真菌漆酶的结构与功能

漆酶是一种含铜的多酚氧化酶,能催化氧化酚类和芳香类化合物,同时伴随4个电子的转移,并将分子氧还原成水。漆酶结构的解析是阐明其催化作用机理、了解蛋白质结构与功能关系的基础。综述近年来对真菌漆酶蛋白结构及其功能研究的进展。     

真菌疏水蛋白的结构和功用

真菌疏水蛋白是一类具有强表面活性的分泌型小分子量蛋白质。疏水蛋白的重要特性是能在亲水—疏水界面通过自我组装形成一层紧密稳定的约10nm厚的两性蛋白膜。概述了疏水蛋白的结构和性质。总结了疏水蛋白的生理功能,并探讨它的各种应用。     

真菌疏水蛋白结构研究进展

真菌疏水蛋白是由高等丝状真菌产生的小分子量(10kD左右)具有双亲性的蛋白质,它们在真菌生长和发育中起着重要的作用。通过研究发现疏水蛋白具有极高的表面活性,可以在界面通过自组装形成双亲性的蛋白膜,从而改变界面的亲疏水性质。值得注意的是,疏水蛋白的不同功能可归因于其双亲性蛋白质结构,使得其在不同的亲水/疏水界面处自组装以形成两性蛋白膜。基于这样的性质,疏水蛋白已经获得了国内外各领域的广泛应用。疏水蛋白潜在的应用价值激励了人们对其蛋白结构的探究从而解释其自组装机理。此篇综述总结了近些年人们通过不同手段及研究方法来解释疏水蛋白发挥功能的结构基础。     

脂多糖结合蛋白的结构和功能

脂多糖（ＬＰＳ）结合蛋白（ＬＢＰ）是存在于下沉人和动物血清中的种糖蛋白,人血清中ＬＢＰ的正常浓度为５～１０μｇ／ｍｌ,急性反应期可升高到２００μｇ／ｍｌ,ＬＰＢ与ＬＰＳ中的类脂Ａ具有高度亲和性,可作为ＬＰＳ载体蛋白,催化ＬＰＳ与ＣＤ１４结合,刺激单核细胞、内皮细胞等,促进Ｔ痰性介绍的释放;ＬＢＰ还可作为调理素,促进单核细胞等吞噬调理后的ＬＰＳ和甘兰阴性细菌,故ＬＢＰ可以调节ＬＰＳ所致的炎症反应。Ｂ     

真菌Peroxins蛋白的性质和功能

过氧化物酶体(Peroxisome)是普遍存在于各种真核细胞中的一类单层膜的细胞器,其内所含的各种酶在细胞的生理代谢过程中发挥着重要作用。目前,在真菌中已报道30多种参与过氧化物酶体的组装、分化和遗传调控的蛋白,这些蛋白被称为Peroxins(编码基因为PEX,编码的蛋白为Pexp)。Peroxins还参与真菌的乙醛酸循环和脂肪酸代谢,并与真菌的致病性密切相关。近年来,随着基因组测序技术的发展和新实验技术手段的应用,Peroxins的功能在日益增多的真菌中被鉴定。本文对真菌中已报道Peroxins的种类及它们在不同真菌中的分布进行总结,对Peroxins的性质和功能进行评述。     

真菌G蛋白信号调控蛋白的功能研究进展

G蛋白信号途径是真菌细胞信号转导网络的枢纽,在细胞的各种生物学调控过程中具有重要作用。G蛋白信号调控蛋白(Rgulators of G protein signaling,RGS)是一类重要的G蛋白信号调控因子,能通过促进G蛋白α亚基(Gα)偶联的GTP水解,使Gα和Gβγ亚基发生聚合,导致G蛋白失活,从而迅速关闭与G蛋白偶联的信号途径。自从第一个RGS蛋白在酿酒酵母中被鉴定以来,目前已经有30多个RGS蛋白在重要的模式真菌中被报道,包括构巢曲霉、绿僵菌、稻瘟病菌、玉米赤霉菌、轮枝镰孢菌、新型隐球菌和白色念珠菌等。RGS蛋白在真菌的营养菌丝生长、产孢、毒素和色素生产、致病性和有性生殖等过程中发挥着重要作用。本文对真菌中已报道RGS蛋白的功能进行了总结,对真菌RGS蛋白的结构特征和调控机制进行了评述。     

冠状病毒S蛋白的结构和功能

冠状病毒S蛋白具有受体结合活性和膜融合活性,在组织嗜性、细胞融合和毒力等方面具有重要作用。本综述了S蛋白的一般结构特征及其与细胞受体和膜融合的关系,并介绍了最近发现的SARS病毒S蛋白与其他冠状病毒的异同。     

Zinc homeostasis and functions of zinc in the brain

The brain barrier system, i.e., the blood-brain and blood-cerebrospinal fluid barriers, is important for zinc homeostasis in the brain. Zinc is supplied to the brain via both barriers. A large portion of zinc serves as zinc metalloproteins in neurons and glial cells. Approximately 10% of the total zinc in the brain, probably ionic zinc, exists in the synaptic vesicles, and may serve as an endogenous neuromodulator in synaptic neurotransmission. The turnover of zinc in the brain is much slower than in peripheral tissues such as the liver. However, dietary zinc deprivation affects zinc homeostasis in the brain. Vesicular zinc-enriched regions, e.g., the hippocampus, are responsive to dietary zinc deprivation, which causes brain dysfunctions such as learning impairment and olfactory dysfunction. Olfactory recognition is reversibly disturbed by the chelation of zinc released from amygdalar neuron terminals. On the other hand, the susceptibility to epileptic seizures, which may decrease vesicular zinc, is also enhanced by zinc deficiency. Therefore, zinc homeostasis in the brain is closely related to neuronal activity. Even in adult animals and probably adult humans, adequate zinc supply is important for brain functions and prevention of neurological diseases.     

Structural studies of an engineered zinc biosensor reveal an unanticipated mode of zinc binding

Protein engineering was used previously to convert maltose-binding protein (MBP) into a zinc biosensor. Zn(2+) binding by the engineered MBP was thought to require a large conformational change from "open" to "closed", similar to that observed when maltose is bound by the wild-type protein. We show that although this re-designed MBP molecule binds Zn(2+) with high affinity as previously reported, it does not adopt a closed conformation in solution as assessed by small-angle X-ray scattering. High-resolution crystallographic studies of the engineered Zn(2+)-binding MBP molecule demonstrate that Zn(2+) is coordinated by residues on the N-terminal lobe only, and therefore Zn(2+) binding does not require the protein to adopt a fully closed conformation. Additional crystallographic studies indicate that this unexpected Zn(2+) binding site can also coordinate Cu(2+) and Ni(2+) with only subtle changes in the overall conformation of the protein. This work illustrates that the energetic barrier to domain closure, which normally functions to maintain MBP in an open concentration in the absence of ligand, is not easily overcome by protein design. A comparison to the mechanism of maltose-induced domain rearrangement is discussed.     

Importance of long-time simulations for rare event sampling in zinc finger proteins

Molecular dynamics (MD) simulation methods have seen significant improvement since their inception in the late 1950s. Constraints of simulation size and duration that once impeded the field have lessened with the advent of better algorithms, faster processors, and parallel computing. With newer techniques and hardware available, MD simulations of more biologically relevant timescales can now sample a broader range of conformational and dynamical changes including rare events. One concern in the literature has been under which circumstances it is sufficient to perform many shorter timescale simulations and under which circumstances fewer longer simulations are necessary. Herein, our simulations of the zinc finger NEMO (2JVX) using multiple simulations of length 15, 30, 1000, and 3000 ns are analyzed to provide clarity on this point.     

菌根真菌的生理生态功能

菌根真菌是土壤中重要生物成员之一,不仅具有丰富的遗传多样性和物种多样性,其功能也是丰富多样,主要体现在：1）影响陆生植物起源、进化、演化与分布;2）促进植物的生长发育;3）提高植物的抗逆性;4）修复污染与退化土壤、改善土壤质量与健康状况;5）促进农林牧业的生产;6）保持生态平衡、稳定生态系统及其可持续生产力.随着技术发展和研究的深入,菌根真菌新功能将会不断被发现.     

Selection of synthetic proteins to modulate the human frataxin function

Frataxin is a kinetic activator of the mitochondrial supercomplex for iron-sulfur cluster assembly. Low frataxin expression or a decrease in its functionality results in Friedreich's Ataxia (FRDA). With the aim of creating new molecular tools to study this metabolic pathway, and ultimately, to explore new therapeutic strategies, we have investigated the possibility of obtaining small proteins exhibiting a high affinity for frataxin. In this study, we applied the ribosome display approach, using human frataxin as the target. We focused on Affi_224, one of the proteins that we were able to select after five rounds of selection. We have studied the interaction between both proteins and discussed some applications of this specific molecular tutor, concerning the modulation of the supercomplex activity. Affi_224 and frataxin showed a K_D value in the nanomolar range, as judged by surface plasmon resonance analysis. Most likely, it binds to the frataxin acidic ridge, as suggested by the analysis of chemical shift perturbations (nuclear magnetic resonance) and computational simulations. Affi_224 was able to increase Cys NFS1 desulfurase activation exerted by the FRDA frataxin variant G130V. Importantly, Affi_224 interacts with frataxin in a human cellular model. Our results suggest quaternary addition may be a new tool to modulate frataxin function in vivo. Nevertheless, more functional experiments under physiological conditions should be carried out to evaluate Affi_224 effectiveness in FRDA cell models.     

菌根真菌的生理生态功能

菌根真菌是土壤中重要生物成员之一,不仅具有丰富的遗传多样性和物种多样性,其功能也是丰富多样,主要体现在：1）影响陆生植物起源、进化、演化与分布;2）促进植物的生长发育;3）提高植物的抗逆性;4）修复污染与退化土壤、改善土壤质量与健康状况;5）促进农林牧业的生产;6）保持生态平衡、稳定生态系统及其可持续生产力.随着技术发展和研究的深入,菌根真菌新功能将会不断被发现.     

Local motions in a benchmark of allosteric proteins

Allosteric proteins have been studied extensively in the last 40 years, but so far, no systematic analysis of conformational changes between allosteric structures has been carried out. Here, we compile a set of 51 pairs of known inactive and active allosteric protein structures from the Protein Data Bank. We calculate local conformational differences between the two structures of each protein using simple metrics, such as backbone and side-chain Cartesian displacement, and torsion angle change and rearrangement in residue-residue contacts. Thresholds for each metric arise from distributions of motions in two control sets of pairs of protein structures in the same biochemical state. Statistical analysis of motions in allosteric proteins quantifies the magnitude of allosteric effects and reveals simple structural principles about allostery. For example, allosteric proteins exhibit substantial conformational changes comprising about 20% of the residues. In addition, motions in allosteric proteins show strong bias toward weakly constrained regions such as loops and the protein surface. Correlation functions show that motions communicate through protein structures over distances averaging 10-20 residues in sequence space and 10-20 A in Cartesian space. Comparison of motions in the allosteric set and a set of 21 nonallosteric ligand-binding proteins shows that nonallosteric proteins also exhibit bias of motion toward weakly constrained regions and local correlation of motion. However, allosteric proteins exhibit twice as much percent motion on average as nonallosteric proteins with ligand-induced motion. These observations may guide efforts to design flexibility and allostery into proteins.     

Disorder transitions and conformational diversity cooperatively modulate biological function in proteins

Structural differences between conformers sustain protein biological function. Here, we studied in a large dataset of 745 intrinsically disordered proteins, how ordered‐disordered transitions modulate structural differences between conformers as derived from crystallographic data. We found that almost 50% of the proteins studied show no transitions and have low conformational diversity while the rest show transitions and a higher conformational diversity. In this last subset, 60% of the proteins become more ordered after ligand binding, while 40% more disordered. As protein conformational diversity is inherently connected with protein function our analysis suggests differences in structure‐function relationships related to order‐disorder transitions.     

Application of biasing‐potential replica‐exchange simulations for loop modeling and refinement of proteins in explicit solvent

Comparative or homology modeling of a target protein based on sequence similarity to a protein with known structure is widely used to provide structural models of proteins. Depending on the target‐template similarity these model structures may contain regions of limited structural accuracy. In principle, molecular dynamics (MD) simulations can be used to refine protein model structures and also to model loop regions that connect structurally conserved regions but it is limited by the currently accessible simulation time scales. A recently developed biasing potential replica exchange (BP‐REMD) method was used to refine loops and complete decoy protein structures at atomic resolution including explicit solvent. In standard REMD simulations several replicas of a system are run in parallel at different temperatures allowing exchanges at preset time intervals. In a BP‐REMD simulation replicas are controlled by various levels of a biasing potential to reduce the energy barriers associated with peptide backbone dihedral transitions. The method requires much fewer replicas for efficient sampling compared with T‐REMD. Application of the approach to several protein loops indicated improved conformational sampling of backbone dihedral angle of loop residues compared to conventional MD simulations. BP‐REMD refinement simulations on several test cases starting from decoy structures deviating significantly from the native structure resulted in final structures in much closer agreement with experiment compared to conventional MD simulations. Proteins 2010. © 2010 Wiley‐Liss, Inc.