Protein crystallization for genomics: throughput versus output

Structural genomics involves many steps in order to reach from Gene to structure. This article focuses on the crystallization step in this chain of tasks. It is becoming increasingly evident that the current high throughput procedures for crystallising proteins do not always produce the expected output of high quality crystals required for structure determination by x-ray crystallography. This problem is discussed and suggestions for raising the output are presented.     

Parkinsonism-associated Protein DJ-1/Park7 Is a Major Protein Deglycase That Repairs Methylglyoxal- and Glyoxal-glycated Cysteine,Arginine, and Lysine Residues

Glycation is an inevitable nonenzymatic covalent reaction between proteins and endogenous reducing sugars or dicarbonyls (methylglyoxal, glyoxal) that results in protein inactivation. DJ-1 was reported to be a multifunctional oxidative stress response protein with poorly defined function. Here, we show that human DJ-1 is a protein deglycase that repairs methylglyoxal- and glyoxal-glycated amino acids and proteins by acting on early glycation intermediates and releases repaired proteins and lactate or glycolate, respectively. DJ-1 deglycates cysteines, arginines, and lysines (the three major glycated amino acids) of serum albumin, glyceraldehyde-3-phosphate dehydrogenase, aldolase, and aspartate aminotransferase and thus reactivates these proteins. DJ-1 prevented protein glycation in an Escherichia coli mutant deficient in the DJ-1 homolog YajL and restored cell viability in glucose-containing media. These results suggest that DJ-1-associated Parkinsonism results from excessive protein glycation and establishes DJ-1 as a major anti-glycation and anti-aging protein.     

Effect of sucrose,stevia and xylitol on rheological properties of gels from blends of chestnut and rice flours

The development of high quality gluten-free products requires the understanding of the phenomena that dictate the ingredient interactions commonly used in foodstuff. In this work, the main objective was to develop alternative gluten-free gelled desserts from blends of chestnut flour (Cf) and whole (Rw), Agulha (Ra) or Carolino (Rc) rice flours. The impact of sucrose, stevia and xylitol on textural, rheological and structural properties of selected gels was investigated. Texture results indicated that studied gels in the presence of sucrose and xylitol decreased significantly the firmness. Rheological outcomes showed that the temperature ramps on heating of Cf/Rw gels were similar to those obtained for Cf/Ra, whereas Cf/Rc gels presented a particular pattern. The presence of sucrose resulted in a significant decrease in the values of storage and loss moduli. Confocal microscopic images showed that the sugar addition leads to a less aggregated structure with fracture lines well marked.     

Thermodynamics of protein folding: a microscopic view

Statistical thermodynamics provides a powerful theoretical framework for analyzing, understanding and predicting the conformational properties of biomolecules. The central quantity is the potential of mean force or effective energy as a function of conformation, which consists of the intramolecular energy and the solvation free energy. The intramolecular energy can be reasonably described by molecular mechanics-type functions. While the solvation free energy is more difficult to model, useful results can be obtained with simple approximations. Such functions have been used to estimate the intramolecular energy contribution to protein stability and obtain insights into the origin of thermodynamic functions of protein folding, such as the heat capacity. With reasonable decompositions of the various energy terms, one can obtain meaningful values for the contribution of one type of interaction or one chemical group to stability. Future developments will allow the thermodynamic characterization of ever more complex biological processes.     

食用豆类种质资源粗蛋白及粗淀粉含量的评价

对"十五"期间收集、整理并存入国家种质库的1696份食用豆类种质资源的主要品质性状进行了鉴定评价.结果表明,9种食用豆类种质资源的粗蛋白、粗淀粉平均含量分别为24.93%、45.11%,不同食用豆类种质资源中各品质性状变异程度不同,其中菜豆和鹰嘴豆的粗蛋白和豇豆的粗淀粉含量变异最大.不同来源的食用豆类种质资源品质性状比较结果表明,国内绿豆种质资源粗蛋白含量明显优于国外种质资源.通过鉴定筛选出一批品质性状优良的食用豆类种质,并对使用的评价标准进行了讨论.     

Biophysics and Thermodynamics: The Scientific Building Blocks of Bio-inspired Drug Delivery Nano Systems

Biophysics and thermodynamics are considered as the scientific milestones for investigating the properties of materials. The relationship between the changes of temperature with the biophysical variables of biomaterials is important in the process of the development of drug delivery systems. Biophysics is a challenge sector of physics and should be used complementary with the biochemistry in order to discover new and promising technological platforms (i.e., drug delivery systems) and to disclose the ‘silence functionality’ of bio-inspired biological and artificial membranes. Thermal analysis and biophysical approaches in pharmaceuticals present reliable and versatile tools for their characterization and for the successful development of pharmaceutical products. The metastable phases of self-assembled nanostructures such as liposomes should be taken into consideration because they represent the thermal events can affect the functionality of advanced drug delivery nano systems. In conclusion, biophysics and thermodynamics are characterized as the building blocks for design and development of bio-inspired drug delivery systems.KEY WORDS: biophysics, drug delivery nano systems, pharmaceutics, thermal analysis, thermodynamics     

The Collagen-like Protein gp12 Is a Temperature-dependent Reversible Binder of SPP1 Viral Capsids

Icosahedral capsids of viruses are lattices of defined geometry and homogeneous size. The (quasi-)equivalent organization of their protein building blocks provides, in numerous systems, the binding sites to assemble arrays of viral polypeptides organized with nanometer precision that protrude from the capsid surface. The capsid of bacterial virus (bacteriophage) SPP1 exposes, at its surface, the 6.6-kDa viral polypeptide gp12 that binds to the center of hexamers of the major capsid protein. Gp12 forms an elongated trimer with collagen-like properties. This is consistent with the fold of eight internal GXY repeats of gp12 to build a stable intersubunit triple helix in a prokaryotic setting. The trimer dissociates and unfolds at near physiological temperatures, as reported for eukaryotic collagen. Its structural organization is reacquired within seconds upon cooling. Interaction with the SPP1 capsid hexamers strongly stabilizes gp12, increasing its T_m to 54 °C. Above this temperature, gp12 dissociates from its binding sites and unfolds reversibly. Multivalent binding of gp12 trimers to the capsid is highly cooperative. The capsid lattice also provides a platform to assist folding and association of unfolded gp12 polypeptides. The original physicochemical properties of gp12 offer a thermoswitchable system for multivalent binding of the polypeptide to the SPP1 capsid surface.     

Induction of a Stress Protein in Developing Cell Cultures of the Rat Cerebellum

Abstract: We examined the ability of developing cere-bellar cell cultures to synthesize a 71,000 MW stress protein (SP71) in response to heat shock and Cd²⁺ treatment. The induction of SP71 synthesis appeared to be dependent on both the age of the culture and the stressor used. Heat shock induced SP71 synthesis in freshly prepared cells and in cell cultures at each age examined, whereas Cd²⁺ was effective only in cultures at 7 days of age and older. These findings are discussed with reference to the development of various cell types in these cultures.     

Amyloid features and neuronal toxicity of mature prion fibrils are highly sensitive to high pressure

Prion proteins (PrP) can aggregate into toxic and possibly infectious amyloid fibrils. This particular macrostructure confers on them an extreme and still unexplained stability. To provide mechanistic insights into this self-assembly process, we used high pressure as a thermodynamic tool for perturbing the structure of mature amyloid fibrils that were prepared from recombinant full-length mouse PrP. Application of high pressure led to irreversible loss of several specific amyloid features, such as thioflavin T and 8-anilino-1-naphthalene sulfonate binding, alteration of the characteristic proteinase K digestion pattern, and a significant decrease in the β-sheet structure and cytotoxicity of amyloid fibrils. Partial disaggregation of the mature fibrils into monomeric soluble PrP was observed. The remaining amyloid fibrils underwent a change in secondary structure that led to morphologically different fibrils composed of a reduced number of proto-filaments. The kinetics of these reactions was studied by recording the pressure-induced dissociation of thioflavin T from the amyloid fibrils. Analysis of the pressure and temperature dependence of the relaxation rates revealed partly unstructured and hydrated kinetic transition states and highlighted the importance of collapsing and hydrating inter- and intramolecular cavities to overcome the high free energy barrier that stabilizes amyloid fibrils.     

Native mutant huntingtin in human brain: evidence for prevalence of full-length monomer

Huntington disease (HD) is caused by polyglutamine expansion in the N terminus of huntingtin (htt). Analysis of human postmortem brain lysates by SDS-PAGE and Western blot reveals htt as full-length and fragmented. Here we used Blue Native PAGE (BNP) and Western blots to study native htt in human postmortem brain. Antisera against htt detected a single band broadly migrating at 575-850 kDa in control brain and at 650-885 kDa in heterozygous and Venezuelan homozygous HD brains. Anti-polyglutamine antisera detected full-length mutant htt in HD brain. There was little htt cleavage even if lysates were pretreated with trypsin, indicating a property of native htt to resist protease cleavage. A soluble mutant htt fragment of about 180 kDa was detected with anti-htt antibody Ab1 (htt-(1-17)) and increased when lysates were treated with denaturants (SDS, 8 M urea, DTT, or trypsin) before BNP. Wild-type htt was more resistant to denaturants. Based on migration of in vitro translated htt fragments, the 180-kDa segment terminated ≈htt 670-880 amino acids. If second dimension SDS-PAGE followed BNP, the 180-kDa mutant htt was absent, and 43-50 kDa htt fragments appeared. Brain lysates from two HD mouse models expressed native full-length htt; a mutant fragment formed if lysates were pretreated with 8 M urea + DTT. Native full-length mutant htt in embryonic HD(140Q/140Q) mouse primary neurons was intact during cell death and when cell lysates were exposed to denaturants before BNP. Thus, native mutant htt occurs in brain and primary neurons as a soluble full-length monomer.     

The denatured state dictates the topology of two proteins with almost identical sequence but different native structure and function

The protein folding problem is often studied by comparing the mechanisms of proteins sharing the same structure but different sequence. The recent design of the two proteins G_A88 and G_B88, displaying different structures and functions while sharing 88% sequence identity (49 out of 56 amino acids), allows the unique opportunity for a complementary approach. At which stage of its folding pathway does a protein commit to a given topology? Which residues are crucial in directing folding mechanisms to a given structure? By using a combination of biophysical and computational techniques, we have characterized the folding of both G_A88 and G_B88. We show that, contrary to expectation, G_B88, characterized by a native α+β fold, displays in the denatured state a content of native-like helical structure greater than G_A88, which is all-α in its native state. Both experiments and simulations indicate that such residual structure may be tuned by changing pH. Thus, despite the high sequence identity, the folding pathways for these two proteins appear to diverge as early as in the denatured state. Our results suggest a mechanism whereby protein topology is committed very early along the folding pathway, being imprinted in the residual structure of the denatured state.     

Rheological Behavior of Food Emulsions Mixed with Saliva: Effect of Oil Content, Salivary Protein Content, and Saliva Type

In this paper, we studied the effect of saliva on the rheological properties of β-lactoglobulin- and lysozyme-stabilized emulsions, prepared at pH = 6.7 in relation to variation of emulsions- and saliva-related parameters. The effect of oil–volume fraction (2.5% w/w to 10% w/w), salivary protein concentration (0.1 to 0.8 mg ml⁻¹), and the use of both stimulated and unstimulated saliva was investigated. Viscosity and storage modulus were measured before (η _emul and G′_emul, respectively) and after addition of saliva (η _mix and G′_mix). To better estimate the changes due to saliva-induced flocculation of the emulsions, the ratios η _mix/η _emul, G′_mix/G′_emul were calculated. In addition, tan δ (=the ratio of the loss and storage moduli) was investigated to evaluate the viscoelastic behavior of the emulsion/saliva mixtures. Increasing the oil–volume fraction and salivary protein concentration resulted in an increase in η _mix/η _emul and G′_mix/G′_emul, while a decrease in tan δ of the emulsion/saliva mixtures is occurring. When compared with unstimulated saliva, mixing β-lactoglobulin-stabilized emulsions with stimulated saliva led to a reduction in η _mix/η _emul and G′_mix/G′_emul, and an augment of tan δ at all measured deformations. In case of lysozyme-stabilized emulsions, the use of stimulated saliva increased G′_mix/G′_emul for γ < 3 when compared to unstimulated saliva. The effect of stimulated saliva on the η _mix/η _emul and tan δ in this mixture is similar to that of unstimulated saliva. These results indicate that the influence of stimulated saliva on the rheological parameters of emulsion/saliva mixtures largely depends on the type of emulsions. To conclude, our findings demonstrate that the rheological behavior of emulsions upon mixing with saliva is greatly affected by both saliva and emulsion properties.     

Small and Large Deformation Rheology of Acid Gels from Transglutaminase Treated Milks

The purpose of this study was to evaluate the effects of microbial transglutaminase on the rheological and mechanical properties of gels from a commercial UHT milk made by acidification with d-gluconic-acid-δ-lactone. Although further heating of UHT milk, primarily carried out to inactivate the enzyme, showed a significant impact on gel firmness, we observed no enzyme-related effects at small deformation. The impact of the additional thermal treatment was also evident in large deformation measurements. In these experiments, gels from enzyme-treated milk revealed much higher elasticity and rupture force. Prolonged incubation time or increased enzyme concentration resulted in lower gel firmness (small deformation), indicating a reduced number of total bonds as a result of the restriction of proper rearrangements during acidification. Large deformation measurements revealed a heat-induced amplification of this effect, i.e., lower rupture forces at almost constant elasticity levels. In gels from milk, which was not subjected to thermal enzyme inactivation, we observed a further increase in both parameters. This is presumably caused by a combination of residual enzyme activity and of additional substrate, liberated during acidification.     

Protein arginine methyltransferases and hepatocellular carcinoma: A review

Hepatocellular carcinoma (HCC) is one of the most frequently diagnosed cancers with a high mortality rate worldwide. The complexity of HCC initiation and progression poses a great challenge to the diagnosis and treatment. An increasing number of studies have focused on the emerging roles of protein arginine methylation in cancers, including tumor growth, invasion, metastasis, metabolism, immune responses, chemotherapy sensitivity, etc. The family of protein arginine methyltransferases (PRMTs) is the most important proteins that mediate arginine methylation. The deregulation of PRMTs’ expression and functions in cancers have been gradually unveiled, and many PRMTs inhibitors are in preclinical and clinical investigations now. This review focuses predominantly on the aberrant expression of PRMTs, underlying mechanisms, as well as their potential applications in HCC, and provide novel insights into HCC therapy.     

Synchrotron Protein Footprinting: A Technique to Investigate Protein-Protein Interactions

Abstract

Traditional approaches for macromolecular structure elucidation, including NMR, crystallography and cryo-EM have made significant progress in defining the structures of protein-protein complexes. A substantial number of macromolecular structures, however, have not been examined with atomic detail due to sample size and heterogeneity, or resolution limitations of the technique; therefore, the general applicability of each method is greatly reduced. Synchrotron footprinting attempts to bridge the gap in these methods by monitoring changes in accessible surface areas of discrete macromolecular moieties. As evidenced by our previous studies on RNA folding and DNA-protein interactions, the three-dimensional structure is probed by examining the reactions of these moieties with hydroxyl radicals generated by synchrotron X-rays. Here we report the application of synchrotron foot- printing to the investigation of protein-protein interactions, as the novel technique has been utilized to successfully map the contact sites of gelsolin segment-1 in the gelsolin segment 1/actin complex. Footprinting results demonstrate that phenylalanine 104, located on the actin binding helix of gelsolin segment 1, is protected from hydroxyl radical modification in the presence of actin. This change in reactivity results from the specific protection of gel- solin segment-1, consistent with the substantial decrease in solvent accessibility of F104 upon actin binding, as calculated from the crystal structural of the gelsolin segment 1/actin complex. The results presented here establish synchrotron footprinting as a broadly applicable method to probe structural features of macromolecular complexes that are not amenable to conventional approaches.     

Protein kinases and protein phosphatases in prokaryotes: a genomic perspective

For many years, the regulation of protein structure and function by phosphorylation and dephosphorylation was considered a relatively recent invention that arose independently in each phylogenetic domain. Over time, however, incidents of apparent domain trespass involving the presence of 'eukaryotic' protein kinases or protein phosphatases in prokaryotic organisms were reported with increasing frequency. Today, genomics has provided the means to examine the phylogenetic distribution of 'eukaryotic' protein kinases and protein phosphatases in a comprehensive and systematic manner. The results of these genome searches challenge previous conceptions concerning the origins and evolution of this versatile regulatory mechanism.     

单宁酸对根田鼠食物摄入量和蛋白质消化率的效应

在食物中含10 %和20%蛋白质的条件下, 采用食物平衡法测定了单宁酸对根田鼠食物摄入量和蛋白质消化率的作用。食物蛋白质含量为10 %时, 第1～5 天, 单宁酸对根田鼠食物摄入量具有显著的抑制作用, 自第6天, 其作用不明显, 以3 %和6 %单宁酸处理的根田鼠, 其食物蛋白质消化率较对照组分别降低22 %和47.67 %;在食物蛋白质含量为20 %的条件下, 单宁酸对根田鼠的食物摄入量和蛋白质消化率无显著作用。上述结果验证了植物次生化合物能抑制植食性小哺乳动物食物摄入量及蛋白质消化率的假设。     

Reversible and non-reversible thermal denaturation of lysozyme with varying pH at low ionic strength

DSC analysis has been used to quantify the reversibility of unfolding following thermal denaturation of lysozyme. Since the temperature at which protein unfolding occurs, T_m, varies with different solution conditions, the effect on the melting temperature and the degree of refolding after thermal denaturation in low ionic strength sodium phosphate buffers (5–1000 mM) over a range of pH (5–9) in the presence/absence of disaccharides is examined. This study compares the enthalpies of unfolding during successive heating cycles to quantify reversibility following thermal denaturation. The disaccharides, trehalose and maltose were used to assess if the disaccharide induced increase in T_m is reflected in the reversibility of thermally induced denaturation. There was extensive overlap between the T_m values where non-reversible and reversible thermal denaturation occurred. Indeed, for pH 6, at the highest and lowest T_m, no refolding was observed whereas refolding was observed for intermediate values, but with similar T_m values having different proportions of refolded protein. We established a method to measure the degree of reversible unfolding following thermal denaturation and hence indirectly, the degree to which protein is lost to irreversible aggregation, and show that solution conditions which increase melt transition temperatures do not automatically confer an increase in reversibility. This type of analysis may prove useful in assessing the stability of proteins in both the biopharmaceutical and food industries.     

Dinucleotide Receptor Modulation by Protein Kinases (Protein Kinases A and C) and Protein Phosphatases in Rat Brain Synaptic Terminals

Abstract: The diadenosine polyphosphates, diadenosine tetraphosphate and diadenosine pentaphosphate (Ap₅A), can activate an ionotropic dinucleotide receptor that induces Ca²⁺ transients into synaptosomes prepared from rat brain. This receptor, also termed the P₄ purinoceptor, is sensitive only to adenine dinucleotides and is insensitive to ATP. Studies on the modulatory role of protein kinase A (PKA), protein kinase C (PKC), and protein phosphatases on the response of diadenosine polyphosphate receptors were performed by measuring the changes in the intracellular Ca²⁺ levels with fura-2. Activation and inhibition of PKA were carried out by means of forskolin and the PKA inhibitory peptide (PKA-IP), respectively. The Ap₅A response was inhibited by forksolin to 35% of control values, but PKA-IP induced an increase of 37%. The effect of PKC activation was similar to that observed for PKA. PKC stimulation with phorbol 12,13-dibutyrate produced an inhibition of 67%, whereas the PKC inhibitors staurosporine and PKC inhibitory peptide enhanced the responses elicited by Ap₅A to 40% in both cases. Protein phosphatase inhibitors diminished the responses elicited by Ap₅A to 17% in the case of okadaic acid, to 50% for microcystin, and to 45% in the case of cyclosporin A. Thus, the activity of dinucleotide receptors in rat brain synaptosomes appears to be modulated by phosphorylation/dephosphorylation. These processes could be of physiological significance in the control of transmitter release from neurons that are postsynaptic to nerves that release diadenosine polyphosphates.     

Elucidation of acid-induced unfolding and aggregation of human immunoglobulin IgG1 and IgG2 Fc

Understanding the underlying mechanisms of Fc aggregation is an important prerequisite for developing stable and efficacious antibody-based therapeutics. In our study, high resolution two-dimensional nuclear magnetic resonance (NMR) was employed to probe structural changes in the IgG1 Fc. A series of (1)H-(15)N heteronuclear single-quantum correlation NMR spectra were collected between pH 2.5 and 4.7 to assess whether unfolding of C(H)2 domains precedes that of C(H)3 domains. The same pH range was subsequently screened in Fc aggregation experiments that utilized molecules of IgG1 and IgG2 subclasses with varying levels of C(H)2 glycosylation. In addition, differential scanning calorimetry data were collected over a pH range of 3-7 to assess changes in C(H)2 and C(H)3 thermostability. As a result, compelling evidence was gathered that emphasizes the importance of C(H)2 stability in determining the rate and extent of Fc aggregation. In particular, we found that Fc domains of the IgG1 subclass have a lower propensity to aggregate compared with those of the IgG2 subclass. Our data for glycosylated, partially deglycosylated, and fully deglycosylated molecules further revealed the criticality of C(H)2 glycans in modulating Fc aggregation. These findings provide important insights into the stability of Fc-based therapeutics and promote better understanding of their acid-induced aggregation process.