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Ensemble-function relationships: From qualitative to quantitative relationships between protein structure and function

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JOURNAL OF STRUCTURAL BIOLOGY 2025年第1期217卷 108152页

作者： Yabukarski, Filip Bristol Myers Squibb Prot Homeostasis Struct Biol Grp San Diego CA 92121 USA

structure-function relationships are deeply rooted in modern biochemistry and structural biology and have provided the basis for our understanding of how protein structure defines function. While structure-function relationships continue to provide invaluable qualitative information, they cannot, in principle, provide the quantitative information ultimately needed to fully understand how proteins function and to make quantitative predictions about changes in activity from changes in sequence and structure. These limitations appear to arise from fundamental principles of physics, which dictate that proteins exist as interchanging ensembles of conformations, rather than as static structures that underly conventional structure-function relationships. This perspective discusses the concept of ensemble-function relationships as quantitative relationships that build on and extend traditional structure-function relationships. The concepts of free energy landscapes and conformational ensembles and their application to proteins are reviewed. The perspective summarizes a range of approaches that can provide conformational ensemble information and focuses on X-ray crystallography methods for obtaining experimental protein conformational ensembles. Focusing on enzymes as archetypes of protein function, recent literature examples are reviewed that used ensemble-function relationships to understand how protein residues contribute to function and how changes in protein sequence and structure impact activity, leading to new models and providing previously inaccessible mechanistic insights. Potential applications of conformational ensembles and ensemble-function relationships to protein design are examined. The perspective concludes with current limitations of the ensemble-function relationships and potential paths forward toward the next generation of quantitative ensemble-function models.

关键词： Protein structure structure-function relationships X-ray crystallography Conformational ensembles Ensemble-function relationships

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structure-function relationships in Hydrophobins: Probing the Role of Charged Side Chains

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APPLIED AND ENVIRONMENTAL MICROBIOLOGY 2013年第18期79卷 5533-5538页

作者： Lienemann, Michael Gandier, Julie-Anne Joensuu, Jussi J. Iwanaga, Atsushi Takatsuji, Yoshiyuki Haruyama, Tetsuya Master, Emma Tenkanen, Maija Linder, Markus B. VTT Tech Res Ctr Finland Espoo Finland Univ Toronto Dept Chem Engn & Appl Chem Toronto ON Canada Kyushu Inst Technol Dept Biol Funct & Engn Kitakyushu Fukuoka 804 Japan Univ Helsinki Dept Food & Environm Sci Helsinki Finland Aalto Univ Sch Chem Technol Dept Biotechnol & Chem Technol Espoo Finland

Hydrophobins are small fungal proteins that are amphiphilic and have a strong tendency to assemble at interfaces. By taking advantage of this property, hydrophobins have been used for a number of applications: as affinity tags in protein purification, for protein immobilization, such as in foam stabilizers, and as dispersion agents for insoluble drug molecules. Here, we used site-directed mutagenesis to gain an understanding of the molecular basis of their properties. We especially focused on the role of charged amino acids in the structure of hydrophobins. For this purpose, fusion proteins consisting of Trichoderma reesei hydrophobin I (HFBI) and the green fluorescent protein (GFP) that contained various combinations of substitutions of charged amino acids (D30, K32, D40, D43, R45, K50) in the HFBI structure were produced. The effects of the introduced mutations on binding, oligomerization, and partitioning were characterized in an aqueous two-phase system. It was found that some substitutions caused better surface binding and reduced oligomerization, while some showed the opposite effects. However, all mutations decreased partitioning in surfactant systems, indicating that the different functions are not directly correlated and that partitioning is dependent on finely tuned properties of hydrophobins. This work shows that not all functions in self-assembly are connected in a predictable way and that a simple surfactant model for hydrophobin function is insufficient.

关键词： relationships hydrophobins Probing assemblies structure-function relationships hydrophobin partitions Exploration with a probe Green Fluorescent Proteins

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Multiscale structure and function of the aortic valve apparatus

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PHYSIOLOGICAL REVIEWS 2024年第4期104卷 1487-1532页

作者： El-Nashar, Hussam Sabry, Malak Tseng, Yuan-Tsan Francis, Nadine Latif, Najma Parker, Kim H. Moore Jr, James E. Yacoub, Magdi H. Magdi Yacoub Fdn Aswan Heart Res Ctr Cairo Egypt Imperial Coll London Dept Bioengn London England Kings Coll London Dept Biomed Engn London England Magdi Yacoub Inst Heart Sci Ctr London England Imperial Coll London Natl Heart & Lung Inst London England

Whereas studying the aortic valve in isolation has facilitated the development of life-saving procedures and technologies, the dynamic interplay of the aortic valve and its surrounding structures is vital to preserving their function across the wide range of conditions encountered in an active lifestyle. Our view is that these structures should be viewed as an integrated functional unit, here referred to as the aortic valve apparatus (AVA). The coupling of the aortic valve and root, left ventricular outflow tract, and blood circulation is crucial for AVA's functions: unidirectional flow out of the left ventricle, coronary perfusion, reservoir function, and support of left ventricular function. In this review, we explore the multiscale biological and physical phenomena that underlie the simultaneous fulfillment of these functions. A brief overview of the tools used to investigate the AVA, such as medical imaging modalities, experimental methods, and computational modeling, specifically fluid-structure interaction (FSI) simulations, is included. Some pathologies affecting the AVA are explored, and insights are provided on treatments and interventions that aim to maintain quality of life. The concepts explained in this article support the idea of AVA being an integrated functional unit and help identify unanswered research questions. Incorporating phenomena through the molecular, micro, meso, and whole tissue scales is crucial for understanding the sophisticated normal functions and diseases of the AVA.

关键词： aortic root aortic valve biomechanics molecular, developmental and cellular mechanisms structure-function relationships

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HadBD dehydratase from Mycobacterium tuberculosis fatty acid synthase type II: A singular structure for a unique function

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PROTEIN SCIENCE 2024年第4期33卷 e4964-e4964页

作者： Bories, Pascaline Rima, Julie Tranier, Samuel Marcoux, Julien Grimoire, Yasmina Tomaszczyk, Mathilde Launay, Anne Fata, Karine Marrakchi, Hedia Burlet-Schiltz, Odile Mourey, Lionel Ducoux-Petit, Manuelle Bardou, Fabienne Bon, Cecile Quemard, Annaik Univ Toulouse III Paul Sabatier UPS Univ Toulouse Inst Pharmacol & Biol Structurale IPBS CNRS Toulouse France Univ Toulouse Univ Toulouse III Paul Sabatier UPS Serv TP Biochim Toulouse France IPBS CNRS UPS UMR5089 205 Route NarbonneBP 64182 F-31077 Toulouse 4 France

Worldwide, tuberculosis is the second leading infectious killer and multidrug resistance severely hampers disease control. Mycolic acids are a unique category of lipids that are essential for viability, virulence, and persistence of the causative agent, Mycobacterium tuberculosis (Mtb). Therefore, enzymes involved in mycolic acid biosynthesis represent an important class of drug targets. We previously showed that the (3R)-hydroxyacyl-ACP dehydratase (HAD) protein HadD is dedicated mainly to the production of ketomycolic acids and plays a determinant role in Mtb biofilm formation and virulence. Here, we discovered that HAD activity requires the formation of a tight heterotetramer between HadD and HadB, a HAD unit encoded by a distinct chromosomal region. Using biochemical, structural, and cell-based analyses, we showed that HadB is the catalytic subunit, whereas HadD is involved in substrate binding. Based on HadBDMtb crystal structure and substrate-bound models, we identified determinants of the ultra-long-chain lipid substrate specificity and revealed details of structure-function relationship. HadBDMtb unique function is partly due to a wider opening and a higher flexibility of the substrate-binding crevice in HadD, as well as the drastically truncated central alpha-helix of HadD hotdog fold, a feature described for the first time in a HAD enzyme. Taken together, our study shows that HadBDMtb, and not HadD alone, is the biologically relevant functional unit. These results have important implications for designing innovative antivirulence molecules to fight tuberculosis, as they suggest that the target to consider is not an isolated subunit, but the whole HadBD complex.

关键词： (3R)-hydroxyacyl-ACP dehydratase HadBD catalytic subunit crystal structure fatty acid synthase type II system hotdog helix Mycobacterium tuberculosis mycolic acids structure-function relationships substrate-binding subunit ultra-long-chain substrates

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Heme-based Oxygen Sensors: structure-function relationships

Heme-based Oxygen Sensors: Structure-function Relationships

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2014第五届国际工业酶与生物催化大会

作者： Toru Shimizu Shantou University Medical College

Heme proteins play important roles in O2 storage(myoglobin), O2 transfer(hemoglobin), O2 activation(cytochrome P450), electron transfer(cytochromes), and many more functions. In addition to these well-known prototypical heme proteins, is an emerging class of heme-based oxygen sensors. In general, the heme-based oxygen sensor is composed of two domains: an N-terminal sensor domain and a C-terminal functional domain. The heme iron complex bound to the sensor domain acts as the O2 sensor. Association of the O2 molecule to the heme iron complex or dissociation from it alters the protein structure in the heme-bound sensor domain. In this process, binding of the O2 molecule is the first signal and the protein structural alteration near the heme-bound site becomes the second signal. This second signal is then transduced to the C-terminal functional domain, switching on(or off) the associated activity, which may consist of phosphodiesterase(PDE), diguanylate cyclase(DGC), histidine kinase(HK), and methyl-accepting chemotaxis. Our group has been studying the structure and function relationships of representative oxygen sensors such as Ec DOS, YddV and AfGcHK that are involved in PDE, DGC and HK reactions, respectively. Interestingly,catalytic activities of those oxygen sensors are regulated by NO and CO. Furthermore, enhancement of the PDE activity of Ec DOS by H2 S is novel to be noted. I discuss the molecular mechanism of the roles of the heme iron complex and the gaseous molecule in the catalytic regulation of those oxygen sensors.

关键词： Heme-based Oxygen Sensors structure-function relationships

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Ion type-based formation rules and functional properties of polysaccharide-starch aerogels with chitooligosaccharide, xanthan gum, and locust bean gum: A comparative study

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FOOD RESEARCH INTERNATIONAL 2025年 202卷 115674页

作者： Lin, Qian Zhao, Wenqing Liang, Wei Wang, Xinyu Zeng, Jie Gao, Haiyan Li, Wenhao Northwest A&F Univ Coll Food Sci & Engn Yangling 712100 Shaanxi Peoples R China Henan Inst Sci & Technol Sch Food Sci Xinxiang 453003 Henan Peoples R China

Polysaccharide ion types may play a regulatory role in the functionalization development of starchpolysaccharide-based gels, although the relevant mechanisms remain to be elucidated. This study provides a simple and effective strategy for developing gels suitable for different adsorption scenarios by adding different ratios and ion types of polysaccharides. The addition of locust bean gum (LBG, neutral charge) and xanthan gum (XG, -/negative charge) increased the viscosity of wheat gels, with XG increasing more significantly at the same addition. Meanwhile, chito oligosaccharides (COS, +/positive charge) decreased the viscosity of wheat gels. SEM showed that the gels' pore size became larger after adding polysaccharides. FT-IR results showed that adding all three polysaccharides resulted in a more disordered structure and a decrease in the hardness of the gels. However, due to the different charges, the adsorption property results showed that adding the anionic polysaccharide XG increased the methylene blue adsorption capacity dramatically, while COS showed the opposite trend. The obtained results are expected to facilitate the high-value processing and utilization of polysaccharide resources and the on-demand construction of gel materials with promising textural or adsorption performance in food processing or industrial manufacture.

关键词： Different ionic polysaccharides Starch-polysaccharide composite gels Interaction mechanism structure-function relationships

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Linking xylem structure and function: the comparative method in from the cold

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NEW PHYTOLOGIST 2022年第3期235卷 815-820页

作者： Olson, Mark E. Univ Nacl Autonoma Mexico Inst Biol Tercer Circuito SnCiudad Univ Mexico City 04510 DF Mexico

The field of functional xylem biology aims to understand how xylem structure gives rise to xylem function. This effort requires understanding processes at very tiny scales, from nanometric-level variation in the intricacies of pit membrane structure (Li et al., 2016;Kaack et al., 2021) to the intermolecular interactions involved in the formation of gas bubbles in xylem sap (Schenk et al., 2015, 2017). It requires understanding how these very smalllevel events give rise to whole-plant properties, such as bulk water flow through the xylem or whole-plant transpiration and carbon (C) capture (Tyree & Ewers, 1991;Comstock & Sperry, 2000;Enquist et al., 2007). It is necessary to understand how some individuals within populations in the distant past survived and reproduced better than their conspecifics all because of certain structure-function relations manifest at these different scales (Carlquist, 1975). This understanding extends to estimating forest productivity at a landscape level, modeling `average' plant structure, or predicting which trees will die across a drought-stricken landscape (West et al., 1999;Christoffersen et al., 2016;Trugman et al., 2021). Given the size of the task facing the field, the toolbox of xylem functional biology is a very large one indeed. The recent study published in this issue of New Phytologist by Savage et al. (2022;pp. 953-964) is a model of how this toolbox can, and must, seamlessly integrate data and theory from across levels, from the very small scale of processes within xylem conduits to the millionsplus years scale of evolutionary time. Before highlighting just some of the inferential richness in Savage et al. (2022), let me first explore why the integration of levels is such a challenge, and the empirical turn that this challenge demands.

关键词： cold tolerance evolution freezing-induced embolism leaf phenology north-temperate forests structure-function relationships xylem

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High spatiotemporal resolution transmission electron microscopy and diffraction: Progress from subnanosecond laser-induced structural dynamics to femtosecond quantum tomography

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NANO TODAY 2025年 61卷

作者： Aseyev, Sergei A. Mironov, Boris N. Poydashev, Denis G. Ryabov, Evgeny A. Miller, R. J. Dwayne Li, Zheng Zhang, Ming Ischenko, Anatoly A. RAS Inst Spect Fizicheskaya St 5 Moscow 108840 Russia Univ Toronto Dept Chem Toronto ON M5S 3H6 Canada Univ Toronto Dept Phys Toronto ON M5S 3H6 Canada Peking Univ State Key Lab Mesoscop Phys Beijing 100871 Peoples R China Peking Univ Collaborat Innovat Ctr Quantum Matter Sch Phys Beijing 100871 Peoples R China Shanxi Univ Collaborat Innovat Ctr Extreme Opt Taiyuan 030006 Shanxi Peoples R China Peking Univ Yangtze Delta Inst Optoelect Nantong 226010 Jiangsu Peoples R China MIREA Russian Technol Univ Inst Fine Chem Technol Dept Analyt Chem Vernadsky Ave 86 Moscow 119571 Russia

The use of short photoelectron pulses, pioneered in the 1980s, opened up the possibility of studying structural dynamics with high spatiotemporal resolution. The combination of nano-pico-femtosecond lasers with electron- based technology has become extremely fruitful for observing the behavior of atoms and molecules on their natural length and time scales. In imaging mode, this concept soon led to the creation of 4D transmission electron microscopy. In the electron diffraction mode, the achievement of ultrabright electron sources provided a unique opportunity to shoot molecular movies with atomic resolution. These sources are at their fundamental space charge limit with sufficient brightness to literally light up atomic motions. The high sensitivity of this approach, combined with low radiation damage, made it possible to atomically resolve reaction dynamics with nanograms of material. In contrast to the X-ray free electron lasers (XFELs), the development of ultrabright electron sources made it possible to conduct experiments on very thin films of promising materials in small-scale facilities in standard laboratories. The extension to quantum tomography has recently opened a new page in the study of matter using short electron bunches. Here we review the development of ultrafast transmission electron microscopy and diffraction techniques that enable detection of structural dynamics on the primary timescales.

关键词： Ultrafast transmission electron microscopy Simultaneous real space imaging Structural dynamics structure-function relationships Ultrafast laser-induced processes Transition state crossing Femtosecond quantum tomography

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Exopolysaccharide production by salt-tolerant bacteria: Recent advances, current challenges, and future prospects

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INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES 2024年第Part2期264卷 130731页

作者： Gan, Longzhan Huang, Xin He, Zhicheng He, Tengxia Guizhou Univ Coll Life Sci Key Lab Plant Resource Conservat & Germplasm Innov Minist Educ Guiyang 550025 Guizhou Peoples R China

Natural biopolymers derived from exopolysaccharides (EPSs) are considered eco-friendly and sustainable alternatives to available traditional synthetic counterparts. Salt-tolerant bacteria inhabiting harsh ecological niches have evolved a number of unique adaptation strategies allowing them to maintain cellular integrity and assuring their long-term survival;among these, producing EPSs can be adopted as an effective strategy to thrive under high-salt conditions. A great diversity of EPSs from salt-tolerant bacteria have attracted widespread attention recently. Because of factors such as their unique structural, physicochemical, and functional characteristics, EPSs are commercially valuable for the global market and their application potential in various sectors is promising. However, large-scale production and industrial development of these biopolymers are hindered by their low yields and high costs. Consequently, the research progress and future prospects of salt-tolerant bacterial EPSs must be systematically reviewed to further promote their application and commercialization. In this review, the structure and properties of EPSs produced by a variety of salt-tolerant bacterial strains isolated from different sources are summarized. Further, feasible strategies for solving production bottlenecks are discussed, which provides a scientific basis and direct reference for more scientific and rational EPS development.

关键词： Biopolymer Exopolysaccharide Extremophile Salt-tolerant bacteria Biosynthesis structure-function relationships Production strategy

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Defects in Inorganic Mechanoluminescent Phosphors: Insights and Impacts

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ADVANCED functionAL MATERIALS 2025年

作者： Li, Wenhao Wu, Sheng Ren, Jing Xiong, Puxian Harbin Engn Univ Coll Phys & Optoelect Engn Key Lab Photon Mat & Devices Phys Ocean Applicat Minist Ind & Informat Technol China Harbin 150001 Peoples R China South China Normal Univ Guangdong Basic Res Ctr Excellence Struct & Fundam Sch Phys Guangdong Prov Key Lab Quantum Engn & Quantum Mat Guangzhou 510006 Peoples R China Univ Hong Kong Dept Elect & Elect Engn Hong Kong 999077 Peoples R China

Mechanoluminescence (ML), the light emission of materials in response to mechanical stimuli, has gained significant attention in various fields due to the in situ and real-time "force to light" converting ability. Defects dominate the ML process, either for accommodating carriers or as sites for carrier recombination. However, comprehensive discussions on ML-based defects are rarely reported. The review opens with an exploration of recent progress in ML research, highlighting the central role of defects in ML. A range of defect types commonly exist in ML materials are firstly introduced, which aims to highlight the profound influences on ML. Subsequently reported defect-dominated phosphors are researched to elucidate the intricate relationship between specific defect types and their influence on ML performance, shedding light on the underlying luminescence mechanisms. Afterward, experimental techniques for defect characterization are also researched to demonstrate how defects work in ML. The role of computational modeling is confirmed to act as a powerful tool for investigating the atomistic mechanisms of defect-related processes and enabling precise control of defects in ML materials. In conclusion, this mini-review underscores the centrality of defects in ML materials, offering an integrated perspective on their profound influence and potential to guide future research endeavors.

关键词： charge carrier defect inorganic luminescence mechanoluminescence structure-function relationships

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