Biopolymers最新文献

{"title":"Biochemical and biophysical characterization of the nucleic acid binding properties of the RNA/DNA binding protein EWS","authors":"Emily E. Selig,&nbsp;Roohi Bhura,&nbsp;Matthew R. White,&nbsp;Shivani Akula,&nbsp;Renee D. Hoffman,&nbsp;Carmel N. Tovar,&nbsp;Xiaoping Xu,&nbsp;Rachell E. Booth,&nbsp;David S. Libich","doi":"10.1002/bip.23536","DOIUrl":"10.1002/bip.23536","url":null,"abstract":"<p>EWS is a member of the FET family of RNA/DNA binding proteins that regulate crucial phases of nucleic acid metabolism. EWS comprises an N-terminal low-complexity domain (LCD) and a C-terminal RNA-binding domain (RBD). The RBD is further divided into three RG-rich regions, which flank an RNA-recognition motif (RRM) and a zinc finger (ZnF) domain. Recently, EWS was shown to regulate R-loops in Ewing sarcoma, a pediatric bone and soft-tissue cancer in which a chromosomal translocation fuses the N-terminal LCD of EWS to the C-terminal DNA binding domain of the transcription factor FLI1. Though EWS was shown to directly bind R-loops, the binding mechanism was not elucidated. In the current study, the RBD of EWS was divided into several constructs, which were subsequently assayed for binding to various nucleic acid structures expected to form at R-loops, including RNA stem-loops, DNA G-quadruplexes, and RNA:DNA hybrids. EWS interacted with all three nucleic acid structures with varying affinities and multiple domains contributed to binding each substrate. The RRM and RG2 region appear to bind nucleic acids promiscuously while the ZnF displayed more selectivity for single-stranded structures. With these results, the structural underpinnings of EWS recognition and binding of R-loops and other nucleic acid structures is better understood.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bip.23536","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9550843","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":"Sorghum bicolor SbHSP110 has an elongated shape and is able of protecting against aggregation and replacing human HSPH1/HSP110 in refolding and disaggregation assays","authors":"Juliana C. Franco,&nbsp;Maria L. C. Nogueira,&nbsp;Gabriela M. Gandelini,&nbsp;Glaucia M. S. Pinheiro,&nbsp;Conrado C. Gonçalves,&nbsp;Leandro R. S. Barbosa,&nbsp;Jason C. Young,&nbsp;Carlos H. I. Ramos","doi":"10.1002/bip.23532","DOIUrl":"10.1002/bip.23532","url":null,"abstract":"<p>Perturbations in the native structure, often caused by stressing cellular conditions, not only impair protein function but also lead to the formation of aggregates, which can accumulate in the cell leading to harmful effects. Some organisms, such as plants, express the molecular chaperone HSP100 (homologous to HSP104 from yeast), which has the remarkable capacity to disaggregate and reactivate proteins. Recently, studies with animal cells, which lack a canonical HSP100, have identified the involvement of a distinct system composed of HSP70/HSP40 that needs the assistance of HSP110 to efficiently perform protein breakdown. As sessile plants experience stressful conditions more severe than those experienced by animals, we asked whether a plant HSP110 could also play a role in collaborating with HSP70/HSP40 in a system that increases the efficiency of disaggregation. Thus, the gene for a putative HSP110 from the cereal <i>Sorghum bicolor</i> was cloned and the protein, named SbHSP110, purified. For comparison purposes, human HsHSP110 (HSPH1/HSP105) was also purified and investigated in parallel. First, a combination of spectroscopic and hydrodynamic techniques was used for the characterization of the conformation and stability of recombinant SbHSP110, which was produced folded. Second, small-angle X-ray scattering and combined predictors of protein structure indicated that SbHSP110 and HsHSP110 have similar conformations. Then, the chaperone activities, which included protection against aggregation, refolding, and reactivation, were investigated, showing that SbHSP110 and HsHSP110 have similar functional activities. Altogether, the results add to the structure/function relationship study of HSP110s and support the hypothesis that plants have multiple strategies to act upon the reactivation of protein aggregates.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10784015","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":"Effects of the geometry of reinforcement on physical properties of sodium caseinate/TiO2 nanocomposite films for applications in food packaging","authors":"Nurys Tatiana Hoyos Merlano,&nbsp;Lucas Guz,&nbsp;Virginia Borroni,&nbsp;Roberto Jorge Candal,&nbsp;María Lidia Herrera","doi":"10.1002/bip.23531","DOIUrl":"https://doi.org/10.1002/bip.23531","url":null,"abstract":"<p>Plastic materials for food packaging are being replaced by biodegradable films based on biopolymers due to the adverse effects they have had on animal life and the environment. In this study, nanocomposite films containing 2.5 wt% sodium caseinate and 2 wt% glycerol were reinforced with 0.1 or 0.2 wt% nano TiO₂ prepared in two forms: spheres (P25) and tubes. The effects of nanoreinforcement geometry on mechanical, tensile, barrier, thermogravimetric, and optical properties, and distribution of nanoparticles were described. The interactions among film components were analyzed by Fourier transform infrared spectroscopy (FTIR). Addition of nanotubes significantly increased <i>E</i>' (341 wt%) and <i>E</i>\" (395 wt%) moduli, the Young modulus <i>E</i> (660 wt%), the residual mass at 500°C (38 wt%), and color change (6.78) compared to control film. The compositional mapping studies showed that P25 nanoparticles were homogeneously distributed between the surfaces of the film while nanotubes were found on the bottom surface. The changes in position of the FTIR spectra signals as compared to pure protein signals indicated strong matrix/reinforcement interactions. In addition, the changes in intensity in 1100, 1033, and 1638 cm⁻¹ FTIR signals suggested formation of a protein/Tween 20 ester. The geometry of reinforcement was highly relevant regarding physical properties, showing nanotubes as being very successful for enhancing tensile properties.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50149036","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":"Chasing long-range evolutionary couplings in the AlphaFold era","authors":"Theodoros K. Karamanos","doi":"10.1002/bip.23530","DOIUrl":"10.1002/bip.23530","url":null,"abstract":"<p>Coevolution between protein residues is normally interpreted as direct contact. However, the evolutionary record of a protein sequence contains rich information that may include long-range functional couplings, couplings that report on homo-oligomeric states or even conformational changes. Due to the complexity of the sequence space and the lack of structural information on various members of a protein family, it has been difficult to effectively mine the additional information encoded in a multiple sequence alignment (MSA). Here, taking advantage of the recent release of the AlphaFold (AF) database we attempt to identify coevolutionary couplings that cannot be explained simply by spatial proximity. We propose a simple computational method that performs direct coupling analysis on a MSA and searches for couplings that are not satisfied in any of the AF models of members of the identified protein family. Application of this method on 2012 protein families suggests that ~12% of the total identified coevolving residue pairs are spatially distant and more likely to be disordered than their contacting counterparts. We expect that this analysis will help improve the quality of coevolutionary distance restraints used for structure determination and will be useful in identifying potentially functional/allosteric cross-talk between distant residues.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bip.23530","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9166977","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":"Targeting a KRAS i-motif forming sequence by unmodified and gamma-modified peptide nucleic acid oligomers","authors":"Srijani Sarkar,&nbsp;Gabriela Colón-Roura,&nbsp;Alexander Pearse,&nbsp;Bruce A. Armitage","doi":"10.1002/bip.23529","DOIUrl":"10.1002/bip.23529","url":null,"abstract":"<p>Growing interest in i-motif DNA as a transcriptional regulatory element motivates development of synthetic molecules capable of targeting these structures. In this study, we designed unmodified peptide nucleic acid (PNA) and gamma-modified PNA (γPNA) oligomers complementary to an i-motif forming sequence derived from the promoter of the <i>KRAS</i> oncogene. Biophysical techniques such as circular dichroism (CD) spectroscopy, CD melting, and fluorescence spectroscopy demonstrated the successful invasion of the i-motif by PNA and γPNA. Both PNA and γPNA showed very strong binding to the target sequence with high thermal stability of the resulting heteroduplexes. Interestingly fluorescence and CD experiments indicated formation of an intermolecular i-motif structure via the overhangs of target-probe heteroduplexes formed by PNA/γPNA invasion of the intramolecular i-motif. Targeting promoter i-motif forming sequences with high-affinity oligonucleotide mimics like γPNAs may represent a new approach for inhibiting <i>KRAS</i> transcription, thereby representing a potentially useful anti-cancer strategy.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f7/ad/BIP-114-0.PMC10078108.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9320914","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":"Peptide nucleic acid","authors":"Bruce A. Armitage","doi":"10.1002/bip.23523","DOIUrl":"10.1002/bip.23523","url":null,"abstract":"<p>I remember it like it was yesterday, even though it was more than 30 years ago. I was a graduate student at the University of Arizona (U.S.A.), sitting at my desk, eating lunch and perusing the latest issue of <i>Science</i> magazine. I came across an article about an intriguing new molecule called “polyamide nucleic acid” or PNA.^[<span>¹</span>^] (We now define PNA as “peptide nucleic acid,” which is a perfectly fine name, except that PNA technically is not a peptide, it is not found in the nucleus and it is not an acid!) My Ph.D. thesis research had nothing to do with nucleic acid chemistry, but I still found the article fascinating, as the authors—Peter Nielsen, Michael Egholm, Rolf Berg, and the late Ole Buchardt at the University of Copenhagen (Denmark)—reported the ability of PNA to bind complementary DNA targets via a novel strand-invasion mechanism. The exceptionally high affinity of PNA for its targets, its resistance to natural degradation pathways and its fidelity to the Watson–Crick rules for base pairing sparked an intense level of excitement in both the fundamental science and the applications of PNA that continues to this day. Reading that paper certainly triggered my interest in nucleic acids and motivated me to seek out a postdoctoral position in the field. Two years later, I joined the laboratory of Gary Schuster at the University of Illinois (U.S.A.) where, by way of a happy accident, I had the good fortune to begin working with PNA through collaboration with Peter Nielsen's laboratory. 29 years later, my lab continues to work with this amazing molecule and its descendants. That paper changed my life!</p><p>In this Special Collection of <i>Biopolymers</i>, we have gathered original research and review articles that highlight the ongoing evolution of PNA—both its structure and its applications. Backbone modifications that enhance affinity, nucleobase modifications that promote cell uptake, new applications in biosensing and self-assembly, and advances in targeting non-canonical structures, such as double-stranded RNA all demonstrate the versatility of PNA. While the original structure of PNA bedeviled researchers because of technical issues, for example aggregation, the next generation of PNAs have overcome these challenges. Moreover, the exploitation of PNA's peptide-like character via incorporation of amino acid side chains into the backbone, distinguishes PNA from other members of the nucleic acid alphabet soup, for example, LNA, that are more closely related to the natural biopolymers DNA and RNA.</p><p>We hope you enjoy reading these articles and that you will return from time to time as we plan to take advantage of the dynamic nature of a virtual Special Collection to add more contributions in the future. Who knows what is in store for PNA, but the seemingly endless varieties that chemists are producing and the innovative new applications that scientists and biotechnologists continue to d","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bip.23523","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10440018","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":"Advances in biomimetic collagen mineralisation and future approaches to bone tissue engineering","authors":"Michael Eugene Doyle,&nbsp;Kenny Dalgarno,&nbsp;Enrico Masoero,&nbsp;Ana Marina Ferreira","doi":"10.1002/bip.23527","DOIUrl":"10.1002/bip.23527","url":null,"abstract":"<p>With an ageing world population and ~20% of adults in Europe being affected by bone diseases, there is an urgent need to develop advanced regenerative approaches and biomaterials capable to facilitate tissue regeneration while providing an adequate microenvironment for cells to thrive. As the main components of bone are collagen and apatite mineral, scientists in the tissue engineering field have attempted in combining these materials by using different biomimetic approaches to favour bone repair. Still, an ideal bone analogue capable of mimicking the distinct properties (i.e., mechanical properties, degradation rate, porosity, etc.) of cancellous bone is to be developed. This review seeks to sum up the current understanding of bone tissue mineralisation and structure while providing a critical outlook on the existing biomimetic strategies of mineralising collagen for bone tissue engineering applications, highlighting where gaps in knowledge exist.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bip.23527","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9320468","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":"Advances in G-quadruplexes-based fluorescent imaging","authors":"Jiao-Na Han,&nbsp;Mingmin Ge,&nbsp;Pengfei Chen,&nbsp;Shi Kuang,&nbsp;Zhou Nie","doi":"10.1002/bip.23528","DOIUrl":"10.1002/bip.23528","url":null,"abstract":"<p>G-quadruplexes (G4s), the noncanonical nucleic acid secondary structure, form within guanine-rich DNA or RNA sequences. G4s formation can affect chromatin architecture and gene regulation and has been associated with various cellular functions, including DNA replication, transcription, and genome maintenance. Visualizing and detecting G4s precisely in such processes is essential to increasing our understanding of G4s biology. Considerable attention has focused on the G4s targeting molecular imaging studies. Besides, fluorescent light-up aptamers (FLAPs, also referred to as fluorogenic aptamers) have gained momentum, which commonly have a G4 scaffolding for imaging intracellular RNAs and metabolites. In this review, we first introduce several representative fluorescent imaging approaches for tracking G4s in cells and <i>in vivo</i>. We also discuss the potential of G4-containing FLAPs in bioimaging and summarize current developments in this field from the standpoint of fluorescent molecules. Finally, we discuss the present challenges and future potential of G4 imaging and G4-containing FLAPs development.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10417981","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":"Mechanical loading of graphene quantum dots on Staphylococcus aureus surface protein G: A molecular dynamics study","authors":"Sedigheh Mousanezhad,&nbsp;Jamal Davoodi","doi":"10.1002/bip.23526","DOIUrl":"10.1002/bip.23526","url":null,"abstract":"<p>This research studies graphene quantum dots (GQDs) adsorption on <i>Staphylococcus aureus</i> surface protein G (SasG) using the molecular dynamics simulation method that in addition to investigating various aspects of adsorption, including edge and surface effects of GQDs, and effects of orientation and size of GQDs, proposes a new study method in edge effects studies. Through our simulations to find edge effects, we found that even if GQD approaches the protein with its edges, GQDs' edges are not freely adsorbed on the protein because when the particles interact with each other, GQD rotates and then adsorbs the protein with its surface; therefore, GQD having initial velocity was applied to the protein to force the protein to interact with GQDs' edges to find both surface and edge effects. This is a new way of investigating that we propose to study edge effects in the molecular dynamics simulation method.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40363401","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":"Energetically unfavorable protein angles: Exploration of a conserved dihedral angle in triosephosphate isomerase","authors":"Patrick W. Allen,&nbsp;Jordan A. Cook,&nbsp;Anh N. Colquhoun,&nbsp;Eric J. Sorin,&nbsp;Enrico Tapavicza,&nbsp;Jason P. Schwans","doi":"10.1002/bip.23525","DOIUrl":"10.1002/bip.23525","url":null,"abstract":"<p>Over the past 3.5 billion years of evolution, enzymes have adopted a myriad of conformations to suit life on earth. However, torsional angles of proteins have settled into limited zones of energetically favorable dihedrals observed in Ramachandran plots. Areas outside said zones are believed to be disallowed to all amino acids, except glycine, due to steric hindrance. Triosephosphate isomerase (TIM), a homodimer with a catalytic rate approaching the diffusion limit, contains an active site lysine residue (K13) with dihedrals within the fourth quadrant (Φ = +51/Ψ = −143). Both the amino acid and the dihedral angles are conserved across all species of TIM and known crystal structures regardless of ligand. Only crystal structures of the engineered monomeric version (1MSS) show accepted β-sheet dihedral values of Φ = -135/Ψ = +170 but experiments show a 1000-fold loss in activity. Based on these results, we hypothesized that adopting the unfavorable torsion angle for K13 contributes to catalysis. Using both, computational and experimental approaches, four residues that interact with K13 (N11, M14, E97, and Q64) were mutated to alanine. In silico molecular dynamics (MD) simulations were performed using 2JK2 unliganded human TIM as a starting structure. Ramachandran plots, containing K13 dihedral values reveal full or partial loss of disallowed zone angles. N11A showed no detectable catalytic activity and lost the unfavorable K13 dihedral angles across four separate force fields during simulation while all other mutants plus wild type retained activity and retained the conserved K13 dihedral angles.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40356970","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}