rich Aβ₁₋₄₂ aggregates with a particular size and molecular structure.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"42 5","pages":"575 - 585"},"PeriodicalIF":3.0,"publicationDate":"2023-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10930-023-10138-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5032078","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":"Expression, Purification, and Crystallization of the Vγ9Vδ2 T-cell Receptor Recognizing Protein/Peptide Antigens","authors":"Chaofei Cheng,&nbsp;Zhendong Zhao,&nbsp;Guangzhi Liu","doi":"10.1007/s10930-023-10151-3","DOIUrl":"10.1007/s10930-023-10151-3","url":null,"abstract":"<div><p>γδ T cells, especially Vγ9Vδ2 T cells, play an important role in mycobacterial infection. We have identified some Vγ9Vδ2 T cells that recognize protein/peptide antigens derived from mycobacteria, which may induce protective immune responses to mycobacterial infection. To clarify the structural basis of the molecular recognition mechanism, we tried many methods to express the Vγ9Vδ2 T-cell receptor (TCR). The Vγ9Vδ2 TCR was not expressed well in a prokaryotic expression system or a baculovirus expression system, even after extensive optimization. In a mammalian cell expression system, the Vγ9Vδ2 TCR was expressed in the form of a soluble heterodimer, which was suitable for crystal screening. Reduced-temperature cultivation (cold shock) increased the yield of the recombinant TCR. The recombinant purified TCR was used for crystal trials, and crystals that could be used for X-ray diffraction were obtained. Although we have not yet determined the crystal structure of the Vγ9Vδ2 TCR, we have established a procedure for Vγ9Vδ2 TCR expression and purification, which is useful for basic research and potentially for clinical application.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"42 6","pages":"778 - 791"},"PeriodicalIF":3.0,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10930-023-10151-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10058071","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":"gmXtal: Cooking Crystals with GROMACS","authors":"Pavel Buslaev,&nbsp;Gerrit Groenhof","doi":"10.1007/s10930-023-10141-5","DOIUrl":"10.1007/s10930-023-10141-5","url":null,"abstract":"<div><p>Molecular dynamics (MD) simulations are routinely performed of biomolecules in solution, because this is their native environment. However, the structures used in such simulations are often obtained with X-ray crystallography, which provides the atomic coordinates of the biomolecule in a crystal environment. With the advent of free electron lasers and time-resolved techniques, X-ray crystallography can now also access metastable states that are intermediates in a biochemical process. Such experiments provide additional data, which can be used, for example, to optimize MD force fields. Doing so requires that the simulation of the biomolecule is also performed in the crystal environment. However, in contrast to simulations of biomolecules in solution, setting up a crystal is challenging. In particular, because not all solvent molecules are resolved in X-ray crystallography, adding a suitable number of solvent molecules, such that the properties of the crystallographic unit cell are preserved in the simulation, can be difficult and typically is a trial-and-error based procedure requiring manual interventions. Such interventions preclude high throughput applications. To overcome this bottleneck, we introduce <b>gmXtal</b>, a tool for setting up crystal simulations for MD simulations with GROMACS. With the information from the protein data bank (rcsb.org) <b>gmXtal</b> automatically (i) builds the crystallographic unit cell; (ii) sets the protonation of titratable residues; (iii) builds missing residues that were not resolved experimentally; and (iv) adds an appropriate number of solvent molecules to the system. <b>gmXtal</b> is available as a standalone tool https://gitlab.com/pbuslaev/gmxtal.</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":"200 - 206"},"PeriodicalIF":1.9,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11058868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10058074","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}