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structure-function relationship of long noncoding RNAs: Advances and challenges

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2022年第5期12卷 e1609-e1609页

作者： Longkumer, Imliyangla Mishra, Seema Univ Hyderabad Sch Life Sci Dept Biochem Hyderabad Telangana India

Long noncoding RNAs (lncRNAs) are an emerging and a promising class of RNAs, and the lncRNA field is an intense research area. Once trashed as the junk regions of the genome, lncRNAs have now proved to be one of the crucial elements of a functional genome. These comprise a major chunk of the transcriptome, and similar to proteins, the sequence-structure-function paradigm holds true for lncRNAs as well. While some of the earliest lncRNAs like Xist and H19 have been well-characterized, many of the emerging lncRNAs remain in oblivion. The low sequence conservation of lncRNAs has prompted researchers to decipher its conserved structure in order to gain an insight into the functional mechanisms. Here, we explore the concept of the sequence-structure-function relationship of lncRNAs, and the biophysical and biochemical laws governing a lncRNA structure which are just beginning to be understood. Proceeding from specific structures, much of the functions of lncRNAs revolve around their regulatory roles, through myriad modes of action. Throughout this review, we discuss the powerful computational as well as some experimental approaches that are applied in a synergistic fashion and highlight promising studies that have proved crucial towards an understanding of lncRNA structure and functional mechanisms. We also discuss at length, the existing challenges and the possible strategies to circumvent it. Given the unknown realm, the patterns and insights generated from these studies will be extremely useful in deciphering the way nature selects and uses a specific lncRNA to regulate a specific gene or gene sets in health and disease. This article is categorized under: structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Free Energy Methods structure and Mechanism > Molecular structures

关键词： computational tools and databases long noncoding RNAs structure-function

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Heat-treated bean flour: Exploring techno-functionality via starch-protein structure-function analysis

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FOOD HYDROCOLLOIDS 2024年 157卷

作者： Navneet Martinez, Mario M. Joye, Iris J. Univ Guelph Dept Food Sci Guelph ON Canada Aarhus Univ Ctr Innovat Food CiFOOD Dept Food Sci Agro Food Pk 48 DK-8200 Aarhus N Denmark

The study aimed to modify the structure of two major components ( i.e. , starch and protein) in bean flour to enhance bean flour's techno-functionality. The bean flour was processed by two very different temperature treatments - dry heat (DH) and extrusion. The effect of processing on starch and protein was analyzed by characterizing their physicochemical properties. While processing did not alter, as expected, the total starch (35-47 % (db)) and protein (24-25 % (db)) content of the bean flours, it did significantly change the microstructure and molecular architecture of starch and proteins. DH processing mainly affected protein conformation while minimally affecting starch structure. Conversely, extrusion caused extensive structural modifications of both starch and protein in bean flour. Both DH and extrusion processing decreased intramolecular beta-sheet secondary structure of bean protein. Additionally, both unprocessed and thermally processed bean flours were characterized for their techno-functional properties. The heat treatments (DH and extrusion) did not only result in colour variations, but they also modified the particle size distribution, pasting profile, rheological properties, and water absorption and solubility indices of the bean flour. The structure-function relationship of bean flour components (starch and protein) and bean flour's functionality implied that thermal processing treatments led to changes in the protein/starch matrix which were reflected in the techno-functionality of processed bean flours. However, the changes induced by each of the different types of processing were very different, thus, unlocking different opportunities for functionalization of bean flours for food manufacturing and product development applications.

关键词： Dry beans structure-function Microscopy FT-IR Rheology Wheat substitute

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structure-function relationship of small peptides generated during the ripening of Spanish dry-cured ham: Peptidome, molecular stability and computational modelling

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FOOD CHEMISTRY 2022年 375卷 131673-131673页

作者： Li, Chengliang Mora, Leticia Toldra, Fidel Inst Agroquim & Tecnol Alimentos IATA CSIC Ave Agustin Escardino 7 Paterna 46980 Valencia Spain

A systematic insight into the structure-function properties of small bioactive peptides is of great importance. Herein, peptidomics and computational methodology were adopted to investigate the stabilization patterns and building blocks of antioxidant peptides resulting from proteolysis during the ripening of Spanish dry-cured ham (9-24 months of processing). The results showed that native peptides underwent manufacture-induced steric/ redox stress, while homogeneous/heterogeneous p-pi/pi-pi interaction significantly improved the ABTS(center dot+) inhibition activity of hydrophobic peptides. However, for more hydrophilic peptides, the intrinsic pi-interaction system (i.e., cation-pi and pi-pi packing) substantially interfered with ABTS(center dot+) /DPPH center dot scavenging events when compared to the aromatic residues. Semi-quantitative peptidomics and molecular simulation/docking revealed that VFSSQGQSELILLQK and LCPSPDGLYL are two potential antioxidant peptides at the late ripening-drying. They had distinctive self-folding destinies following solvation owing to varying charged/hydrophobic properties of termini and hydrogen atom donor, allowing different flexibility of backbone and interactive surface towards free radicals ex situ followed by electron/proton transfer.

关键词： Dry-cured ham Antioxidant peptides Ripening Peptidomics Intrinsic pi-interaction system In silico approach Molecular docking structure-function

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Longitudinal evaluation of circumpapillary structure-function and vasculature-function relationships in acute and sub-acute nonarteritic anterior ischemic optic neuropathy

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PHOTODIAGNOSIS AND PHOTODYNAMIC THERAPY 2024年 49卷 104345-104345页

作者： Gong, Yi Sun, Shuo Wang, Manqiao Luan, Rong Liu, Boshi Yu, Rongguo Li, Xiaorong Tianjin Med Univ Eye Inst Natl Clin Res Ctr Ocular Dis Tianjin Key Lab Retinal Funct & DisTianjin Branch Tianjin Peoples R China Tianjin Med Univ Sch Optometry Eye Hosp Tianjin Peoples R China

Purpose: To investigate the global and regional correlations between longitudinal structure-function (S-F) and vasculature-function (V-F) using circumpapillary retinal nerve fiber layer (cpRNFL) thickness measurements, circumpapillary vessel density (cpVD) and the corresponding/final visual outcomes at different stages of nonarteritic anterior ischemic optic neuropathy (NAION). Methods: Thirty eyes of 30 patients with acute NAION were included. LogMAR best-corrected visual acuity (BCVA), mean deviation (MD) and visual field index (VFI), cpRNFL thickness and cpVD across different retinal layers were examined at baseline, 2 weeks and 1 month after diagnosis. Potential correlations between the Optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA) parameters and visual outcomes were investigated in both acute and sub-acute NAION. Results: Significant global and regional correlations in S-F relationship were identified exclusively in sub-acute stage (p < 0.05). However, among the OCTA parameters for the acute NAION, the temporal cpVD in superficial vessel complex (SVC) and inner retinal layer (IRL) exhibited positive correlations with corresponding and final visual acuity and visual field outcomes. In the sub-acute stage of NAION, the cpVD of global or temporal section in radial peripapillary capillary (RPC), SVC and IRL were positively correlated with visual outcomes. Conclusion: Significant longitudinal V-F relationships exist both globally and regionally, in acute and sub-acute NAION. The cpVD parameters of the SVC and IRL are potentially valuable for evaluating corresponding and final visual outcomes and highlights the importance of monitoring cpVD over cpRNFL thickness in acute NAION.

关键词： Nonarteritic anterior ischemic optic neuropathy Optical coherence tomography Optical coherence tomography angiography structure-function Vasculature-function

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Wet shells and dry tales: the evolutionary 'Just-So' stories behind the structure-function of biominerals

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JOURNAL OF THE ROYAL SOCIETY INTERFACE 2022年第191期19卷 20220336-20220336页

作者： Lemanis, Robert Tadayon, Kian Reich, Elke Joshi, Gargi Johannes Best, Richard Stevens, Kevin Zlotnikov, Igor Tech Univ Dresden CUBE Ctr Mol Bioengn B Dresden Germany Ruhr Univ Bochum Inst GeolMineral & Geophys Bochum Germany

The ability of evolution to shape organic form involves the interactions of multiple systems of constraints, including fabrication, phylogeny and function. The tendency to place function above everything else has characterized some of the historical biological literature as a series of 'Just-So' stories that provided untested explanations for individual features of an organism. A similar tendency occurs in biomaterials research, where features for which a mechanical function can be postulated are treated as an adaptation. Moreover, functional adaptation of an entire structure is often discussed based on the local characterization of specimens kept in conditions that are far from those in which they evolved. In this work, environmental- and frequency-dependent mechanical characterization of the shells of two cephalopods, Nautilus pompilius and Argonauta argo, is used to demonstrate the importance of multi-scale environmentally controlled characterization of biogenic materials. We uncover two mechanistically independent strategies to achieve deformable, stiff, strong and tough highly mineralized structures. These results are then used to critique interpretations of adaptation in the literature. By integrating the hierarchical nature of biological structures and the environment in which they exist, biomaterials testing can be a powerful tool for generating functional hypotheses that should be informed by how these structures are fabricated and their evolutionary history.

关键词： structure-function biominerals mechanical properties adaptation

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Using augmented reality in molecular case studies to enhance biomolecular structure-function explorations in undergraduate classrooms

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JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2024年第2期25卷 e00019-24-e00019-24页

作者： Vardar-Ulu, Didem Ragab, Saif Eldeen Agrawal, Swati Dutta, Shuchismita Boston Univ Boston MA 02215 USA Univ Mary Washington Fredericksburg VA USA Rutgers State Univ Piscataway NJ USA

Molecular case studies (MCSs) are open educational resources that use a storytelling approach to engage students in biomolecular structure-function explorations, at the interface of biology and chemistry. Although MCSs are developed for a particular target audience with specific learning goals, they are suitable for implementation in multiple disciplinary course contexts. Detailed teaching notes included in the case study help instructors plan and prepare for their implementation in diverse contexts. A newly developed MCS was simultaneously implemented in a biochemistry and a molecular parasitology course at two different institutions. Instructors participating in this cross-institutional and multidisciplinary implementation collaboratively identified the need for quick and effective ways to bridge the gap between the MCS authors' vision and the implementing instructor's interpretation of the case-related molecular structure-function discussions. Augmented reality (AR) is an interactive and engaging experience that has been used effectively in teaching molecular sciences. Its accessibility and ease-of-use with smart devices (e.g., phones and tablets) make it an attractive option for expediting and improving both instructor preparation and classroom implementation of MCSs. In this work, we report the incorporation of ready-to-use AR objects as checkpoints in the MCS. Interacting with these AR objects facilitated instructor preparation, reduced students' cognitive load, and provided clear expectations for their learning. Based on our classroom observations, we propose that the incorporation of AR in MCSs can facilitate its successful implementation, improve the classroom experience for educators and students, and make MCSs more broadly accessible in diverse curricular settings.

关键词： molecular case studies hands-on learning molecular visualization augmented reality biochemistry structure-function molecular parasitology

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The chemokine X-factor: structure-function analysis of the CXC motif at CXCR4 and ACKR3

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JOURNAL OF BIOLOGICAL CHEMISTRY 2020年第40期295卷 13927-13939页

作者： Wedemeyer, Michael J. Mahn, Sarah A. Getschman, Anthony E. Crawford, Kyler S. Peterson, Francis C. Marchese, Adriano McCorvy, John D. Volkman, Brian F. Med Coll Wisconsin Dept Biochem Milwaukee WI 53226 USA Med Coll Wisconsin Dept Cell Biol Neurobiol & Anat Milwaukee WI 53226 USA

The human chemokine family consists of 46 protein ligands that induce chemotactic cell migration by activating a family of 23 G protein-coupled receptors. The two major chemokine subfamilies, CC and CXC, bind distinct receptor subsets. A sequence motif defining these families, the X position in the CXC motif, is not predicted to make significant contacts with the receptor, but instead links structural elements associated with binding and activation. Here, we use comparative analysis of chemokine NMR structures, structural modeling, and molecular dynamic simulations that suggested the X position reorients the chemokine N terminus. Using CXCL12 as a model CXC chemokine, deletion of the X residue (Pro-10) had little to no impact on the folded chemokine structure but diminished CXCR4 agonist activity as measured by ERK phosphorylation, chemotaxis, and G(i/o)-mediated cAMP inhibition. functional impairment was attributed to over 100-fold loss of CXCR4 binding affinity. Binding to the other CXCL12 receptor, ACKR3, was diminished nearly 500-fold. Deletion of Pro-10 had little effect on CXCL12 binding to the CXCR4 N terminus, a major component of the chemokine-GPCR interface. Replacement of the X residue with the most frequent amino acid at this position (P10Q) had an intermediate effect between WT and P10del in each assay, with ACKR3 having a higher tolerance for this mutation. This work shows that the X residue helps to position the CXCL12 N terminus for optimal docking into the orthosteric pocket of CXCR4 and suggests that the CC/CXC motif contributes directly to receptor selectivity by orienting the chemokine N terminus in a subfamily-specific direction.

关键词： G protein-coupled receptor (GPCR) cell migration nuclear magnetic resonance (NMR) signal transduction structure-function chemokine CC CXC motif chemokine network

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Unraveling Forest Complexity: Resource Use Efficiency, Disturbance, and the structure-function Relationship

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JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES 2022年第6期127卷 e2021JG006748-e2021JG006748页

作者： Murphy, Bailey A. May, Jacob A. Butterworth, Brian J. Andresen, Christian G. Desai, Ankur R. Univ Wisconsin Dept Atmospher & Ocean Sci Madison WI 53706 USA Univ Wisconsin Dept Geog Madison WI 53706 USA Univ Colorado Cooperat Inst Res Environm Sci Boulder CO 80309 USA NOAA Phys Sci Lab Boulder CO USA

Structurally complex forests optimize resources to assimilate carbon more effectively, leading to higher productivity. Information obtained from Light Detection and Ranging (LiDAR)-derived canopy structural complexity (CSC) metrics across spatial scales serves as a powerful indicator of ecosystem-scale functions such as gross primary productivity (GPP). However, our understanding of mechanistic links between forest structure and function, and the impact of disturbance on the relationship, is limited. Here, we paired eddy covariance measurements of carbon and water fluxes from nine forested sites within the 10 x 10 km CHEESEHEAD19 study domain in Northern Wisconsin, USA with drone LiDAR measurements of CSC to establish which CSC metrics were strong drivers of GPP, and tested potential mediators of the relationship. Mechanistic relationships were inspected at five resolutions (0.25, 2, 10, 25, and 50 m) to determine whether relationships persisted with scale. Vertical heterogeneity metrics were the most influential in predicting productivity for forests with a significant degree of heterogeneity in management, forest type, and species composition. CSC metrics included in the structure-function relationship as well as driver strength was dependent on metric calculation resolution. The relationship was mediated by light use efficiency (LUE) and water use efficiency (WUE), with WUE being a stronger mediator and driver of GPP. These findings allow us to improve representation in ecosystem models of how CSC impacts light and water-sensitive processes, and ultimately GPP. Improved models enhance our capacity to accurately simulate forest responses to management, furthering our ability to assess climate mitigation strategies.

关键词： forest complexity scaling structure-function LiDAR forest management eddy covariance

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structure-function analysis defines the minimal functional C-terminal domain of the variant surface glycoprotein of Trypanosoma brucei

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The Journal of biological chemistry 2025年 110260页

作者： Nicola G Jones Markus Engstler Department of Cell and Developmental Biology University of Würzburg Würzburg Germany. Electronic address: nicola.jones@uni-wuerzburg.de. Department of Cell and Developmental Biology University of Würzburg Würzburg Germany. Electronic address: markus.engstler@uni-wuerzburg.de.

In their mammalian hosts, African trypanosomes abundantly express GPI-anchored variant surface glycoproteins (VSGs) on their cell surfaces. These provide a protective surface coat that has been studied best in Trypanosoma brucei. The genome of this single-celled parasite contains more than 2000 VSG genes and pseudogenes, a rich foundation based on which only one functional VSG is expressed at any given time. This allows coat exchange by antigenic variation which is an elegant means of repeatedly evading the immune response of the mammalian host. All proteins of the VSG family are composed of a larger, elongated N-terminal domain that is most exposed and a smaller C-terminal domain that is sandwiched between the N-terminal domain and the GPI-anchor, which connects the protein to the outer leaflet of the plasma membrane. Whereas the sequence variability in the N-terminal domain of different members of the VSG family is essential for antigenic variation, the role of the C-terminal domain remains less clear and other species such as T. congolense and T. vivax do not possess a similarly structured C-terminal domain in their VSGs. Here, we systematically mutated the C-terminal domain of selected T. brucei VSGs and define a minimal domain required for VSG function. We show that the size of the minimal C-terminal domain resembles that of T. congolense VSGs and structured regions are not essential. We further propose that the evolutionary pressure to conserve the build of the C-terminal domain is related to functions beyond protein structure.

关键词： Glycosylphosphatidylinositol (GPI) anchor Trypanosoma brucei Trypanosoma congolense cell surface mutagenesis protein domain structure-function variant surface glycoprotein

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Development of structure-function coupling in human brain networks during youth

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2020年第1期117卷 771-778页

作者： Baum, Graham L. Cui, Zaixu Roalf, David R. Ciric, Rastko Betzel, Richard F. Larsen, Bart Cieslak, Matthew Cook, Philip A. Xia, Cedric H. Moore, Tyler M. Ruparel, Kosha Oathes, Desmond J. Alexander-Bloch, Aaron F. Shinohara, Russell T. Raznahan, Armin Gur, Raquel E. Gur, Ruben C. Bassett, Danielle S. Satterthwaite, Theodore D. Univ Penn Dept Psychiat Philadelphia PA 19104 USA Childrens Hosp Philadelphia Lifespan Brain Inst Philadelphia PA 19104 USA Stanford Univ Dept Bioengn Stanford CA 94305 USA Indiana Univ Dept Psychol & Brain Sci Bloomington IN 47405 USA Univ Penn Dept Radiol Philadelphia PA 19104 USA Yale Univ Sch Med Dept Psychiat New Haven CT 06510 USA Univ Penn Dept Biostat Epidemiol & Informat Penn Stat Imaging & Visualizat Ctr Philadelphia PA 19104 USA Univ Penn Ctr Biomed Image Comp & Analyt Philadelphia PA 19104 USA NIMH Dev Neurogen Unit Bethesda MD 20814 USA Univ Penn Dept Neurol Philadelphia PA 19104 USA Univ Penn Dept Bioengn Philadelphia PA 19104 USA Univ Penn Dept Elect & Syst Engn Philadelphia PA 19104 USA Univ Penn Dept Phys & Astron Philadelphia PA 19104 USA Santa Fe Inst Santa Fe NM 87501 USA

The protracted development of structural and functional brain connectivity within distributed association networks coincides with improvements in higher-order cognitive processes such as executive function. However, it remains unclear how white-matter architecture develops during youth to directly support coordinated neural activity. Here, we characterize the development of structure-function coupling using diffusion-weighted imaging and n-back functional MRI data in a sample of 727 individuals (ages 8 to 23 y). We found that spatial variability in structure-function coupling aligned with cortical hierarchies of functional specialization and evolutionary expansion. Furthermore, hierarchy-dependent age effects on structure-function coupling localized to transmodal cortex in both cross-sectional data and a subset of participants with longitudinal data (n = 294). Moreover, structure-function coupling in rostrolateral prefrontal cortex was associated with executive performance and partially mediated age-related improvements in executive function. Together, these findings delineate a critical dimension of adolescent brain development, whereby the coupling between structural and functional connectivity remodels to support functional specialization and cognition.

关键词： brain development MRI connectome cortical organization structure-function

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