Biophysical chemistry最新文献

{"title":"Mechanistic insights into G-protein activation via phosphorylation mediated non-canonical pathway","authors":"Kunal Shewani ,&nbsp;Midhun K. Madhu ,&nbsp;Rajesh K. Murarka","doi":"10.1016/j.bpc.2024.107234","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107234","url":null,"abstract":"<div><p>Activation of heterotrimeric G-proteins (<span><math><mi>G</mi><mi>αβγ</mi></math></span>) downstream to receptor tyrosine kinases (RTKs) is a well-established crosstalk between the signaling pathways mediated by G-protein coupled receptors (GPCRs) and RTKs. While GPCR serves as a guanine exchange factor (GEF) in the canonical activation of <span><math><mi>G</mi><mi>α</mi></math></span> that facilitates the exchange of GDP for GTP, the mechanism through which RTK phosphorylations induce <span><math><mi>G</mi><mi>α</mi></math></span> activation remains unclear. Recent experimental studies revealed that the epidermal growth factor receptor (EGFR), a well-known RTK, phosphorylates the helical domain tyrosine residues Y154 and Y155 and accelerates the GDP release from the <span><math><mi>G</mi><mi>α</mi><mi>i</mi><mn>3</mn></math></span>, a subtype of <span><math><mi>G</mi><mi>α</mi></math></span>-protein. Using well-tempered metadynamics and extensive unbiased molecular dynamics simulations, we captured the GDP release event and identified the intermediates between bound and unbound states through Markov state models. In addition to weakened salt bridges at the domain interface, phosphorylations induced the unfolding of helix <span><math><mi>α</mi><mi>F</mi></math></span>, which contributed to increased flexibility near the hinge region, facilitating a greater distance between domains in the phosphorylated <span><math><mi>G</mi><mi>α</mi><mi>i</mi><mn>3</mn></math></span>. Although the larger domain separation in the phosphorylated system provided an unobstructed path for the nucleotide, the accelerated release of GDP was attributed to increased fluctuations in several conserved regions like P-loop, switch 1, and switch 2. Overall, this study provides atomistic insights into the activation of G-proteins induced by RTK phosphorylations and identifies the specific structural motifs involved in the process. The knowledge gained from the study could establish a foundation for targeting non-canonical signaling pathways and developing therapeutic strategies against the ailments associated with dysregulated G-protein signaling.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140542635","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}

{"title":"Structural analysis of ATP bound to the F1-ATPase β-subunit monomer by solid-state NMR- insight into the hydrolysis mechanism in F1","authors":"Yasuto Todokoro ,&nbsp;Yoshiyuki Miyasaka ,&nbsp;Hiromasa Yagi ,&nbsp;Masatsune Kainosho ,&nbsp;Toshimichi Fujiwara ,&nbsp;Hideo Akutsu","doi":"10.1016/j.bpc.2024.107232","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107232","url":null,"abstract":"<div><p>ATP-hydrolysis-associated conformational change of the <em>β</em>-subunit during the rotation of F₁-ATPase (F₁) has been discussed using cryo-electron microscopy (cryo-EM). Since it is worthwhile to further investigate the conformation of ATP at the catalytic subunit through an alternative approach, the structure of ATP bound to the F₁<em>β</em>-subunit monomer (<em>β</em>) was analyzed by solid-state NMR. The adenosine conformation of ATP-<em>β</em> was similar to that of ATP analog in F₁ crystal structures. ³¹P chemical shift analysis showed that the P^α and P^β conformations of ATP-<em>β</em> are gauche-trans and trans-trans, respectively. The triphosphate chain is more extended in ATP-<em>β</em> than in ATP analog in F₁ crystals. This appears to be in the state just before ATP hydrolysis. Furthermore, the ATP-<em>β</em> conformation is known to be more closed than the closed form in F₁ crystal structures. In view of the cryo-EM results, ATP-<em>β</em> would be a model of the most closed <em>β</em>-subunit with ATP ready for hydrolysis in the hydrolysis stroke of the F₁ rotation.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140535191","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}

{"title":"New insights into the interaction of emodin with lipid membranes","authors":"Antonio R. da Cunha ,&nbsp;Evandro L. Duarte ,&nbsp;Gabriel S. Vignoli Muniz ,&nbsp;Kaline Coutinho ,&nbsp;M. Teresa Lamy","doi":"10.1016/j.bpc.2024.107233","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107233","url":null,"abstract":"<div><p>Emodin is a natural anthraquinone derivative found in nature, widely known as an herbal medicine. Here, the partition, location, and interaction of emodin with lipid membranes of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) are experimentally investigated with different techniques. Our studies have considered the neutral form of emodin (EMH) and its anionic/deprotonated form (EM⁻), and their interaction with a more and less packed lipid membrane, DMPC at the gel and fluid phases, respectively. Though DSC results indicate that the two species, EMH and EM⁻, similarly disrupt the packing of DMPC bilayers, spin labels clearly show that EMH causes a stronger bilayer disruption, both in gel and fluid DMPC. Fluorescence spectroscopy shows that both EMH and EM⁻ have a high affinity for DMPC: the binding of EM⁻ to both gel and fluid DMPC bilayers was found to be quite similar, and similar to that of EMH to gel DMPC, <em>K</em>_p = (1.4 ± 0.3)<em>x</em>10³. However, EMH was found to bind twice more strongly to fluid DMPC bilayers, <em>K</em>_p = (3.2 ± 0.3)<em>x</em>10³. Spin labels and optical absorption spectroscopy indicate that emodin is located close to the lipid bilayer surface, and suggest that EM⁻ is closer to the lipid/water interface than EMH, as expected. The present studies present a relevant contribution to the current understanding of the effect the two species of emodin, EMH and EM⁻, present on different microregions of an organism, as local <em>pH</em> values can vary significantly, can cause in a neutral lipid membrane, either more or less packed, liked gel and fluid DMPC, respectively, and could be extended to lipid domains of biological membranes.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140347563","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}

{"title":"The structure, self-assembly and dynamics of lipid nanodiscs revealed by computational approaches","authors":"Beibei Wang ,&nbsp;D. Peter Tieleman","doi":"10.1016/j.bpc.2024.107231","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107231","url":null,"abstract":"<div><p>Nanodisc technology is increasingly being used in structural, biochemical and biophysical studies of membrane proteins. The computational approaches have revealed many important features of nanodisc assembly, structures and dynamics. Therefore, we reviewed the application of computational approaches, especially molecular modeling and molecular dyncamics (MD) simulations, to characterize nanodiscs, including the structural models, assembly and disassembly, protocols for modeling, structural properties and dynamics, and protein-lipid interactions in nanodiscs. More amazing computational studies about nanodiscs are looked forward to in the future.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140342247","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}

{"title":"Dissecting the effect of ALS mutation S375G on the conformational properties and aggregation dynamics of TDP-43370-375 fragment","authors":"Zhengdong Xu ,&nbsp;Jianxin Zhang ,&nbsp;Jiaxing Tang ,&nbsp;Yehong Gong ,&nbsp;Yu Zou ,&nbsp;Qingwen Zhang","doi":"10.1016/j.bpc.2024.107230","DOIUrl":"10.1016/j.bpc.2024.107230","url":null,"abstract":"<div><p>The aggregation of transactive response deoxyribonucleic acid (DNA) binding protein of 43 kDa (TDP-43) into ubiquitin-positive inclusions is closely associated with amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and chronic traumatic encephalopathy. The 370–375 fragment of TDP-43 (³⁷⁰GNNSYS³⁷⁵, TDP-43_370-375), the amyloidogenic hexapeptides, can be prone to forming pathogenic amyloid fibrils with the characteristic of steric zippers. Previous experiments reported the ALS-associated mutation, serine 375 substituted by glycine (S375G) is linked to early onset disease and protein aggregation of TDP-43. Based on this, it is necessary to explore the underlying molecular mechanisms. By utilizing all-atom molecular dynamics (MD) simulations of 102 μs in total, we investigated the impact of S375G mutation on the conformational ensembles and oligomerization dynamics of TDP-43_370-375 peptides. Our replica exchange MD simulations show that S375G mutation could promote the unstructured conformation formation and induce peptides to form a loose packed oligomer, thus inhibiting the aggregation of TDP-43_370-375. Further analyses suggest that S375G mutation displays a reduction effect on the number of total hydrogen bonds and contacts among TDP-43_370-375 peptides. Hydrogen bonding and polar interactions among TDP-43_370-375 peptides, as well as Y374-Y374 π-π stacking interaction, are attenuated by S375G mutation. Additional microsecond MD simulations demonstrate that S375G mutation could prohibit the conformational conversion to β-structure-rich aggregates and possess an inhibitory effect on the oligomerization dynamics of TDP-43_370-375. This study offers for the first time of molecular insights into the S375G mutation affecting the aggregation of TDP-43_370-375 at the atomic level, and may open new avenues in the development of future site-specific mutation therapeutics.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140403921","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}

{"title":"Probing pharmaceutically important amino acids L-isoleucine and L-tyrosine Solubilities: Unraveling the solvation thermodynamics in diverse mixed solvent systems","authors":"Jit Chakraborty ,&nbsp;Kalachand Mahali ,&nbsp;A.M.A. Henaish ,&nbsp;Jahangeer Ahmed ,&nbsp;Saad M. Alshehri ,&nbsp;Sanjay Roy","doi":"10.1016/j.bpc.2024.107229","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107229","url":null,"abstract":"<div><p>The study specifically investigates the solubilities of L-isoleucine and L-tyrosine in water-mixed solvent systems (DMF, DMSO, and ACN), exploring the behaviour of amino acids in complex environments. The experimental methods prioritize meticulous solvent purification to ensure reliable results. The work explores solubility data, uncovering temperature-dependent trends and intricate interactions influencing solubility in the chosen mixed solvent systems. The study emphasizes the impact of thermodynamic properties, solvent-solvent interactions, and amino acid structure on solubility patterns. The broader implications highlight the relevance of understanding amino acid behaviour in diverse solvent environments, offering potential applications in cosmetics and pharmaceutical industries. The distinct solubility patterns contribute valuable insights, enhancing on the understanding of the solution stability and interactions of L-isoleucine and L-tyrosine in different solvent systems. In conclusion, work suggests the enhanced utilization of L-isoleucine and L-tyrosine in various industries, driven by a profound understanding of their solubility in mixed solvent systems. The research expands our knowledge of amino acid behaviour, paving the way for advancements in industries relying on protein-based products and technologies.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140328307","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}

{"title":"Metallo-β-lactamase inhibitors: A continuing challenge for combating antibiotic resistance","authors":"Su-Jin Kang ,&nbsp;Do-Hee Kim ,&nbsp;Bong-Jin Lee","doi":"10.1016/j.bpc.2024.107228","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107228","url":null,"abstract":"<div><p>β-lactam antibiotics are the most successful and commonly used antibacterial agents, but the emergence of resistance to these drugs has become a global health threat. The expression of β-lactamase enzymes produced by pathogens, which hydrolyze the amide bond of the β-lactam ring, is the major mechanism for bacterial resistance to β-lactams. In particular, among class A, B, C and D β-lactamases, metallo-β-lactamases (MBLs, class B β-lactamases) are considered crucial contributors to resistance in gram-negative bacteria. To combat β-lactamase-mediated resistance, great efforts have been made to develop β-lactamase inhibitors that restore the activity of β-lactams. Some β-lactamase inhibitors, such as diazabicyclooctanes (DBOs) and boronic acid derivatives, have also been approved by the FDA. Inhibitors used in the clinic can inactivate mostly serine-β-lactamases (SBLs, class A, C, and D β-lactamases) but have not been effective against MBLs until now. In order to develop new inhibitors particularly for MBLs, various attempts have been suggested. Based on structural and mechanical studies of MBL enzymes, several MBL inhibitor candidates, including taniborbactam in phase 3 and xeruborbactam in phase 1, have been introduced in recent years. However, designing potent inhibitors that are effective against all subclasses of MBLs is still extremely challenging. This review summarizes not only the types of β-lactamase and mechanisms by which β-lactam antibiotics are inactivated, but also the research finding on β-lactamase inhibitors targeting these enzymes. These detailed information on β-lactamases and their inhibitors could give valuable information for novel β-lactamase inhibitors design.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140320858","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}

{"title":"Improving synthesis and binding affinities of nucleic acid aptamers and their therapeutics and diagnostic applications","authors":"Malaya Mili ,&nbsp;Vinay Bachu ,&nbsp;Pooja Rani Kuri ,&nbsp;Naveen Kumar Singh ,&nbsp;Pranab Goswami","doi":"10.1016/j.bpc.2024.107218","DOIUrl":"10.1016/j.bpc.2024.107218","url":null,"abstract":"<div><p>Nucleic acid aptamers have captivated the attention of analytical and medicinal scientists globally due to their several advantages as recognition molecules over conventional antibodies because of their small size, simple and inexpensive synthesis, broad target range, and high stability in varied environmental conditions. These recognition molecules can be chemically modified to make them resistant to nuclease action in blood serum, reduce rapid renel clearance, improve the target affinity and selectivity, and make them amenable to chemically conjugate with a support system that facilitates their selective applications. This review focuses on the development of efficient aptamer candidates and their application in clinical diagnosis and therapeutic applications. Significant advances have been made in aptamer-based diagnosis of infectious and non-infectious diseases. Collaterally, the progress made in therapeutic applications of aptamers is encouraging, as evident from their use in diagnosing cancer, neurodegenerative diseases, microbial infection, and in imaging. This review also updates the progress on clinical trials of many aptamer-based products of commercial interests. The key development and critical issues on the subject have been summarized in the concluding remarks.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140271378","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}

{"title":"H2 production under stress: [FeFe]‑hydrogenases reveal strong stability in high pressure environments","authors":"Kristina Edenharter ,&nbsp;Michel W. Jaworek ,&nbsp;Vera Engelbrecht ,&nbsp;Roland Winter ,&nbsp;Thomas Happe","doi":"10.1016/j.bpc.2024.107217","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107217","url":null,"abstract":"<div><p>Hydrogenases are a diverse group of metalloenzymes that catalyze the conversion of H₂ into protons and electrons and the reverse reaction. A subgroup is formed by the [FeFe]‑hydrogenases, which are the most efficient enzymes of microbes for catalytic H₂ conversion. We have determined the stability and activity of two [FeFe]‑hydrogenases under high temperature and pressure conditions employing FTIR spectroscopy and the high-pressure stopped-flow methodology in combination with fast UV/Vis detection. Our data show high temperature stability and an increase in activity up to the unfolding temperatures of the enzymes. Remarkably, both enzymes reveal a very high pressure stability of their structure, even up to pressures of several kbars. Their high pressure-stability enables high enzymatic activity up to 2 kbar, which largely exceeds the pressure limit encountered by organisms in the deep sea and sub-seafloor on Earth.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0301462224000462/pdfft?md5=63a9b00b8624f7892908de829beda053&pid=1-s2.0-S0301462224000462-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140134449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Understanding the bio-crystallization: An insight to therapeutic relevance","authors":"Vivek Pandey ,&nbsp;Tejasvi Pandey","doi":"10.1016/j.bpc.2024.107216","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107216","url":null,"abstract":"<div><p>In the realm of biomedical engineering and materials science, the synthesis of biomaterials plays a pivotal role in advancing therapeutic strategies for regeneration of tissues. The deliberate control of crystallization processes in biomaterial synthesis has emerged as a key avenue for tailoring the properties of these materials, enabling the design of innovative solutions for a wide array of medical applications. This review delves into the interplay between controlled crystallization and biomaterial synthesis, exploring its multifaceted applications in the therapeutic domains. The investigation encompasses a wide spectrum of matrices, ranging from small molecules to large biomolecules, highlighting their unique contributions in modulating crystallization processes. Furthermore, the review critically assesses the analytical techniques and methodologies employed to probe and characterize the depths of crystallization dynamics. Advanced imaging, spectroscopic, and computational tools are discussed in the context of unraveling the intricate mechanisms governing nucleation and crystallization processes within the organic matrix. Finally we delve in the applications of such advance material in therapeutics of hard and soft tissues.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140103759","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}