Biopolymers最新文献

{"title":"Polyglycine Strands Within a Collagen Triple Helix","authors":"Wasin Tiarawut,&nbsp;Gabriel Saenz,&nbsp;Jinyi Yang,&nbsp;Ronald T. Raines","doi":"10.1002/bip.70127","DOIUrl":"10.1002/bip.70127","url":null,"abstract":"<p>The collagen triple helix is the most abundant protein structural motif in animals. It tolerates any amino acid in its Xaa and Yaa positions but demands glycine (Gly) at every third position, where the residue packs into the sterically forbidding core of the triple helix and donates the recurring interstrand N–H⋯OC hydrogen bond that stitches the three strands together. (2<i>S</i>)-Proline (Pro) and (2<i>S</i>,4<i>R</i>)-4-hydroxyproline (Hyp) are enriched far above their proteome-wide abundance because they preorganize individual strands into the polyproline II conformation, lowering the entropic cost of folding. We asked whether the triple helix is intrinsically stable enough to form from strands that carry no such preorganization, that is, from polyglycine. To offset the conformational entropy of a Gly-rich tract, we embedded Gly₆ within flanking triple-helical (Pro-Hyp-Gly)_<i>n</i> clamps in Ac-(Pro-Hyp-Gly)₆-Gly₆-(Pro-Hyp-Gly)₅-Pro-Hyp-NH₂ and compared it with an otherwise identical peptide in which Gly₆ was replaced by two [2-(2-aminoethoxy)ethoxy]acetic acid units, a flexible, length-matched spacer that lacks most of the regularly spaced backbone amides of Gly₆. Circular dichroism spectroscopy revealed the diagnostic positive band at 225 nm. The molar ellipticity of the spacer-containing control was 86% of that of the Gly₆-containing peptide, matching the 35/41 = 85% ratio of residues capable of triple-helix formation and consistent with the Gly₆ segment contributing to the triple-helical signal. Thermal denaturation yielded a <i>T</i>_m of 46.8°C for the Gly₆-containing peptide, 6.3°C higher than that of the matched spacer control. This added stability indicates that the polyglycine tract is not merely accommodated within the helix but contributes stabilizing interstrand hydrogen bonds. Together, these data indicate that three polyglycine strands can form a collagen triple helix when flanked by triple-helical clamps. This result is consistent with the idea that the triple-helical architecture predates the recruitment of Pro and Hyp, informs the evolutionary origin of collagen, and offers a blunt-ended, symmetric scaffold for designing peptidic triple helices.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":"117 6","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bip.70127","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149191213","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":"Molecular Interactions Between Bacteriorhodopsin Protein Embedded Within Purple Membrane and the Surfaces of Polyvinyl Alcohol (PVA) and Graphene","authors":"Elia Haghbin,&nbsp;Leslie Abbott,&nbsp;Isaac Macwan","doi":"10.1002/bip.70126","DOIUrl":"https://doi.org/10.1002/bip.70126","url":null,"abstract":"<div>\u0000 \u0000 <p>Bacteriorhodopsin (bR), the light-driven proton pump of <i>Halobacterium salinarum</i>, is a promising candidate for bioelectronic and optoelectronic applications. Its utility in hybrid systems depends on how surrounding materials influence structural stability and photocycle dynamics. In this work, all-atom molecular dynamics simulations are conducted under isothermal–isobaric conditions to evaluate bR in three environments: its native purple membrane, adsorption onto graphene sheets, and incorporation within a polyvinyl alcohol (PVA) matrix. Across all systems, bR displayed preferential adsorption on the extracellular side of the membrane. Graphene promoted strong and stable interactions, preserving native electrostatic contacts, enhancing Van der Waals forces, and allowing conformational flexibility essential for photocycle transitions. In contrast, PVA generated weaker stabilization, a water-rich interface, and disruption of key electrostatic interactions, which constrained protein adaptability. These findings identify graphene as a favorable surface for maintaining both structural integrity and functional dynamics of bR, supporting its integration within PVA based scaffolds toward the development of bio-nano interfaces.</p>\u0000 </div>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":"117 6","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981415","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":"Biogenic Silver Nanoparticles-Loaded Collagen–L-Lysine Matrices in Gel and Spray Formulations for Improved Skin Wound Repair","authors":"Ruma Devi,&nbsp;Pratik Das,&nbsp;Purnendu Ghosh,&nbsp;Sudipta Roy,&nbsp;Tathagata Adhikary,&nbsp;Satyabrata Nigamananda Sahoo,&nbsp;Sovan Lal Banerjee,&nbsp;Samiran Mondal,&nbsp;Piyali Basak,&nbsp;Mangal Roy,&nbsp;Samit Kumar Nandi","doi":"10.1002/bip.70123","DOIUrl":"10.1002/bip.70123","url":null,"abstract":"<div>\u0000 \u0000 <p>Biogenic silver nanoparticles (AgNPs) are emerging as valuable candidates in biomedical research, offering advantages such as cost-effectiveness, eco-friendly preparation methods, and superior biocompatibility. Owing to the challenges in the treatment of chronic skin injury, this study utilizes biogenic AgNPs (synthesized using Shilajit as a reducing and stabilizing agent) to develop gel and spray formulations (constituting fish collagen and <span>l</span>-lysine) for wound-healing applications. FTIR analysis indicated the involvement of functional groups from the Shilajit extract in synthesizing crystalline spherical AgNPs of 140–160 nm diameter. EDAX analysis reported 0.6% (by weight) silver in both formulations, with major elemental peaks for nitrogen, carbon, and oxygen, indicating the presence of polysaccharides. The MTT assay on HDFa cells confirmed that both preparations were nontoxic, as validated by FDA staining, which signified intact cell morphology. In vivo findings demonstrated that ShilAgNPs-Fcol-Lys formulations promote rapid wound closure, effective extracellular matrix (ECM) deposition, advanced neovascularization, and improved tissue remodeling compared with controls and standard treatments. Well-organized collagen deposition and efficient remodeling were confirmed by histology and immunohistochemistry, with the spray formulation performing better than the gel. Thus, ShilAgNPs-Fcol-Lys formulations offer a biocompatible, safe, and cost-effective alternative for treating deep excisional wounds.</p>\u0000 </div>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":"117 5","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148910601","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":"Pre-Esterification Dry Heat Treatment Enhances the Functional Properties of Starch Citrate: Enzyme Resistance and Water Absorption","authors":"Anna Dogadina,&nbsp;Denis Tryakhov,&nbsp;Svetlana Grishkova,&nbsp;Daniel Maslennikov","doi":"10.1002/bip.70125","DOIUrl":"10.1002/bip.70125","url":null,"abstract":"<div>\u0000 \u0000 <p>This study investigates how pre-esterification dry heat treatment (DHT) of corn starch at 170°C, 180°C, and 200°C influences the functional properties of subsequently synthesized starch citrates. Structural and morphological changes induced by DHT and esterification were analyzed using scanning electron microscopy, X-ray diffractometry, and Fourier-Transform Infrared spectroscopy. Starch citrates were characterized for their resistance to pancreatic α-amylase and amyloglucosidase, as well as their water absorption capacity (WAC) at 37°C. Results demonstrated a strong correlation between DHT temperature and the functional properties of the final citrate. Increasing the DHT temperature significantly increased the resistant starch fraction and WAC. Specifically, citrates from native starch had a resistant starch (RS) fraction of 91%, while citrates from starch pre-treated at 200°C exhibited a markedly increased RS fraction of 98% and a 64% increase in WAC. These findings indicate that DHT is an effective pre-treatment for enhancing the dietary fiber potential and hydration properties of starch citrates.</p>\u0000 </div>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":"117 5","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148918306","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":"Bacterial Cellulose Membranes for Dye Removal: Adsorption Behavior, Thermodynamics, Regeneration, and Performance in Simulated Wastewater","authors":"Francisca L. Aranda,&nbsp;Yovany Oropesa,&nbsp;Elizabeth Parra Gatica,&nbsp;Julio Sánchez,&nbsp;Angelo Oñate,&nbsp;Manuel F. Meléndrez,&nbsp;Orlando Rojas,&nbsp;Daniel A. Palacio","doi":"10.1002/bip.70124","DOIUrl":"10.1002/bip.70124","url":null,"abstract":"<div>\u0000 \u0000 <p>Bacterial cellulose is a sustainable biopolymeric material with considerable potential for wastewater treatment due to its nanofibrous structure and abundance of hydroxyl groups. In this study, BC membranes were evaluated as adsorbents for organic dyes, focusing on pH effects, adsorption behavior, and reusability. Adsorption performance was influenced by pH, with significant differences among some conditions; pH 7 was selected for subsequent experiments based on adsorption performance and its practical relevance. Kinetic studies showed rapid initial adsorption followed by a slower approach to equilibrium, while the maximum experimental adsorption capacity for methylene blue (MB) reached 100.15 mg g⁻¹. BC membranes were separately evaluated with MB, crystal violet, and methyl orange in the presence of inorganic salts, showing effective but dye-dependent removal. Reusability tests showed a progressive decline, with a 37.26% loss after five adsorption–desorption cycles. FTIR analysis indicated preservation of the main structural features of BC after adsorption. Hydrogen bonding and electrostatic interactions are proposed as plausible contributors to adsorption. Overall, BC membranes showed promising adsorption performance, although regeneration requires further optimization.</p>\u0000 </div>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":"117 5","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148905075","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":"Unraveling the Asymmetric Hydration Dynamics and Water-Mediated Stabilization in Collagen Heterotrimers","authors":"Anand Balupuri,&nbsp;Dong-Hyun Son,&nbsp;Nam Sook Kang","doi":"10.1002/bip.70122","DOIUrl":"10.1002/bip.70122","url":null,"abstract":"<div>\u0000 \u0000 <p>Collagen's triple helix structure is fundamental to the mechanical integrity of bodily tissues, and its stability is vital for optimal physiological function. While the stabilization mechanisms of simple, symmetric collagen homotrimers have been previously studied, the hydration dynamics of native-like collagen heterotrimers which comprise the vast majority of human collagens remain largely unexplored. In this study, we investigated the complex role of water in stabilizing heterotrimeric collagen model peptides (CMPs) using extensive molecular dynamics (MD) simulations. We examined structurally diverse AAB-type and ABC-type heterotrimers exhibiting varying experimental stability profiles to investigate how sequence asymmetry influences hydration organization and collagen stability. Our simulations revealed that water molecules dynamically organize around these complex structures, forming topological water networks (TWNs) via intermolecular hydrogen bonds. Quantitative analyses of peptide–water interactions, hydration-water dynamics, and normalized TWN counts, together with residue- and chain-resolved TWN characterization, demonstrated that hydration-shell organization is strongly sequence dependent and differs among heterotrimers with distinct thermal stabilities. In particular, the more thermally stable heterotrimers exhibited a greater propensity for hydration-shell water molecules to participate in cyclic TWNs, accompanied by reduced hydration-water mobility and favorable interchain hydrogen-bonding interactions. These findings extend our previous observations on collagen homotrimers and provide new atomistic insight into the sequence-dependent organization of hydration water surrounding collagen heterotrimers, suggesting that organized hydration water contributes to collagen stability in concert with interchain hydrogen bonding and hydration-water dynamics rather than acting as an independent stabilization mechanism.</p>\u0000 </div>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":"117 5","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863519","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":"High-Efficiency Carboxymethylation Achieved by Enhancing Hydroxyl Accessibility Through Glycerol Pretreatment of Bacterial Cellulose","authors":"Bangqi Fu,&nbsp;Guoqiang Chen,&nbsp;Xuedong Chen,&nbsp;Linyuan Chen,&nbsp;Yanjun Jiang,&nbsp;Lei Wang,&nbsp;Chengbo Gu,&nbsp;Haibo Zhang","doi":"10.1002/bip.70121","DOIUrl":"10.1002/bip.70121","url":null,"abstract":"<div>\u0000 \u0000 <p>Due to its dense crystalline structure and extensive hydrogen bonding network, cellulose exhibits limited reactive accessibility and reactivity, which severely restricts the reaction efficiency, degree of substitution, and uniformity of cellulose modifications such as carboxymethylation. To overcome these limitations, this study developed a novel glycerol-based pretreatment strategy to disrupt the hydrogen bonding network of bacterial cellulose (BC), thereby improving its reactive accessibility. The results confirmed that glycerol pretreatment significantly enhanced the reactivity of BC. The reaction time for preparing carboxymethyl cellulose (CMC) from glycerol-pretreated powdered BC was reduced from 2 to 1 h, representing a 100% improvement in reaction efficiency. In addition, glycerol pretreatment facilitated the exposure of hydroxyl groups in BC, thereby increasing the degree of substitution of CMC from 0.297 to 0.433 and from 0.427 to a peak value of 0.626, an approximately 46% enhancement. In addition, the CMC films prepared from glycerol-pretreated BC exhibited significantly improved light transmittance, reaching over 95% in the wavelength range of 300–1000 nm. This study provides theoretical support and technical guidance for the efficient production of CMC, expands its application potential in high-end fields, and promotes the high-value utilization of cellulose resources.</p>\u0000 </div>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":"117 5","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863501","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":"Inherent α-Helix Around Tyrosine 183 in the Intrinsically Disordered Tail of the Multi-Site Docking Platform Gab1","authors":"Anne Dietrich,&nbsp;Marc Lewitzky,&nbsp;Tobias Gruber,&nbsp;Jochen Balbach,&nbsp;Stephan M. Feller,&nbsp;Ulrich Weininger","doi":"10.1002/bip.70120","DOIUrl":"10.1002/bip.70120","url":null,"abstract":"<p>The biological function of intrinsically disordered proteins is frequently coupled to short linear motifs, which serve as protein binding sites. This goes often hand in hand with local transient structural element formation. The intrinsically disordered C-terminal region of the multi-site docking protein Grb2-associated binder 1 (Gab1) contains several well-characterized phosphotyrosine pairs, whereas the Tyr162 and Tyr183 epitopes have remained practically unstudied. Here, we combine computational prediction, circular dichroism and high-resolution NMR spectroscopy (chemical shift and relaxation analyses) to structurally characterize a Gab1 fragment containing residues 142–203. The here determined NMR structure shows an α-helix for residues Pro180 to Ile187, with Tyr183 positioned centrally, while all other parts of the fragment, including the region around Tyr162, are disordered. This helical conformation is maintained upon changes in pH, variation of peptide lengths and phosphorylation status. The inherent helix around Tyr183 distinguishes the local structural environment of Tyr162 and Tyr183 within the intrinsically disordered Gab1 tail and provides a structural framework for future studies on interaction partners and potential functional roles of this structural motif.</p>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":"117 5","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13435814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148668310","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":"Role of Water in Starch Mechanical Treatment","authors":"Denis E. Tryakhov,&nbsp;Mikhail A. Mikhailenko,&nbsp;Daniel V. Maslennikov","doi":"10.1002/bip.70119","DOIUrl":"https://doi.org/10.1002/bip.70119","url":null,"abstract":"<div>\u0000 \u0000 <p>The impact of initial moisture content (1.5%–20%) on the ball-milling of pea starch was investigated across multiple structural levels. Scanning electron microscopy revealed moisture-dependent deformation mechanisms: plastic flow and agglomeration in high-moisture granules versus pseudo-brittle fracture in low-moisture samples. Despite these differences, XRD-detectable crystallinity was eliminated within 5 min of treatment, independent of initial moisture content. Fourier transform infrared spectroscopy confirmed the loss of short-range molecular order, including helical and hydrogen-bonded contributions. Gel permeation chromatography demonstrated more severe molecular degradation in low-moisture starch, suggesting a possible two-stage degradation behavior, with a rapid initial decrease of molar mass followed by a slower regime as the material becomes predominantly amorphous. Consequently, ball-milling enhanced solubility in both cold (30°C) and hot (90°C) water, increasing it from less than 1% and ~25% to 60%–70%, respectively. The increased cold-water solubility is explained by the loss of crystallinity. In contrast, the rise in hot-water solubility indicates a more profound structural disintegration. We propose that this is related to the mechanochemical degradation of amylopectin, which may suppress the formation of amylopectin-rich remnants during gelatinization and thereby promote dissolution.</p>\u0000 </div>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":"117 5","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148533854","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":"Fluorescent Leaf-Like Structures Formed by Self-Assembly of Green Fluorescent Protein","authors":"Hsi-Chi Lu,&nbsp;Yi-Lin Huang,&nbsp;Woan-Ling Chen,&nbsp;Pei-Kang Gu,&nbsp;Yesong Gu","doi":"10.1002/bip.70118","DOIUrl":"https://doi.org/10.1002/bip.70118","url":null,"abstract":"<div>\u0000 \u0000 <p>Green fluorescent protein (GFP) was originally obtained from <i>Aequorea victoria</i> and was successfully synthesized through recombinant technology. In this study, we revealed novel, fascinating insights into the properties of this well-known GFP by examining a traditional GFP separation process involving aqueous two-phase systems and several liquid chromatographs. We investigated the impact of organic solvents and salts on the conformation of GFP by measuring its fluorescence intensity and circular dichroism spectrum, and then proposed an optimized process to improve the yield of fluorescent GFP. We have noticed that fluorescent GFP migrates anomalously to ~37 kDa on non-heating SDS-PAGE due to retention of its compact β-barrel conformation, whereas the commonly reported 27 kDa migration corresponds to the fully heat-denatured, non-fluorescent form. Nevertheless, the most exciting discovery is that the purified GFP exhibited a remarkable ability to self-assemble into an intriguing fluorescent leaf-like structure upon evaporation-concentration under ambient conditions. To our knowledge, this represents the first direct visualization of such macroscopic fluorescent leaf-like assemblies formed by recombinant GFP, with fluorescence retained throughout the assembled morphology. This captivating phenomenon may have promising implications for protein-based nanomaterials and will inspire further exploration of protein self-assembly nanotechnology.</p>\u0000 </div>","PeriodicalId":8866,"journal":{"name":"Biopolymers","volume":"117 5","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148533855","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}