Comparative 11A structure of two molluscan hemocyanins from 3D cryo-electron microscopy

Hemocyanins are giant extracellular proteins that transport oxygen in the hemolymph of many molluscs. Molluscan hemocyanins are cylindrical decamers or didecamers of a 350-400 kDa subunit that contains seven or eight different covalently linked globular functional units (FUs), arranged in a linear manner. Each FU carries a single copper active site and reversibly binds one dioxygen molecule. As a consequence, the decamer can carry up to 70 or 80 O(2) molecules. Although complete sequence information is now available from several molluscan hemocyanins, many details of the quaternary structure are still unclear, including the topology of the 10 subunits within the decamer. Here we show 3D reconstructions from cryo-electron micrographs of the hemocyanin decamer of Nautilus pompilius (Cephalopoda) and Haliotis tuberculata (Gastropoda) at a resolution of 11A (FSC(1/2-bit) criterion). The wall structure of both hemocyanins is very similar and shows, as in previous reconstructions, three tiers with 20 functional units each that encircle the cylinder wall, and the 10 oblique minor and major wall grooves. However, the six types of wall FUs of the polypeptide subunit, termed a-b-c-d-e-f, are now for the first time individually discernable by their specific orientation, shape, and connections. Also, the internal collar complex of the decamers shows superior resolution which, in this case, reveals striking differences between the two hemocyanins. The five arcs (FU-g pairs) of the central collar (in both hemocyanins) and the five slabs (FU-h pairs) of the peripheral collar (only present in Haliotis hemocyanin), as well as their connections to the wall and to each other are now more clearly defined. The arc is attached to the wall through a feature termed the anchor, a previously undescribed structural element of the hemocyanin wall.     

Binding and Fluorescence Resonance Energy Transfer (FRET) of Ruthenium(II)-Bipyridine-Calixarene System with Proteins—Experimental and Docking Studies

The investigation of the interaction of ruthenium(II)-bipyridine-tert-butylcalix[4]arene complexes (Rubc2 and Rubc3) with proteins (BSA and ovalbumin) using absorption, emission, excited state lifetime and circular dichroism techniques and by docking studies show that luminophore-receptor system bind strongly with proteins. An enhancement of absorption as well as emission intensity of Ru(II)-calixarene complexes in the presence of proteins, but the quenching of the emission intensity of proteins in the presence of Ru(II)-calixarene complexes are the interesting observations. The enhancement of emission intensity of Ru(II)-calixarene complex, in the presence of proteins, is due to the fluorescence resonance energy transfer (FRET) from protein to Ru(II)-calixarene complex. Among the two Ru(II)-calixarene complexes synthesized Rubc3 has more efficient binding and energy transfer than Rubc2 and BSA, with a large cavity size, has the advantage for binding over ovalbumin. Docking studies reveal that the presence of tert-butylcalix[4]arene moiety in Ru(II)-calixarene complexes facilitates binding with proteins. After the binding of Rubc2 and Rubc3 with proteins, the nearby fluorophores present in proteins are in optimal distance from the ruthenium centre for efficient FRET process to occur.     

The Competitive Dynamic Binding of Some Blood Proteins Adsorbed on Gold Nanoparticles

Nanoparticle (NP) surfaces are modified immediately by the adsorption of proteins when injected into human blood, leading to the formation of a protein corona. The protein‐coated NPs may be recognized by living cells. Furthermore, the adsorption of serum proteins is a continuous competitive dynamic process that is the key to exploring the bioapplication and biosafety of NPs. In this study, the competitive dynamic adsorption of some serum proteins on gold nanoparticles (AuNPs) is investigated by fluorescence emission, dynamic light scattering, and sodium dodecyl sulfate‐polyacrylamide gel electrophoresis. Serum proteins with different AuNPs binding affinities are used to address the competitive dynamic process of protein‐AuNP interactions in vitro. The results show that more abundant serum proteins, such as human serum albumin, adsorb on AuNPs first, and then the higher binding affinity and lower concentration serum proteins, such as fibrinogen (FIB), replace the abundant and lower binding affinity serum proteins. However, the lower binding affinity serum proteins, such as hemoglobin, do not replace the higher binding affinity proteins from the protein‐AuNP conjugates. During the dynamic exchange process, the larger the binding affinities difference between two proteins, the faster the exchange rate. This dynamic exchange process usually takes longer in inner protein‐AuNP conjugates (hard corona) than the external surface of protein‐AuNP conjugates (soft corona).     

蛋白质顺磁标记技术与生物核磁共振中的赝接触位移

未配对电子与蛋白质分子自旋核的作用能提供丰富的长程结构信息,这些顺磁信息通常可用顺磁弛豫增强、赝接触位移和残余偶极耦合描述,其中赝接触位移包含生物大分子内重要的距离和角度信息.稀土离子具有相似的配位化学性质和不同的顺磁物理特性,而大多稀土离子具有磁各向异性,在与大分子作用过程中会产生赝接触位移.由于大多数蛋白质没有顺磁中心,获得这些顺磁信息需要通过定点选择标记蛋白质来实现.该文旨在对近年来蛋白质顺磁标记的方法和进展进行介绍,在顺磁标记基础上阐述赝接触位移在结构生物学中的应用.     

Molecular properties of muscarinic acetylcholine receptors

Muscarinic acetylcholine receptors, which comprise five subtypes (M₁-M₅ receptors), are expressed in both the CNS and PNS (particularly the target organs of parasympathetic neurons). M₁-M₅ receptors are integral membrane proteins with seven transmembrane segments, bind with acetylcholine (ACh) in the extracellular phase, and thereafter interact with and activate GTP-binding regulatory proteins (G proteins) in the intracellular phase: M₁, M₃, and M₅ receptors interact with Gq-type G proteins, and M₂ and M₄ receptors with Gi/Go-type G proteins. Activated G proteins initiate a number of intracellular signal transduction systems. Agonist-bound muscarinic receptors are phosphorylated by G protein-coupled receptor kinases, which initiate their desensitization through uncoupling from G proteins, receptor internalization, and receptor breakdown (down regulation). Recently the crystal structures of M₂ and M₃ receptors were determined and are expected to contribute to the development of drugs targeted to muscarinic receptors. This paper summarizes the molecular properties of muscarinic receptors with reference to the historical background and bias to studies performed in our laboratories.     

Solid-state NMR studies of proteins immobilized on inorganic surfaces

Solid state NMR is the primary tool for studying the quantitative, site-specific structure, orientation, and dynamics of biomineralization proteins under biologically relevant conditions. Two calcium phosphate proteins, statherin (43 amino acids) and leucine rich amelogenin protein (LRAP; 59 amino acids), have been studied in depth and have different dynamic properties and 2D- and 3D-structural features. These differences make it difficult to extract design principles used in nature for building materials with properties such as high strength, unusual morphologies, or uncommon phases. Consequently, design principles needed for developing synthetic materials controlled by proteins are not clear. Many biomineralization proteins are much larger than statherin and LRAP, necessitating the study of larger biomineralization proteins. More recent studies of the significantly larger full-length amelogenin (180 residues) represent a significant step forward to ultimately investigate the full diversity of biomineralization proteins. Interactions of amino acids, a silaffin derived peptide, and the model LK peptide with silica are also being studied, along with qualitative studies of the organic matrices interacting with calcium carbonate. Dipolar recoupling techniques have formed the core of the quantitative studies, yet the need for isolated spin pairs makes this approach costly and time intensive. The use of multi-dimensional techniques to study biomineralization proteins is becoming more common, methodology which, despite its challenges with these difficult-to-study proteins, will continue to drive future advancements in this area.     

Electron spin-lattice relaxation rates for high-spin Fe(III) complexes in glassy solvents at temperatures between 6 and 298 K

The temperature dependence of spin-lattice relaxation rates was analyzed for four high-spin nonheme iron proteins between 5 and 20 K, for three high-spin iron porphyrins between 5 and 118 K, and for four high-spin heme proteins between 5 and 150 to 298 K. For the nonheme proteins the zero-field splittings, D, are less than 0.7 cm(-1), and the relaxation is dominated by the Orbach and Raman processes. For the iron porphyrins and heme proteins D is between 4 and 12 cm(-1) and the relaxation is dominated by the Orbach process between about 5 and 100 K and by a local mode at higher temperatures. The relaxation rates for the heme proteins in glassy matrices extrapolated to values at room temperature that are similar to values obtained by NMR relaxivity in fluid solution. This similarity suggests that for high-spin Fe(III) heme proteins with effective intramolecular spin-lattice relaxation processes, the additional motional freedom gained when a relatively large protein goes from glassy solid to liquid solution at room temperature has little impact on spin-lattice relaxation.     

Single molecule diffraction

For solving the atomic structure of organic molecules such as small proteins which are difficult to crystallize, the use of a jet of doped liquid helium droplets traversing a continuous high energy electron beam is proposed as a means of obtaining electron diffraction patterns (serial crystallography). Organic molecules (such as small proteins) within the droplet (and within a vitreous ice jacket) may be aligned by use of a polarized laser beam. Iterative methods for solving the phase problem are indicated. Comparisons with a related plan for pulsed x-ray diffraction from single proteins in a molecular beam are provided.     

Protein Binding on the Surface of Magnetic Nanoparticles

Magnetic nanoparticles (MNPs) are widely used in the areas of biology and biomedicine. The interaction between MNPs and proteins plays a crucial role in the bioapplication of MNPs, and the binding affinity of protein–MNPs is the manifestation of this interaction. The binding affinity of some proteins with MNPs modified in various ways is determined by fluorescence quenching. The results show that the binding affinity depends on the properties of both the MNPs and the proteins. The higher the surface curvature of MNPs, the larger the MNP, and the higher the binding affinity. No significant difference is found in binding affinity between MNPs with different modification methods. For proteins, the binding affinity depends on the properties of individual proteins, such as the amino acid sequence, the native protein conformation in solution, the isoelectric point, and surface potential. In general, the binding affinity is higher for proteins with cysteine residues on the surface. In addition, pH affects the binding affinity between proteins and MNPs; positively charged proteins and lower pH are more suitable for MNP binding due to electrostatic forces.     

水化磷脂层中蛋白质和多肽的高分辨固体核磁共振波谱学

有序样品的固体核磁共振(NMR)已快速发展成测定蛋白质和多肽在“仿真”水化磷脂层中高分辨结构的重要谱学方法. 由于与膜相连的蛋白质和多肽的结构、动力学和功能往往都和其周边自然环境密切相关,因此人们把蛋白质和多肽有序排列于水化磷脂层中进行固体NMR测量, 从而获得与取向相关的各向异性自旋相互作用. 这些取向约束可作为结构参数重构蛋白质在水化磷脂层中的高分辨三维结构. 近十年来在样品制备,NMR探头和实验方法方面的显著发展,极大地促进了有序样品的固体NMR的发展,并使之成为测定与膜相连的蛋白质和多肽结构的有效方法. 该综述介绍有序样品的固体NMR谱学方法,并总结此领域里的最新研究进展.     

用核磁共振方法研究金属离子与蛋白质的相互作用

许多蛋白质含有金属离子,金属离子对蛋白质发挥生物学功能起着很大的作用. 金属离子与蛋白质的相互作用以及参与蛋白质功能调节的方式各种各样：有些金属离子高度专一性地与蛋白质紧密结合,对蛋白质发挥生物学功能起着关键性的作用;有些金属离子只是作为蛋白质发挥功能的辅助因子而瞬态地与蛋白质松散结合. 本文简要介绍目前国际上用NMR方法研究抗磁金属离子和顺磁金属离子与蛋白质相互作用的进展,并具体介绍了NMR方法在钙调蛋白、锌指蛋白、朊病毒蛋白等金属离子蛋白研究上的应用.     

Biomolecular dynamics and binding studies in the living cell

Isolation and preparation of proteins of higher organisms often is a tedious task. In the case of success, the properties of these proteins and their interactions with other proteins can be studied in vitro. If however, these proteins are modified in the cell in order to gain or change function, this is non-trivial to correctly realise in vitro. When, furthermore, the cellular function requires the interplay of more than one or two proteins, in vitro experiments for the analysis of this situation soon become complex. Instead, we thus try to obtain information on the molecular properties of proteins in the living cell. Then, the cell takes care of correct protein folding and modification. A series of molecular techniques are, and new ones become, available which allow for measuring molecular protein properties in the living cell, offering information on concentration (FCS), dynamics (FCS, RICS, FRAP), location (PALM, STED), interactions (F3H, FCCS) and protein proximities (FRET, BRET, FLIM, BiFC). Here, these techniques are presented with their advantages and drawbacks, with examples from our current kinetochore research. The review is supposed to give orientation to researchers planning to enter the field, and inform which techniques help us to gain molecular information on a multi-protein complex. We show that the field of cellular imaging is in a phase of transition: in the future, an increasing amount of physico-chemical data can be determined in the living cell.     

General features of proton longitudinal relaxation in proteins in solution

Time courses of the recovery upon nonselective inversion of all individual proton magnetizations in several globular proteins in aqueous (²H₂O) solution were calculated for varying degrees of rotational correlation time of the molecule (10⁻⁹ s ∼ ∞) and compared with the experimental data on various proteins at 400 MHz. In the calculation, the spinrelaxation mechanism was assumed to be solely the dipolar interaction between protons, and the three-site random jumps of the methyl groups, along with the rotation of the whole molecule, were taken into account. The following conclusions were drawn. ( 1 ) For proteins whose molecular weights are below ∼ 10,000, whole-molecule rotation is a dominant source of relaxation, and the longitudinal relaxation times may vary considerably from proton to proton. (2) For proteins whose molecular weights are above ∼20,000, methyl group rotations assisted by spin diffusion are common and major sources of relaxation, producing T₁ values close to 1 s. In the intermediate region (molecular weight 10,000 ∼ 20,000), both whole-molecule rotation and methyl group rotations contribute significantly to relaxation. (3) In some proteins, segmental motions are as important as methyl group rotations in determining relaxation rate.     

Syndecan-3 and syndecan-4 are enriched in Schwann cell perinodal processes

Background  

Nodes of Ranvier correspond to specialized axonal domains where voltage-gated sodium channels are highly concentrated. In the peripheral nervous system, they are covered by Schwann cells microvilli, where three homologous cytoskeletal-associated proteins, ezrin, radixin and moesin (ERM proteins) have been found, to be enriched. These glial processes are thought to play a crucial role in organizing axonal nodal domains during development. However, little is known about the molecules present in Schwann cell processes that could mediate axoglial interactions. The aim of this study is to identify by immunocytochemistry transmembrane proteins enriched in Schwann cells processes that could interact, directly or indirectly, with axonal proteins.     

Drift coefficients of motor proteins moving along sidesteps

In the paper, we investigate two motor proteins moving along the sidesteps： a motor protein moving along a two- dimensional sidestep and another protein moving along a three-dimensional sidestep. The drift coefficients （or stationary average velocities） of these two motor proteins are calculated. We believe that our investigation of the motor proteins moving along the sidesteps in the present paper can benefit the investigation of the transport of the motor proteins to some extent.     

Illuminate Proteins and Peptides by Elemental Tag for HPLC-ICP-MS Detection

Abstract

High-performance liquid chromatography–inductively coupled plasma mass spectrometry (HPLC-ICP-MS) is becoming a significant complementary technique of HPLC–molecular mass spectrometry for proteins and peptides quantification. However, the naturally occurring heteroelements inside proteins and peptides, such as sulfur, phosphor, and selenium, are not sensitive enough in ICP-MS for low-abundance proteins and peptides, due to their low ionization efficiency or polyatomic spectral interference. In order to make the low-abundance proteins and peptides “visible” by HPLC-ICP-MS, a foreign elemental tag can be employed. The foreign elemental tags are highly sensitive in ICP-MS and almost absent in common biological matrices, which leads to significantly low limits of detection. This review summarizes the major applications of elemental tags in combination with HPLC-ICP-MS detection. The organic mercury tags, iodine tags, ferrocene tags, and macrocyclic metal chelate complex tags are discussed in detail. The recent development of HPLC-ICP-MS in combination with elemental tags demonstrates the great potential in sensitive and accurate proteins and peptides quantification.     

Improved Resolution from Double Constant-Time Evolution of 3D and 4D Triple-Resonance Experiments

Triple-resonance NMR experiments are nearly essential for performing backbone assignments of proteins larger than 15 kDa. Our work extends the double constant-time (2CT) evolution scheme to triple-resonance 3D and 4D experiments. The modifications needed to accomplish 2CT evolution in triple resonance experiments are straight forward, are completely general, and consequently, will yield increased resolution for all out-and-back experiments. We expect that the increased resolution of experiments presented here will be useful in the study of larger proteins (>30 kDa) and in the study of highly helical proteins where¹HN,¹⁵N, and¹³C dimensions are poorly dispersed.     

EPR Spectra of Transition-Metal Proteins: the Benefits of Data Deposition in Standard Formats

Electron paramagnetic resonance (EPR) spectroscopy can provide answers to significant questions about structure and function in biochemistry. Often EPR spectra of proteins containing transition-metal centers and radicals show the influence of electron spin–spin interactions between paramagnets. Analysis of these spectra provides information about distances and molecular orientations. For small proteins, the shape of the EPR spectra is sensitive to freezing effects, and to changes in the solvent environment; intermolecular spin–spin interactions are also observed. For large complex proteins, details of the EPR spectra are often highly conserved in evolution. Reference spectra of paramagnetic proteins are an aid to identification. The sharing of data is becoming a requirement in the public funding of research, and deposition in public databases is already standard for information such as protein structures and gene sequences. This would require the adoption of standard file formats, such as JCAMP-DX (Joint Committee on Atomic and Molecular Physical Data Exchange) or Bruker BES³T (Bruker EPR Standard for Spectrum Storage and Transfer). An archive of EPR spectra of different types of paramagnetic proteins would assist the identification of paramagnetic centers in biological materials. It would increase the profile of research data, allow comparison of different studies, and further interpretation of data in the light of subsequent discoveries.