Biochemistry Biochemistry最新文献_第2页

A Genetically Encoded Redox-Active Nicotinamide Amino Acid. 一种基因编码的具有氧化还原活性的烟酰胺氨基酸。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-11-25 DOI: 10.1021/acs.biochem.4c00530

Michael L Pigula, Yahui Ban, Hengyao You, Peter G Schultz

引用次数: 0

Role of Hydration and Amino Acid Interactions on the Ion Permeation Mechanism in the hNa_V1.5 Channel.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 DOI: 10.1021/acs.biochem.4c00664

Nuria Anguita-Ortiz, Juan J Nogueira

{"title":"Role of Hydration and Amino Acid Interactions on the Ion Permeation Mechanism in the hNaV1.5 Channel.","authors":"Nuria Anguita-Ortiz, Juan J Nogueira","doi":"10.1021/acs.biochem.4c00664","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00664","url":null,"abstract":"This study explores the ion selectivity and conduction mechanisms of the hNaV1.5 sodium channel using classical molecular dynamics simulations under an externally applied electric field. Our findings reveal distinct conduction mechanisms for Na+ and K+, primarily driven by differences in their hydration states when they diffuse close to the channel's selective filter (DEKA) and extracellular ring (EEDD). The Na+ ions undergo partial dehydration in the EEDD region, followed by a rehydration step in the DEKA ring, resulting in longer retention times and a deeper free energy minimum compared to K+. Conversely, the K+ ions exhibit a continuous dehydration process, facilitating a smoother passage through these key regions. These results indicate that ion selectivity and conductance are primarily governed by solvation dynamics, which, in turn, depend on the interactions with key charged residues within the channel. Additionally, we show that the delicate energetic balance between the interactions of the ions with the protein residues and with their solvation shells during the dehydration and rehydration processes is not properly captured by the force field. As a consequence, the selectivity of the channel is not well described, indicating that more accurate computational models must be applied to simulate ion conduction through eukaryotic NaV channels.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833204","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

How Do DNA Molecular Springs Modulate Protein-Protein Interactions: Experimental and Theoretical Results.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-12-03 DOI: 10.1021/acs.biochem.4c00280

Kecheng Zhang, Jingze Duan, Cong Li, Chen Song, Zhixing Chen

{"title":"How Do DNA Molecular Springs Modulate Protein-Protein Interactions: Experimental and Theoretical Results.","authors":"Kecheng Zhang, Jingze Duan, Cong Li, Chen Song, Zhixing Chen","doi":"10.1021/acs.biochem.4c00280","DOIUrl":"10.1021/acs.biochem.4c00280","url":null,"abstract":"Deoxyribonucleic acid (DNA) nanomachines have been widely exploited in enzyme activity regulation, protein crystallization, protein assembly, and control of the protein-protein interaction (PPI). Yet, the fundamental biophysical framework of DNA nanomachines in the case of regulating protein-protein interactions remains elusive. Here, we established a DNA nanospring-mCherry model with mCherry homodimers of different Kd. Using size exclusion chromatography and fluorescence polarization, we profiled the DNA nanospring-mediated manipulation of PPI as an entropy-reducing process. The energy transfer efficiency was a function of the length of the complementary sequence and the geometry of the DNA nanospring construction. With basic force analysis and physical chemistry calculation, we proposed a unified model of the correlation between the dissociation constant, local concentration, construction of DNA nanospring, and kinetics of protein dimerization. Overall, we demonstrated that the DNA nanospring-mCherry conjugate was a simple and practical model to analyze DNA-controlled protein-protein interaction.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3369-3380"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764634","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

Enzymatic Synthesis of a Polyketide/Nonribosomal Peptide Hybrid Antibiotic, Salivabactin.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-12-04 DOI: 10.1021/acs.biochem.4c00515

Di Gu, Rui Zhai, Bailey Daymo, Yuxin Xie, Caroline Luo, Wenjun Zhang

引用次数: 0

Crosstalk of Nucleic Acid Mimics with Lipid Membranes: A Multifaceted Computational and Experimental Study. 核酸模拟物与脂质膜的串扰：多方面的计算和实验研究。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-11-21 DOI: 10.1021/acs.biochem.4c00349

Beatriz T Magalhães, João T S Coimbra, Raquel M Silva, Mariana Ferreira, Rita S Santos, Paula Gameiro, Nuno F Azevedo, Pedro A Fernandes

{"title":"Crosstalk of Nucleic Acid Mimics with Lipid Membranes: A Multifaceted Computational and Experimental Study.","authors":"Beatriz T Magalhães, João T S Coimbra, Raquel M Silva, Mariana Ferreira, Rita S Santos, Paula Gameiro, Nuno F Azevedo, Pedro A Fernandes","doi":"10.1021/acs.biochem.4c00349","DOIUrl":"10.1021/acs.biochem.4c00349","url":null,"abstract":"Nucleic acid mimics (NAMs) have demonstrated high potential as antibacterial drugs. However, very few studies have assessed their possible diffusion across the bacterial envelope. In this work, we studied NAMs' diffusion in lipid bilayer systems that mimic the bacterial outer membrane using molecular dynamics (MD) simulations. Additionally, we examined the interactions of a NAM sequence with lipid membranes and ascertained the partition constants (Kp) through MD and spectroscopic investigations. The NAM sequences were composed of locked nucleic acid (LNA) and 2'-O-methyl (2'-OMe) residues, whereas the membrane models were composed of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) phospholipids. The parametrization protocol followed was validated against literature data and demonstrated the reliability of our approach for simulating NAM sequences. Investigation into the interaction of the sequences with zwitterionic and anionic membranes revealed a preference for hydrogen bond formation with the anionic model over the zwitterionic one. Additionally, potential of mean force (PMF) calculations unveiled a lower free energy barrier for translocation across the zwitterionic bilayer model. Contrarily, the partition constants derived suggested a slightly higher partitioning within the anionic membrane, emphasizing a nuanced interplay of factors. Finally, spectroscopic partition measurements with liposomes presented challenges in quantifying the partition of NAMs due to minimal signal variations. However, a tendency for quenching in anionic vesicles suggested a potential, albeit small, partitioning effect that warrants further investigation. In summary, our study revealed that NAMs will not, in principle, be able to cross an intact bacterial outer membrane by passive diffusion.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3381-3394"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685399","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

Optimized Construction of a Yeast SICLOPPS Library for Unbiased In Vivo Selection of Cyclic Peptides.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-12-06 DOI: 10.1021/acs.biochem.4c00013

Nanna Birkmose, Emilie U Frydendahl, Charlotte R Knudsen

{"title":"Optimized Construction of a Yeast SICLOPPS Library for Unbiased In Vivo Selection of Cyclic Peptides.","authors":"Nanna Birkmose, Emilie U Frydendahl, Charlotte R Knudsen","doi":"10.1021/acs.biochem.4c00013","DOIUrl":"10.1021/acs.biochem.4c00013","url":null,"abstract":"DNA-encoded libraries hold great potential for discovering small, cyclized peptides with drug potential. Split-intein circular ligation of peptides and proteins (SICLOPPS) is a well-established method for in vivo selection of cyclic peptides targeting specific intracellular components. However, the method has mainly been used in prokaryotic cells. In contrast, selection studies performed directly in eukaryotic cells allow for the identification of cyclic peptides promoting a functional outcome, without the need to define a specific cellular target. Here, we report the construction of a Saccharomyces cerevisiae-specific SICLOPPS library of 80 million members, via careful optimization of several steps to increase the size of the library. Individual library members were shown to be correctly expressed and processed in yeast. High-throughput sequencing was conducted on the randomized primer used for library construction and the pure yeast SICLOPPS library isolated from Escherichia coli. A distinct guanine insertion bias was observed in the peptide-encoding, randomized sequence, which was primarily attributed to the degenerate primer used to introduce the randomized sequence. Moreover, high-throughput sequencing was performed on the library before and after the induction of cyclic peptide expression in yeast. Importantly, expression of the SICLOPPS library in S. cerevisiae caused only a marginal further sequence bias. Our work paves the way for selection studies using a large and diverse library to identify cyclic peptides of therapeutic interest that promote a specific phenotypic outcome in eukaryotic organisms, with yeast representing a beneficial model system due to its high transformation efficiency.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3273-3286"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790504","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

Exploring the Structure-Function Relationships in a 5-Aminolevulinic Acid Synthase and the Use of Protein Engineering to Expand its Substrate Range.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 DOI: 10.1021/acs.biochem.4c00599

Ahram Kim, Jon D Stewart

{"title":"Exploring the Structure-Function Relationships in a 5-Aminolevulinic Acid Synthase and the Use of Protein Engineering to Expand its Substrate Range.","authors":"Ahram Kim, Jon D Stewart","doi":"10.1021/acs.biochem.4c00599","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00599","url":null,"abstract":"5-Aminolevulinate synthase (ALAS) is a PLP-dependent enzyme that catalyzes the production of 5-aminolevulinate from succinyl-CoA and glycine. Its ability to catalyze the essentially irreversible C-C bond formation has significant potential in chemoenzymatic synthesis of α-amino ketones. Native ALAS, unfortunately, is extremely substrate-selective, and this seriously limits its synthetic utility. Here, we have used three different protein engineering strategies to overcome this problem for the acyl-CoA substrate. By combining previously reported mutation results and structural analysis, a series of site-saturation mutagenesis/screening efforts were focused on R21, T82, N84, and T362 of Rhodopseudomonas palustris ALAS. These yielded single, double, and triple mutants with significantly improved substrate ranges. The steady-state kinetic parameters of several key variants were determined. These data were analyzed in the framework of the ALAS catalytic mechanism to identify the steps that may have been impacted. The most active variant was used in a larger-scale reaction to demonstrate its synthetic potential. Taken together, our results show how ALAS might become a useful biocatalyst for α-amino ketone synthesis and have also allowed us to comment on the relative merits of each the three protein engineering strategies utilized.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833203","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

Dissecting the Roles of Electrostatic Interactions in Modulating the Folding Stability and Cooperativity of Engrailed Homeodomain. 剖析静电相互作用在调节啮合同源结构域的折叠稳定性和合作性中的作用。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-11-27 DOI: 10.1021/acs.biochem.4c00645

Chengzhen Xu, Xiakun Chu

{"title":"Dissecting the Roles of Electrostatic Interactions in Modulating the Folding Stability and Cooperativity of Engrailed Homeodomain.","authors":"Chengzhen Xu, Xiakun Chu","doi":"10.1021/acs.biochem.4c00645","DOIUrl":"10.1021/acs.biochem.4c00645","url":null,"abstract":"Engrailed homeodomain (EngHD), a highly charged transcription factor regulating over 200 genes, is a fast-folding protein. Recent studies have shown that the abundant charged residues in EngHD not only facilitate protein-DNA interactions but also influence the conformational disorder of its native structure. However, the mechanisms by which electrostatic interactions modulate the folding of EngHD remain unclear. Here, we employ a coarse-grained structure-based model that incorporates the salt-dependent Debye-Hückel model to investigate the (un)folding behavior of EngHD under various salt concentrations. Our findings demonstrate that increasing salt concentrations enhance both folding stability and cooperativity, while the folding barrier height remains relatively constant due to the distinct electrostatic effects on individual residues. By modulating the energetic balance between local and nonlocal interactions, we shift the folding of EngHD from a downhill process to a two-state process. Notably, we observe a nonmonotonic relationship between the strength of local interactions and residue-level coupling degree during (un)folding, likely attributed to the repulsive electrostatic interactions present in the native structure of EngHD. Additionally, we identify a critical turning point in the dependence of folding cooperativity on salt concentration, classified by the energetic balance of local and nonlocal interactions. Our results provide valuable insights into how electrostatic interactions influence the folding of EngHD, contributing to the theoretical framework for engineering highly charged proteins.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3261-3272"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724505","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

Elucidating the Mechanism of Recognition and Binding of Heparin to Amyloid Fibrils of Serum Amyloid A.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 DOI: 10.1021/acs.biochem.4c00529

Conor B Abraham, Emily Lewkowicz, Olga Gursky, John E Straub

{"title":"Elucidating the Mechanism of Recognition and Binding of Heparin to Amyloid Fibrils of Serum Amyloid A.","authors":"Conor B Abraham, Emily Lewkowicz, Olga Gursky, John E Straub","doi":"10.1021/acs.biochem.4c00529","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00529","url":null,"abstract":"Amyloid diseases feature pathologic deposition of normally soluble proteins and peptides as insoluble fibrils in vital organs. Amyloid fibrils co-deposit with various nonfibrillar components including heparan sulfate (HS), a glycosaminoglycan that promotes amyloid formation in vitro for many unrelated proteins. HS-amyloid interactions have been proposed as a therapeutic target for inflammation-linked amyloidosis wherein N-terminal fragments of serum amyloid A (SAA) protein deposit in the kidney and liver. The structural basis for these interactions is unclear. Here, we exploit the high-resolution cryoelectron microscopy (cryo-EM) structures of ex vivo murine and human SAA fibrils in a computational study employing molecular docking, Brownian dynamics simulations, and molecular dynamics simulations to elucidate how heparin, a highly sulfated HS mimetic, recognizes and binds to amyloid protein fibrils. Our results demonstrate that negatively charged heparin chains bind to linear arrays of uncompensated positively charged basic residues along the spines of amyloid fibrils facilitated by electrostatic steering. The predicted heparin binding sites match the location of unidentified densities observed in cryo-EM maps of SAA amyloids, suggesting that these extra densities represent bound HS. Since HS is constitutively found in various amyloid deposits, our results suggest a common mechanism for HS-amyloid recognition and binding.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845299","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

ATAD2 and TWIST1 Interaction Promotes MYC Activation in Colorectal Carcinoma.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 DOI: 10.1021/acs.biochem.4c00360

Anirban Roy, Babu Sudhamalla

{"title":"ATAD2 and TWIST1 Interaction Promotes MYC Activation in Colorectal Carcinoma.","authors":"Anirban Roy, Babu Sudhamalla","doi":"10.1021/acs.biochem.4c00360","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00360","url":null,"abstract":"ATPase family AAA domain-containing protein 2 (ATAD2) is significantly up-regulated in many cancer types and contributes to poor patient outcomes. ATAD2 exhibits a multidomain architecture comprising an N-terminal acidic domain, two AAA+ ATPase domains, a bromodomain, and a C-terminal domain. The AAA+ ATPase domain facilitates protein oligomerization and ATP binding, while the bromodomain recognizes acetylated lysine in histones and nonhistone proteins. ATAD2 involvement in cancer extends across multiple signaling pathways, such as Rb-E2F1, PI3K/AKT, and TGF-β1/Smad3, which promotes cell proliferation and cancer progression. Herein, we report that ATAD2 directly interacts with TWIST1, and both N-terminal regions of proteins mediate the interaction. Immunofluorescence experiments suggested that ATAD2 and TWIST1 primarily colocalize in the nucleus. Notably, our qPCR results revealed the functional significance of ATAD2-TWIST1 interaction by demonstrating their synergistic effect on the transcriptional activation of MYC in colorectal carcinoma cell lines. Moreover, the ChIP-qPCR result further indicates that ATAD2 and TWIST1 significantly localize in the promoter of the MYC gene. In addition, analysis of The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) data suggests a correlation between ATAD2, TWIST1, and MYC overexpression and poor survival rates in colorectal carcinoma. Lastly, the overexpression of ATAD2 and TWIST1 enhances cell proliferation, emphasizing their role in colorectal carcinoma progression through MYC activation. Together, these results suggest that ATAD2 is a crucial factor in TWIST1-dependent MYC gene activation, resulting in an active ATAD2-TWIST1-MYC axis that contributes to colon cancer cell proliferation.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833201","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