Network analysis of transmembrane protein structures

Most studies have shown that globular proteins exist in small-world networks. The present study is an attempt to determine differences in network parameters between transmembrane and globular proteins. Each protein is represented as an undirected graph, where residues represent nodes and inter-residue interactions as the edges. This was then compared to the degree-preserved random controls, to observe if any variation existed. Results indicate that there is a significant difference in shortest path lengths between transmembrane and globular proteins. Hydrophobic amino acids were found to be more spatially distributed in the transmembrane than in globular proteins causing significantly higher values of shortest path lengths (L). Assortativity values too, were found to be significantly higher in the transmembrane than in globular proteins which is due to the highly connected amino acid residues being exposed to the solvent in transmembrane proteins. On analyzing the closeness centrality, it was found that globular proteins have significantly higher values than the transmembrane proteins. We therefore conclude that transmembrane proteins possess small-world characteristics similar to that of globular proteins.     

Biomolecular absorption of ultrasound: II. Molecular structure

Measurements of absorption coefficients in several globular and linear proteins yield no correlations of absorption with alpha-helix content or with the number of polypeptide chains in the protein. Removal of all but the primary structure with denaturing agents that convert proteins to random chains causes only small changes in the absorption of globular proteins. Complete denaturing of linear muscle proteins results in large reductions in absorption. Therefore, it is concluded that absorption in globular proteins is insensitive to structural characteristics while in linear proteins it is dependent upon the amount of alpha-helix content. An alternative explanation of the results is that alpha-helix contributes to absorption in both globular and linear proteins but tertiary structure in globular proteins reduces absorption because of inhibited solvent interactions.     

N-myristoylated proteins,key components in intracellular signal transduction systems enabling rapid and flexible cell responses

N-myristoylation, one of the co- or post-translational modifications of proteins, has so far been regarded as necessary for anchoring of proteins to membranes. Recently, we have revealed that N^α-myristoylation of several brain proteins unambiguously regulates certain protein–protein interactions that may affect signaling pathways in brain. Comparison of the amino acid sequences of myristoylated proteins including those in other organs suggests that this regulation is involved in signaling pathways not only in brain but also in other organs. Thus, it has been shown that myristoylated proteins in cells regulate the signal transduction between membranes and cytoplasmic fractions. An algorithm we have developed to identify myristoylated proteins in cells predicts the presence of hundreds of myristoylated proteins. Interestingly, a large portion of the myristoylated proteins thought to take part in signal transduction between membranes and cytoplasmic fractions are included in the predicted myristoylated proteins. If the proteins functionally regulated by myristoylation, a posttranslational protein modification, were understood as cross-talk points within the intracellular signal transduction system, known signaling pathways could thus be linked to each other, and a novel map of this intracellular network could be constructed. On the basis of our recent results, this review will highlight the multifunctional aspects of protein N-myristoylation in brain.     

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.     

Effects of ultrasound assisted cell wall disruption on physicochemical properties of camellia bee pollen protein isolates

Camellia bee pollen protein isolates were extracted by cell wall disruption using ultrasonication, freeze-thawing, enzymatic hydrolysis, and their combinations. The effects of these methods on microstructure of cell wall, protein release, protein yield, physiochemical properties and structure of proteins were investigated. As compared with physical treatments (ultrasonication, freeze-thawing and their combination), the enzymatic hydrolysis significantly improved the yield of proteins, because it not only promoted the release of proteins from the inside of pollen, but also released proteins in pollen wall. The proteins extracted by enzymatic hydrolysis method also exhibited better solubility, emulsifying and gelation properties due to the partial hydrolysis of proteins by protease. In addition, when ultrasound was combined with freeze-thawing or enzymatic hydrolysis, it could further improve the yield of proteins and the functional properties of proteins, which was mainly related to the changes of protein structure induced by cavitation effect of ultrasound.     

Interstitial protein alterations in rabbit vocal fold with scar

Fibrous and interstitial proteins compose the extracellular matrix of the vocal fold lamina propria and account for its biomechanic properties. Vocal fold scarring is characterized by altered biomechanical properties, which create dysphonia. Although alterations of the fibrous proteins have been confirmed in the rabbit vocal fold scar, interstitial proteins, which are known to be important in wound repair, have not been investigated to date. Using a rabbit model, interstitial proteins decorin, fibromodulin, and fibronectin were examined immunohistologically, two months postinduction of vocal fold scar by means of forcep biopsy. Significantly decreased decorin and fibromodulin with significantly increased fibronectin characterized scarred vocal fold tissue. The implications of altered interstitial proteins levels and their affect on the fibrous proteins will be discussed in relation to increased vocal fold stiffness and viscosity, which characterizes vocal fold scar.     

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).     

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.     

Luminescencence determination of ecotoxicants in protein-based media

The structural changes in the protein macromolecules caused by polycyclic aromatic hydrocarbon (PAH) ecotoxicants were studied using the data on intrinsic fluorescence of proteins and fluorescence of PAH molecules introduced into proteins. A luminescence method for PAH determination in proteins was developed and used to study the interaction of two PAHs (pyrene and anthracene) with proteins of two types (bovine serum albumin and human serum albumin). The results were interpreted using the Stern–Volmer fluorescence quenching model. The association constants and the number of binding sites in the protein–ligand complexes were calculated. The binding of PAHs with proteins was described based on the static version of quenching with formation of nonfluorescent complexes of protein fluorophores with PAHs.     

用不同蛋白质分析方法鉴定玉米分泌蛋白组的比较研究

玉米根系在生长过程中向根际分泌蛋白质类大分子物质。采用双向聚丙烯酰胺凝胶电泳-质谱技术,一维液相色谱-质谱联用(LC/MS)和Shotgun三种不同鉴定方法对无菌条件收集的玉米根系分泌蛋白进行了分离、分析与鉴定,对3种鉴定方法在分泌蛋白分析中的应用做了详细阐述和比较。结果表明,双向电泳通过银染可以看到200个蛋白质点,但由于蛋白量少,通过质谱无法对玉米根系分泌蛋白进行鉴定;用LC/MS鉴定得到了152个蛋白;用Shotgun技术鉴定得到了2 848个蛋白。LC/MS鉴定得到的蛋白全部出现在用Shotgun技术鉴定得到的2 848个蛋白中,后2种方法的结果可以互相验证。Shotgun技术具有更高的灵敏性,更适合对蛋白质浓度低、干扰物多的植物根分泌蛋白组进行鉴定,能够获得完整可靠的信息。     

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.     

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.     

Structural insights and ab initio sequencing within the DING proteins family

DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.     

Chemical synthesis of TASP arrays and their application in protein design

A combinatorial synthesis of de novo proteins is described. The concept of template-assembled synthetic proteins (TASP) has been adapted to an orthogonal assembly of small libraries of purified peptide building blocks. It is combined with the spot synthesis of peptides which is exploited to array cyclic decapeptide templates on cellulose membranes. A cleavable linker on the cellulose allows control of the synthesis. The hydrophilic proteins are constructed by successive cleavage of orthogonal protecting groups on the template, followed by coupling of amphipathic helices in a predefined orientation and finally by incorporation of a cofactor. Libraries of peptides with variation of the amino acids expected to be close to the cofactor were coupled to the cellulose-bound template in all combinations, yielding up to 500 variants of a protein. Cofactors have been inserted either at non-covalent binding sites as heme and Cu2+ or by covalent modification of amino acids as Ru-bipyridine or flavin. The proteins were screened by recording their UV-vis spectra directly on the solid support. The properties screened include the redox potential of heme proteins, charge transfer bands indicating the ligation of Cu-centers, enzymatic activity, and folding stability. Synthesis of the best hits as soluble variants was used for detailed characterization. Iterative improvement in a second screening cycle was efficient in finding novel copper proteins. We discuss the prospects of synthesizing proteins by extending the concept to beta-sandwich proteins and construction of efficient peptide libraries with computer-supported design, as well as the possible usage of improved solid phase materials.     

Tryptophan and Proteins Can Be Entrapped in UV Transmitting Glass

It is demonstrated that tryptophan and proteins (parvalbumin and alcohol dehydrogenase) can be entrapped in silica glass. The silica glass is transparent in the UV spectral region, allowing for spectroscopic studies of immobilized proteins. The fluorescence spectra and phosphorescence spectra and lifetime of entrapped proteins resemble those observed for the molecules in aqueous solution.     

Irreversible Adsorption of Serum Proteins onto Nanoparticles

When a material comes in contact with serum or plasma, proteins will immediately adsorb to its surface. The extent of serum protein adsorption as well as the composition of the protein corona is thought to be decisive for the biological fate. The understanding of the mechanism underlying the concurrent adsorption of multiple proteins and the exact ways by which the adsorbed proteins interact with the biological setting, is still rudimentary. For both cases, a correct estimate of the composition of the protein corona is the key for an improved understanding. The protein corona composition is typically analyzed indirectly through analysis of the supernatant after protein desorption. However, in most cases the particles are not analyzed afterward in order to ensure that all proteins indeed have desorbed. Here, the results related to the analysis of the amounts of proteins in the corona are reported, focusing on the desorbed as well as the fraction of proteins that do not desorb. Irreversible protein adsorption can be observed in some cases. The results show that, in addition of the analysis of the supernatant, analysis of the particles is of critical importance to fully characterize the protein corona formed on nanoparticles.     

Fourier and power law analysis of structural complexity in cornea and lens

The ordered pattern of type I collagen fibrils in the transparent cornea is an example of specialization in the formation of functional ultrastructure. In contrast, the disordered and amorphous distribution of cytoplasmic proteins in the transparent lens resembles the structure of most cells. While the organization of cytoplasmic proteins is often considered to be random, the compartmentalization of functional proteins in biological cells and the organization provided by cytoskeletal elements suggests that non-random patterns of organization are common. Attempts to quantify disordered, amorphous patterns of ultrastructure in cells and tissues have been unsuccessful, in part, because the cellular organization of structural proteins including collagen, keratin, cytoskeletal and crystallin proteins is complex. Characterization of the complex patterns observed in electron micrographs is a fundamental problem in structural biology. This paper reviews the use of Fourier and power law analyses of electron micrographs of cornea and lens as models for ordered and disordered ultrastructure of cells and tissues.     

Predicting the subcellular location of apoptosis proteins based on recurrence quantification analysis and the Hilbertben Huang transform

Apoptosis proteins play an important role in the development and homeostasis of an organism. The elucidation of the subcellular locations and functions of these proteins is helpful for understanding the mechanism of programmed cell death. In this paper, the recurrent quantification analysis, Hilbert-Huang transform methods, the maximum relevance and minimum redundancy method and support vector machine are used to predict the subcellular location of apoptosis proteins. The validation of the jackknife test suggests that the proposed method can improve the prediction accuracy of the subcellular location of apoptosis proteins and its application may be promising in other fields.