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structure-function RELATIONSHIPS FOR THE BIO-INSPIRED DESIGN OF SCALES 19

STRUCTURE-FUNCTION RELATIONSHIPS FOR THE BIO-INSPIRED DESIGN...

ASME 19th International Manufacturing Science and Engineering Conference (MSEC) held jointly with the 52nd North American Research Conference (NAMRC)

作者： Martinez, Itzel Chavez Mistry, Ved Bhate, Dhruv Arizona State Univ Mesa AZ 85212 USA

ISBN: (纸本)9780791888100

The structure of scales, found in organisms ranging from fish to plants, demonstrates a wide range of patterned design. Composed of keratin, collagen, or other biomaterials, scales exhibit a hierarchical organization with diverse patterning strategies. functionally, scales serve several critical roles in organisms' survival and adaptation. The applications of scale-inspired designs span a diverse array of fields, from improving the hydrodynamic efficiency of aircraft and underwater vehicles, to developing advanced wound dressings and prosthetic materials in the biomedical field. Scale-inspired structures have also been integrated into architecture and building materials. Despite some examples, there has been limited exploration of bio-inspired design of scales, which have received a lot of attention with the progress made in computational design and additive manufacturing. We argue there that this is at least partly on account of the limited design principles formally abstracted for scales, which further, may be attributed to a tenuous connection between structure-function relationships that are well described for families of organisms in biology, and engineering applications. Towards addressing this gap, we first develop a new structural and functional classification for scales that cuts across multiple groups of organisms, using a designer's perspective. We show how such a perspective emphasizes design choices as opposed to phylogenetic relationships, commonly used in biological classification. structure-function relationships are then mapped to each other, providing a direction from scale structure to potential applications. We end with a discussion of how such a structure-function map may be embedded into a computational design tool for scales, and how it may also deepen our understanding of the evolution of scales in biology by providing a pathway for engineering studies of structure-function relationships.

关键词： bio-inspired design scales additive manufacturing structure-function cellular materials

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structure-function Studies of GABA (A) Receptors and Related computer-aided Studies

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JOURNAL OF MOLECULAR NEUROSCIENCE 2023年第9-10期73卷 804-817页

作者： Mohamad, Fatin H. Jamali, Muhamad Arif Mohamad Has, Ahmad Tarmizi Che Univ Sains Malaysia Sch Med Sci Dept Anesthesiol Hlth Campus Kota Baharu 16150 Kelantan Malaysia Univ Sains Islam Malaysia Fac Sci & Technol Bandar Baru Nilai Nilai 71800 Negeri Sembilan Malaysia

The gamma-aminobutyric acid type A receptor (GABA (A) receptor) is a membrane protein activated by the neurotransmitter GABA. Structurally, this major inhibitory neurotransmitter receptor in the human central nervous system is a pentamer that can be built from a selection of 19 subunits consisting of alpha(1,2,3,4,5 or 6), beta (1,2 or 3), gamma (1,2 or 3), rho (1,2 or 3), and delta, pi, theta, and epsilon. This creates several possible pentameric arrangements, which also influence the pharmacological and physiological properties of the receptor. The complexity and heterogeneity of the receptors are further increased by the addition of short and long splice variants in several subunits and the existence of multiple allosteric binding sites and expansive ligands that can bind to the receptors. Therefore, a comprehensive understanding of the structure and function of the receptors is required to gain novel insights into the consequences of receptor dysfunction and subsequent drug development studies. Notably, advancements in computational-aided studies have facilitated the elucidation of residual interactions and exploring energy binding, which may otherwise be challenging to investigate. In this review, we aim to summarize the current understanding of the structure and function of GABA (A) receptors obtained from advancements in computational-aided applications.

关键词： GABA (A) receptors structure-function in silico and benzodiazepines

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The structure-function relationships and techno-functions of β-conglycinin

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FOOD CHEMISTRY 2025年 462卷 140950页

作者： Ashaolu, Tolulope Joshua Greff, Babett Varga, Laszlo Duy Tan Univ Inst Global Hlth Innovat Da Nang 550000 Vietnam Duy Tan Univ Fac Med Da Nang 550000 Vietnam SzechenyiIstvan Univ Dept Food Sci H-9200 Mosonmagyarovar Hungary

beta-conglycinin (beta-CG) is a prominent storage protein belonging to the globulin family in soybean (Glycine max) seeds. Along with other soybean proteins, it serves as an important source of essential amino acids and highquality nutrition. However, the digestibility and nutritional value of (3-CG are key factors affecting the nutritional profile of soy-based foods. The heterotrimeric, secondary, and quaternary structures of (3-CG, particularly the spatial arrangement of its alpha, alpha', and (3 subunits, influence its functional properties. Considering these aspects, (3-CG emerges as a significant protein with diverse applications in the food and health sectors. Therefore, this review explores (3-CG's composition, structure, function, health implications, and industrial uses. Salient discussions are presented on its molecular structure, nutrition, digestibility, allergenicity, and techno-functions including emulsification, solubility, gelling, and structure-function complexities. Overall, the multifaceted potential of (3-CG in the healthcare sector and the food industry is evident.

关键词： beta-conglycinin 7S protein Soybean structure-function Food industry

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Multiscale and multimodal signatures of structure-function coupling variability across the human neocortex

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NEUROIMAGE 2024年 302卷 120902-120902页

作者： Facca, Massimiliano Del Felice, Alessandra Bertoldo, Alessandra Padova Neurosci Ctr PNC Padua Italy Univ Padua Dept Neurosci Padua Italy Univ Padua Dept Informat Engn Padua Italy

The relationship between the brain's structural wiring and its dynamic activity is thought to vary regionally, implying that the mechanisms underlying structure-function coupling may differ depending on a region's position within the brain's hierarchy. To better bridge the gap between structure and function, it is crucial to identify the factors shaping this regionality, not only in terms of how static functional connectivity aligns with structure, but also regarding the time-domain variability of this interplay. Here we map structure - function coupling and its time-domain variability and relate them to the heterogeneity of the cortex. We show that these two properties split the cortical landscape into two districts anchored to the opposite ends of the brain's hierarchy. By looking at statistical relationships with layer-specific gene transcription, T1w/T2 w ratio, and synaptic density, we show that macro-scale structure-function coupling may be rooted in the brain's microstructure and meso-scale laminar specialization. Finally, we demonstrate that a lower and more variable alignment of function and structure may bestow the emergence of unique functional dynamics.

关键词： Multimodal neuroimaging Connectivity structure-function Hierarchy Connectome Network

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structure-function analysis for the development of peptide inhibitors for a Gram-positive quorum sensing system

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MOLECULAR MICROBIOLOGY 2022年第6期117卷 1464-1478页

作者： Abdullah, Iman Tajer Ulijasz, Andrew T. Girija, Umakhanth Venkatraman Tam, Sien Andrew, Peter Hiller, Natalia Luisa Wallis, Russell Yesilkaya, Hasan Univ Leicester Dept Resp Sci Leicester Leics England Univ Kirkuk Coll Sci Dept Biol Kirkuk Iraq Loyola Univ Chicago Dept Microbiol & Immunol Maywood IL USA Carnegie Mellon Univ Dept Biol Sci 4400 5th Ave Pittsburgh PA 15213 USA

The Streptococcus pneumoniae Rgg144/SHP144 regulator-peptide quorum sensing (QS) system is critical for nutrient utilization, oxidative stress response, and virulence. Here, we characterized this system by assessing the importance of each residue within the active short hydrophobic peptide (SHP) by alanine-scanning mutagenesis and testing the resulting peptides for receptor binding and activation of the receptor. Interestingly, several of the mutations had little effect on binding to Rgg144 but reduced transcriptional activation appreciably. In particular, a proline substitution (P21A) reduced transcriptional activation by 29-fold but bound with a 3-fold higher affinity than the wild-type SHP. Consistent with the function of Rgg144, the mutant peptide led to decreased utilization of mannose and increased susceptibility to superoxide generator paraquat. Pangenome comparison showed full conservation of P21 across SHP144 allelic variants. Crystallization of Rgg144 in the absence of peptide revealed a comparable structure to the DNA bound and free forms of its homologs suggesting similar mechanisms of activation. Together, these analyses identify key interactions in a critical pneumococcal QS system. Further manipulation of the SHP has the potential to facilitate the development of inhibitors that are functional across strains. The approach described here is likely to be effective across QS systems in multiple species.

关键词： inhibitor design quorum sensing Rgg transcriptional regulators Streptococcus pneumoniae structure-function

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The vertebrate sialylation machinery: structure-function and molecular evolution of GT-29 sialyltransferases

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GLYCOCONJUGATE JOURNAL 2023年第4期40卷 473-492页

作者： Harduin-Lepers, Anne Univ Lille Unite Glycobiol Structurale & Fonct CNRS UMR 8576 UGSF F-59000 Lille France

Every eukaryotic cell is covered with a thick layer of complex carbohydrates with essential roles in their social life. In Deuterostoma, sialic acids present at the outermost positions of glycans of glycoconjugates are known to be key players in cellular interactions including host-pathogen interactions. Their negative charge and hydrophilic properties enable their roles in various normal and pathological states and their expression is altered in many diseases including cancers. Sialylation of glycoproteins and glycolipids is orchestrated by the regulated expression of twenty sialyltransferases in human tissues with distinct enzymatic characteristics and preferences for substrates and linkages formed. However, still very little is known on the functional organization of sialyltransferases in the Golgi apparatus and how the sialylation machinery is finely regulated to provide the ad hoc sialome to the cell. This review summarizes current knowledge on sialyltransferases, their structure-function relationships, molecular evolution, and their implications in human biology.

关键词： Sialic acid Sialyltransferase structure-function Evolution Enzyme activity

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An idea to explore: Engaging high school students in structure-function studies of bacterial sortase enzymes and inhibitors - A comprehensive computational experimental pipeline

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BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION 2023年第6期51卷 606-615页

作者： Godse, Shivani Sapar, Tanvi Amacher, Jeanine F. Tesla STEM High Sch Redmond WA USA Western Washington Univ Dept Chem Bellingham WA USA Western Washington Univ Dept Chem 516 High St MS9150 Bellingham WA 98225 USA

High school science fairs provide an exceptional opportunity for students to gain experience with scientific research, and participation has positive outcomes with respect to chosen careers in the sciences. However, it can be challenging to engage high school students in university-level research outside of formal internship programs. Here, we describe an experimental pipeline for a computational structural biology project that engages high school students. Students are involved at every step of the investigation and utilize freely available software to dock inhibitors onto protein homologues, and then analyze the resulting complexes. Bacterial sortases are transpeptidases on the cell surface of Gram-positive bacteria and are a potential target for the development of antibiotics. Students modeled inhibitors bound to sortases from several organisms, asking questions about affinity and selectivity. Their project was ranked in the top 10% at both regional and state science fairs. This project design is easily adaptable to countless other protein systems and provides a pipeline for collaborative high school student/university professor inquiry.

关键词： computational enzymes high school education science project sortases structure-function

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Enriching Wheat Flour Dough with Dietary Fibers: A structure-function Relationship Investigation

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ACS FOOD SCIENCE & TECHNOLOGY 2024年第9期4卷 2176-2189页

作者： Douiri, Sabrine Ghorbal, Achraf Blecker, Christophe Dhouib, Wala Charradi, Khaled Richel, Aurore Attia, Hamadi Ghorbel, Dorra Univ Sfax Food Anal Valorizat & Safety Lab ENIS Sfax 3038 Tunisia Univ Carthage INSAT Tunis 1080 Tunisia Univ Liege Dept Food Sci & Formulat Gembloux Agrobio Tech B-5030 Gembloux Belgium Univ Gabes Res Unit Adv Mat Appl Mech Innovat Proc & Environm ISSAT Gabes Gabes 6072 Tunisia Technopk Borj Cedria Res & Technol Ctr Energy Nanomat & Syst Renewable Energy Lab BP 095 Hammam Lif Tunisia Univ Liege Lab Biomass & Green Technol Gembloux Agrobio Tech B-5030 Gembloux Belgium

This study investigated the impact of high-level replacement (from 2.5% to 10%) of dietary pea fiber (PF), insoluble wheat straw fiber (IWF), and carboxymethylcellulose (CMC) on wheat flour dough characteristics. IWF included 92.96% cellulose, whereas hemicellulose comprised the majority of PF's insoluble fibers (38.12%), followed by CMC (28.90%). FTIR data from lyophilized enriched dough samples showed that PF and IWF interacted with gluten proteins, improving gluten network structuration, but the CMC hindered it. Furthermore, FTIR data showed that the addition of IWF induced partial gluten dehydration. Doughs with a high DF content showed higher water absorption and resistance to extension but lower extensibility than the control. Dynamic rheology demonstrated that PF and IWF raised the elastic and viscous moduli while decreasing the loss factor, whereas CMC had the reverse effect, supporting structural results. TGA data indicated that CMC reduced the dough thermal stability by destroying the gluten network but IWF and PF increased it. The results revealed that PF and IWF, when added to wheat flour dough, interacted with gluten proteins, enhancing the dough's quality for baking applications. Conversely, the CMC degraded the dough by preventing the formation of the gluten network.

关键词： wheat flour dough dietary fiber gluten structure-function microstructure rheology thermal stability

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structure-function relationship of the platelet glycoprotein VI (GPVI) receptor: does it matter if it is a dimer or monomer?

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PLATELETS 2021年第6期32卷 724-732页

作者： Clark, Joanne C. Damaskinaki, Foteini-Nafsika Cheung, Yam Fung Hilaire Slater, Alexandre Watson, Steve P. Univ Birmingham Coll Med & Dent Sci Inst Cardiovasc Sci Level 1 IBR Birmingham B15 2TT W Midlands England Univ Birmingham Ctr Membrane Prot & Receptors COMPARE The Midlands England Univ Nottingham Ctr Membrane Prot & Receptors COMPARE The Midlands England Univ Nottingham Sch Pharm Biodiscovery Inst Univ Pk Nottingham England Maastricht Univ Cardiovasc Res Inst Maastricht CARIM Dept Biochem Maastricht Netherlands Leibniz Inst Analyt Wissensch ISAS eV Dept Bioanalyt Dortmund Germany

GPVI is a critical signaling receptor responsible for collagen-induced platelet activation and a promising anti-thrombotic target in conditions such as coronary artery thrombosis, ischemic stroke, and atherothrombosis. This is due to the ability to block GPVI while having minimal effects on hemostasis, making it a more attractive target over current dual-antiplatelet therapy (DAPT) with acetyl salicylic acid and P2Y(12) inhibitors where bleeding can be a problem. Our current understanding of how the structure of GPVI relates to function is inadequate and recent studies contradict each other. In this article, we summarize the structure-function relationships underlying the activation of GPVI by its major ligands, including collagen, fibrin(ogen), snake venom toxins and charged exogenous ligands such as diesel exhaust particles. We argue that contrary to popular belief dimerization of GPVI is not required for binding to collagen but serves to facilitate binding through increased avidity, and that GPVI is expressed as a mixture of monomers and dimers on resting platelets, with binding of multivalent ligands inducing higher order clustering.

关键词： GPVI Dimerization Platelets Ligands structure-function

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Comparison of machine learning approaches for structure-function modeling in glaucoma

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ANNALS OF THE NEW YORK ACADEMY OF SCIENCES 2022年第1期1515卷 237-248页

作者： Wong, Damon Chua, Jacqueline Bujor, Inna Chong, Rachel S. Nongpiur, Monisha E. Vithana, Eranga N. Husain, Rahat Aung, Tin Popa-Cherecheanu, Alina Schmetterer, Leopold SER NTU Adv Ocular Engn STANCE Singapore Singapore Nanyang Technol Univ Sch Chem & Biomed Engn Singapore Singapore Singapore Natl Eye Ctr Singapore Eye Res Inst 20 Coll RdLevel 6 Singapore 169856 Singapore Inst Mol & Clin Ophthalmol Basel Switzerland Carol Davila Univ Med & Pharm Bucharest Romania Natl Univ Singapore Yong Loo Lin Sch Med Singapore Singapore Emergency Univ Hosp Dept Ophthalmol Bucharest Romania Med Univ Vienna Dept Clin Pharmacol Vienna Austria Med Univ Vienna Ctr Med Phys & Biomed Engn Vienna Austria

To evaluate machine learning (ML) approaches for structure-function modeling to estimate visual field (VF) loss in glaucoma, models from different ML approaches were trained on optical coherence tomography thickness measurements to estimate global VF mean deviation (VF MD) and focal VF loss from 24-2 standard automated perimetry. The models were compared using mean absolute errors (MAEs). Baseline MAEs were obtained from the VF values and their means. Data of 832 eyes from 569 participants were included, with 537 Asian eyes for training, and 148 Asian and 111 Caucasian eyes set aside as the respective test sets. All ML models performed significantly better than baseline. Gradient-boosted trees (XGB) achieved the lowest MAE of 3.01 (95% CI: 2.57, 3.48) dB and 3.04 (95% CI: 2.59, 3.99) dB for VF MD estimation in the Asian and Caucasian test sets, although difference between models was not significant. In focal VF estimation, XGB achieved median MAEs of 4.44 [IQR 3.45-5.17] dB and 3.87 [IQR 3.64-4.22] dB across the 24-2 VF for the Asian and Caucasian test sets and was comparable to VF estimates from support vector regression (SVR) models. VF estimates from both XGB and SVR were significantly better than the other models. These results show that XGB and SVR could potentially be used for both global and focal structure-function modeling in glaucoma.

关键词： glaucoma machine learning optical coherence tomography structure-function visual field

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