Applications of phospholipid bilayer nanodiscs in the study of membranes and membrane proteins

Phospholipid bilayer Nanodiscs are novel model membranes derived from high-density lipoprotein particles and have proven to be useful in studies of membrane proteins. Membrane protein enzymology has been hampered by the inherent insolubility of membrane proteins in aqueous environments and has necessitated the use of model membranes such as liposomes and detergent-stabilized micelles. Current model membranes display a polydisperse particle size distribution and can suffer from problems of inconsistency and instability. It is also unclear how well they mimic biological lipid bilayers. In contrast, Nanodiscs, the particle size of which is constrained by a coat of scaffold proteins, are relatively monodisperse, stable model membranes with a "nativelike" lipid bilayer. Nanodiscs have already been used to study a variety of membrane proteins, including cytochrome P450s, seven-transmembrane proteins, and bacterial chemoreceptors. These proteins are simultaneously monomerized, solubilized, and incorporated into the well-defined membrane environment provided by Nanodiscs. Nanodiscs may also provide useful insights into the thermodynamics and biophysics of biological membranes and binding of small molecules to membranes.     

Structure and function of basement membranes

Basement membranes (BMs) are present in every tissue of the human body. All epithelium and endothelium is in direct association with BMs. BMs are a composite of several large glycoproteins and form an organized scaffold to provide structural support to the tissue and also offer functional input to modulate cellular function. While collagen I is the most abundant protein in the human body, type IV collagen is the most abundant protein in BMs. Matrigel is commonly used as surrogate for BMs in many experiments, but this is a tumor-derived BM-like material and does not contain all of the components that natural BMs possess. The structure of BMs and their functional role in tissues are unique and unlike any other class of proteins in the human body. Increasing evidence suggests that BMs are unique signal input devices that likely fine tune cellular function. Additionally, the resulting endothelial and epithelial heterogeneity in human body is a direct contribution of cell-matrix interaction facilitated by the diverse compositions of BMs.     

Structure and function of antifreeze proteins

High-resolution three-dimensional structures are now available for four of seven non-homologous fish and insect antifreeze proteins (AFPs). For each of these structures, the ice-binding site of the AFP has been defined by site-directed mutagenesis, and ice etching has indicated that the ice surface is bound by the AFP. A comparison of these extremely diverse ice-binding proteins shows that they have the following attributes in common. The binding sites are relatively flat and engage a substantial proportion of the protein's surface area in ice binding. They are also somewhat hydrophobic -- more so than that portion of the protein exposed to the solvent. Surface-surface complementarity appears to be the key to tight binding in which the contribution of hydrogen bonding seems to be secondary to van der Waals contacts.     

Structure and function of argonaute proteins

Argonaute (Ago) family proteins are multidomain proteins expressed in prokaryotic and eukaryotic organisms. In eukaryotes, Ago proteins are most well known for their roles in RNA silencing. In prokaryotes, the functions of Ago proteins are unknown, but based on their similarity to eukaryotic Ago proteins, they could be involved in nucleic acid-directed regulatory pathways related to RNA silencing. Recent structural and biochemical studies have shed new light on the function of this family of proteins. These studies reveal how these proteins recognize and cleave RNA and suggest a function for prokaryotic family members.     

Effective energy function for proteins in lipid membranes

A simple extension of the EEF1 energy function to heterogeneous membrane-aqueous media is proposed. The extension consists of (a) development of solvation parameters for a nonpolar phase using experimental data for the transfer of amino acid side-chains from water to cyclohexane, (b) introduction of a heterogeneous membrane-aqueous system by making the reference solvation free energy of each atom dependent on the vertical coordinate, (c) a modification of the distance-dependent dielectric model to account for reduced screening of electrostatic interactions in the membrane, and (d) an adjustment of the EEF1 aqueous model in light of recent calculations of the potential of mean force between amino acid side-chains in water. The electrostatic model is adjusted to match experimental observations for polyalanine, polyleucine, and the glycophorin A dimer. The resulting energy function (IMM1) reproduces the preference of Trp and Tyr for the membrane interface, gives reasonable energies of insertion into or adsorption onto a membrane, and allows stable 1-ns MD simulations of the glycophorin A dimer. We find that the lowest-energy orientation of melittin in bilayers varies, depending on the thickness of the hydrocarbon layer.     

哺乳动物中Kelch超家族蛋白的结构与功能

在不同生物体,如病毒、植物、真菌和哺乳动物中,几百种含Kelch构象的蛋白质已经被鉴定出来了,但大部分此类蛋白质的功能未知.而在哺乳动物中,已经有接近41种Kelch蛋白被报道.这些蛋白质在体内参与了很多重要的生理过程.根据Kelch蛋白的域结构不同,把这些哺乳动物中的Kelch蛋白分成了三类(BTB/Kelch蛋白,只含有Kelch结构域的蛋白质,及含其他结构域的Kelch蛋白),并把其已知的功能大致划分为5类:介导蛋白质-蛋白质的相互作用、参与蛋白质降解、信号传导、胞外功能及其他等.另外还认为Keap 1的Kelch结构域其晶体结构应该是研究哺乳动物Kelch蛋白的一个很好的参考模型.     

Structure and function of mismatch repair proteins

DNA mismatch repair is required for maintaining genomic stability and is highly conserved from prokaryotes to eukaryotes. Errors made during DNA replication, such as deletions, insertions and mismatched basepairs, are substrates for mismatch repair. Mismatch repair is strand-specific and targets only the newly synthesized daughter strand. To initiate mismatch repair in Escherichia coli, three proteins are essential, MutS, for mismatch recognition, MutH, for introduction of a nick in the target strand, and MutL, for mediating the interactions between MutH and MutS. Homologues of MutS and MutL important for mismatch repair have been found in nearly all organisms. Mutations in MutS and MutL homologues have been linked to increased cancer susceptibility in both mice and humans. Here, we review the crystal structures of the MutH endonuclease, a conserved ATPase fragment of MutL (LN40), and complexes of LN40 with various nucleotides. Based on the crystal structure, the active site of MutH has been identified and an evolutionary relationship between MutH and type II restriction endonucleases established. Recent crystallographic and biochemical studies have revealed that MutL operates as a molecular switch with its interactions with MutH and MutS regulated by ATP binding and hydrolysis. These crystal structures also shed light on the general mechanism of mismatch repair and the roles of Mut proteins in preventing mutagenesis.     

Structure and function of Toll-like receptor proteins

Beginning in 1997 with the identification of the first human homologue of the Drosophila protein Toll, a family of related molecules have been identified in both humans and other mammals. These Toll-like receptor (TLR) proteins appear to represent a conserved family of innate immune recognition receptors. TLR proteins share extended homology with receptors for the cytokines interleukin 1 (IL-1) and interleukin 18 (IL-18). These receptors are coupled to a signaling pathway that is conserved in mammals, insects, and plants, resulting in cellular activation, thereby stimulating innate immune defenses. A variety of bacterial and fungal products have been identified that serve as TLR ligands, and more recent studies have identified the first endogenous protein ligands for TLR proteins. While TLR signaling is likely to be a key feature of innate immune responses, these proteins may also regulate homeostasis via interaction with endogenous protein ligands.     

Structure and function of seed lipid-body-associated proteins

Many organisms among the different kingdoms store reserve lipids in discrete subcellular organelles called lipid bodies. In plants, lipid bodies can be found in seeds but also in fruits (olives, ...), and in leaves (plastoglobules). These organelles protect plant lipid reserves against oxidation and hydrolysis until seed germination and seedling establishment. They can be stabilized by specific structural proteins, namely the oleosins and caleosins, which act as natural emulsifiers. Considering the putative role of some of them in controlling the size of lipid bodies, these proteins may constitute important targets for seed improvement both in term of oil seed yield and optimization of technological processes for extraction of oil and storage proteins. We present here an overview of the data on the structure of these proteins, which are scarce, and sometimes contradictory and on their functional roles.     

Plant membranes: Structure,assembly and function

Book Review

Plant membranes: Structure, assembly and functionJ.L. Harwood and T.J. Walton (Eds.), London: The Biochemical Society, 1988, 251 pages. £25. ISBN 0-904498-23-9     

Non-ionic detergent assists formation of supercharged nanodiscs and insertion of membrane proteins

Nanodiscs are used to stabilize membrane proteins in a lipid environment and enable investigations of the function and structure of these. Membrane proteins are often only available in small amounts, and thus the stability and ease of use of the nanodiscs are essential. We have recently explored circularizing and supercharging membrane scaffolding proteins (MSPs) for nanodisc formation and found increased temporal stability at elevated temperatures. In the present study, we investigate six different supercharged MSPs and their ability to form nanodiscs: three covalently circularized and the three non-circularized, linear versions. Using standard reconstitution protocols using cholate as the reconstitution detergent, we found that two of the linear constructs formed multiple lipid-protein species, whereas adding n-Dodecyl-B-D-maltoside (DDM) with the cholate in the reconstitution gave rise to single-species nanodisc formation for these MSPs. For all MSPs, the formed nanodiscs were analyzed by small-angle X-ray scattering (SAXS), which showed similar structures for each MSP, respectively, suggesting that the structures of the formed nanodiscs are independent of the initial DDM content, as long as cholate is present. Lastly, we incorporated the membrane protein proteorhodopsin into the supercharged nanodiscs and observed a considerable increase in incorporation yield with the addition of DDM. For the three circularized MSPs, a single major species appeared in the size exclusion chromatography (SEC) chromatogram, suggesting monodisperse nanodiscs with proteorhodopsin incorporated, which is in strong contrast to the samples without DDM showing almost no incorporation and high polydispersity.     

昆虫固醇转运蛋白的结构与功能

在昆虫中, 胆固醇不仅是细胞膜的重要成分之一, 也是昆虫蜕皮激素生物合成的前体。由于昆虫体内缺少两种合成胆固醇所必需的关键性酶, 所以昆虫不能自主地从简单的前体化合物从头合成胆固醇, 而必须通过吸收食物中的甾醇转化为胆固醇来满足生长、发育和繁殖的需要。胆固醇在组织和细胞内的运输主要由固醇转运蛋白 (sterol carrier proteins, SCPs) 执行。因此, 对固醇转运蛋白结构与功能的研究对于阐明昆虫中固醇运输具有重要的意义。本文对固醇转运蛋白的基因和蛋白结构、 细胞内表达和定位、 翻译后修饰、 蛋白三维结构、底物特异性和可能的运输途径等方面的研究进展进行了综述, 并对其作为害虫防治分子靶标的可能性进行了初步的讨论。研究发现, 不同物种的SCP蛋白的基因编码形式和蛋白剪切形式不同; 双翅目昆虫埃及伊蚊Aedes aegypti和黑腹果蝇Drosophila melanogaster除了SCP-x基因可编码SCP-x和SCP-2蛋白外, 还有另外的SCP-2和类SCP-2 (SCP-2L)基因编码SCP-2和类SCP-2蛋白; 而鳞翅目昆虫棉贪夜蛾Spodoptera littoralis、 斜纹夜蛾Spodoptera litura和家蚕Bombyx mori中SCP-x 基因的表达和转录方式与脊椎动物的SCP-x 基因类似, 通过转录和翻译后剪切形成SCP-2蛋白。SCP-x和SCP-2蛋白定位于过氧化物酶体。SCP-2蛋白由5个α-螺旋和5个β-折叠组成, 其中α5-螺旋可影响蛋白与底物的结合。SCP-2蛋白以不同的亲和力与固醇、胆固醇衍生物、脂肪酸、脂酰辅酶A和磷脂等化合物结合。超表达斜纹夜蛾SlSCP-x 和SlSCP-2基因可增加细胞对胆固醇的吸收; 而利用RNAi技术抑制幼虫体内SlSCP-x表达, 可导致血淋巴中的胆固醇含量降低, 并导致幼虫生长缓慢, 蜕皮化蛹延迟。     

Structure and function of proteins involved in milk allergies

Allergy to milk proteins has been defined as any adverse reaction mediated by immunological mechanisms to one or several of proteins found in milk. The milk allergy has been classified according to the onset of symptoms as immediate or delayed type. The milk allergy seems to be manifested by three major proteins found in milk: α-lactalbumin, β-lactoglobulin and caseins. The structural comparison of allergenic sites in α-lactalbumin and β-lactoglobulin with the structure of lactoferrin has clearly shown that yet another major milk protein lactoferrin also possesses allergenic sites and thus may qualify to be an allergen. The heat treatment of milk proteins considerably reduces their allergenicity.     

Structure and function of heterotrimeric G proteins in plants

Heterotrimeric G proteins are mediators that transmit the external signals via receptor molecules to effector molecules. The G proteins consist of three different subunits: alpha, beta, and gamma subunits. The cDNAs or genes for all the alpha, beta, and gamma subunits have been isolated from many plant species, which has contributed to great progress in the study of the structure and function of the G proteins in plants. In addition, rice plants lacking the alpha subunit were generated by the antisense method and a rice mutant, Daikoku d1, was found to have mutation in the alpha-subunit gene. Both plants show abnormal morphology such as dwarfism, dark green leaf, and small round seed. The findings revealed that the G proteins are functional molecules regulating some body plans in plants. There is evidence that the plant G proteins participate at least in signaling of gibberellin at low concentrations. In this review, we summarize the currently known information on the structure of plant heterotrimeric G proteins and discuss the possible functions of the G proteins in plants.