The Folding Transition-State Ensemble of a Four-Helix Bundle Protein: Helix Propensity as a Determinant and Macromolecular Crowding as a Probe

The four-helix bundle protein Rd-apocyt b₅₆₂, a redesigned stable variant of apocytochrome b₅₆₂, exhibits two-state folding kinetics. Its transition-state ensemble has been characterized by Φ-value analysis. To elucidate the molecular basis of the transition-state ensemble, we have carried out high-temperature molecular dynamics simulations of the unfolding process. In six parallel simulations, unfolding started with the melting of helix I and the C-terminal half of helix IV, and followed by helix III, the N-terminal half of helix IV and helix II. This ordered melting of the helices is consistent with the conclusion from native-state hydrogen exchange, and can be rationalized by differences in intrinsic helix propensity. Guided by experimental Φ-values, a putative transition-state ensemble was extracted from the simulations. The residue helical probabilities of this transition-state ensemble show good correlation with the Φ-values. To further validate the putative transition-state ensemble, the effect of macromolecular crowding on the relative stability between the unfolded ensemble and the transition-state ensemble was calculated. The resulting effect of crowding on the folding kinetics agrees well with experimental observations. This study shows that molecular dynamics simulations combined with calculation of crowding effects provide an avenue for characterize the transition-state ensemble in atomic details.     

Histone Octamer Helical Tubes Suggest that an Internucleosomal Four-Helix Bundle Stabilizes the Chromatin Fiber

A major question in chromatin involves the exact organization of nucleosomes within the 30-nm chromatin fiber and its structural determinants of assembly. Here we investigate the structure of histone octamer helical tubes via the method of iterative helical real-space reconstruction. Accurate placement of the x-ray structure of the histone octamer within the reconstructed density yields a pseudoatomic model for the entire helix, and allows precise identification of molecular interactions between neighboring octamers. One such interaction that would not be obscured by DNA in the nucleosome consists of a twofold symmetric four-helix bundle formed between pairs of H2B-α3 and H2B-αC helices of neighboring octamers. We believe that this interface can act as an internucleosomal four-helix bundle within the context of the chromatin fiber. The potential relevance of this interface in the folding of the 30-nm chromatin fiber is discussed.     

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid phase by using combinatorial chemistry. One of the most well studied classes of peptidomimetics is peptoids. Peptoids are easy to synthesize and have been shown to be proteolysis-resistant and cell-permeable. Over the past decade, many useful protein ligands have been identified through screening of peptoid libraries. However, most of the ligands identified from peptoid libraries do not display high affinity, with rare exceptions. This may be due, in part, to the lack of chiral centers and conformational constraints in peptoid molecules. Recently, we described a new synthetic route to access peptide tertiary amides (PTAs). PTAs are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. With side chains on both α-carbon and main chain nitrogen atoms, the conformation of these molecules are greatly constrained by sterical hindrance and allylic 1,3 strain. (Figure 1) Our study suggests that these PTA molecules are highly structured in solution and can be used to identify protein ligands. We believe that these molecules can be a future source of high-affinity protein ligands. Here we describe the synthetic method combining the power of both split-and-pool and sub-monomer strategies to synthesize a sample one-bead one-compound (OBOC) library of PTAs.     

Water and Backbone Dynamics in a Hydrated Protein

Rotational immobilization of proteins permits characterization of the internal peptide and water molecule dynamics by magnetic relaxation dispersion spectroscopy. Using different experimental approaches, we have extended measurements of the magnetic field dependence of the proton-spin-lattice-relaxation rate by one decade from 0.01 to 300 MHz for ¹H and showed that the underlying dynamics driving the protein ¹H spin-lattice relaxation is preserved over 4.5 decades in frequency. This extension is critical to understanding the role of ¹H₂O in the total proton-spin-relaxation process. The fact that the protein-proton-relaxation-dispersion profile is a power law in frequency with constant coefficient and exponent over nearly 5 decades indicates that the characteristics of the native protein structural fluctuations that cause proton nuclear spin-lattice relaxation are remarkably constant over this wide frequency and length-scale interval. Comparison of protein-proton-spin-lattice-relaxation rate constants in protein gels equilibrated with ²H₂O rather than ¹H₂O shows that water protons make an important contribution to the total spin-lattice relaxation in the middle of this frequency range for hydrated proteins because of water molecule dynamics in the time range of tens of ns. This water contribution is with the motion of relatively rare, long-lived, and perhaps buried water molecules constrained by the confinement. The presence of water molecule reorientational dynamics in the tens of ns range that are sufficient to affect the spin-lattice relaxation driven by ¹H dipole-dipole fluctuations should make the local dielectric properties in the protein frequency dependent in a regime relevant to catalytically important kinetic barriers to conformational rearrangements.     

Dehydrated gelatin drops: a good method for fungi maintenance and preservation

Some techniques have been proposed to maintain fungi culture collection. However, any choice must ensure the cultural stability and its phenotypic characteristics. This work proposes an adaptation of a preservation method considered by few literature reports: the dehydrated gelatin drops method (DGD). A total of 27 strains of fungi of clinical interest, including four dermatophyte fungi isolates, six filamentous non-dermatophyte fungi, five environment isolated filamentous fungi, six dimorphic fungi and six yeasts were maintained by this method for a seven year period at room temperature. After that time, the macro and micro characteristics of each fungus were studied, allowing the evaluation of the DGD method. In our experience, none of the strains maintained by DGD were found to be contaminated by bacteria or other fungi and no apparent changes were observed in morphology or macroscopic features.     

The Atrioventricular Node, his Bundle and Bundle Branches-a New Histologic Technique

A technique for examination of the conducting system of the heart is described. A block of tissue embracing the ostium of the coronary sinus, the pars membranacea, the septal leaflet of the tricuspid valve, and appropriate amounts of interatrial and interventricular septum is flattened and fixed in a Kaiserling I solution. Blocks are subsequently cleared in methyl salicylate and trimmed. Sections are cut from the blocks after paraffin embedding beginning from the endocardial surfaces of the right heart chambers. The sections are mounted and stained on 35 mm unperforated leader film and covered with an acrylic preservative. For examination of the conducting system many fewer sections are required than with previous techniques.     

Hydrated conidia of Metarhizium anisopliae release a family of metalloproteases

Metarhizium anisopliae spores release isoforms of metalloprotease during hydration over a 4-day incubation period. The isoforms were identified and characterized by using one-dimensional native PAGE (1-DE nPAGE) and one-dimensional SDS non-dissociating (1-DE nSDS-PAGE) zymography. The ability of these isozymes to degrade gelatin varied as revealed by 2-D spot densitometry. 1-DE nPAGE zymography revealed five isoforms of gelatinase from Tween wash of conidia. Where as, one to three activities with different intensities appeared on gel from washing of conidia to incubation in water till day 4. The relative migrations of these activities on 1-DE nPAGE zymograms appeared as fast, medium and slow on gel. The 2-D spot densitometry of zymograms indicated isoforms have different proteolytic activity as quantified by pixel intensities. SDS-PAGE zymography indicated the release of two isozymes of Mr 103 and 12 kDa during Tween treatment of conidia. However, during the first washing step with water and incubation of spores at day 2 and 3, respectively, only 12 kDa protein was evident. Majority of these proteases were inhibited by EDTA, but stimulated by CaCl(2), and MgCl(2). The presence of isozymes in conidia and their release during hydration must have functional significance for fungi and in this case it should provide advantages to M. anisopliae in its saprobic or pathogenic modalities. To our knowledge this is the first report describing release of metalloprotease isozymes from conidia.     

X-Ray and IR-Studies on the Dehydrated Fish Flesh

Many actinomycetes, newly isolated from soil, converted (?)-carvone to either (?)-trans-carveol or (?)-cis-carveol or to a mixture of both compounds, and known metabolic products, such as (+)-dihydrocarvone, (+)-isodihydrocarvone, (+)-neodihydrocarveol, (?)-dihydrocarveol, (+)-isodihydrocarveol and (+)-neoisodihydrocarveol.

Identification of the metabolic products and the metabolic pathways of (?)-carvone were described in a strain of Streptomyces, A-5–1 and a strain of Nocardia, 1-3-11. A summary shows the reaction mechanism pattern of (?)-carvone conversion by actinomycetes.     

Calorimetric and Microstructural Investigation of Frozen Hydrated Gluten

The thermal and microstructural properties of frozen hydrated gluten were studied by using differential scanning calorimetry (DSC), modulated DSC, and low-temperature scanning electron microscopy (cryo-SEM). This work was undertaken to investigate the thermal transitions observed in frozen hydrated gluten and relate them to its microstructure. The minor peak that is observed just before the major endotherm (melting of bulk ice) was assigned to the melting of ice that is confined to capillaries formed by gluten. The Defay–Prigogine theory for the depression of melting point of fluids confined in capillaries was put forward in order to explain the calorimetric results. The pore radius size of the capillaries was calculated by using four different empirical models. Kinetic analysis of the growth of the pore radius size revealed that it follows first-order kinetics. Cryo-SEM observations revealed that gluten forms a continuous homogeneous and not fibrous network. Results of the present investigation showed that is impossible to assign a T _g value for hydrated frozen gluten because of the wide temperature range over which the gluten matrix vitrifies, and therefore the construction of state diagrams is not feasible at subzero temperatures for this material. Furthermore, the gluten matrix is deteriorated with two different mechanisms from ice recrystallization, one that results from the growth of ice that is confined in capillaries and the other from the growth of bulk ice.     

Screening and Identification of a Specific Binding Peptide to Ovarian Cancer Cells from a Phage-Displayed Peptide Library

To select specific binding peptides for imaging and detection of human ovarian cancer. The phage 12-mer peptide library was used to select specific phage clones to ovarian cancer cells. After four rounds of biopanning, the binding specificity of randomly selected phage clones to ovarian cancer cells was determined by enzyme-linked immunosorbent assay (ELISA). DNA sequencing and homology analysis were performed on specifically bound phages. The binding ability of the selected peptides to SKOV3 cells was confirmed by fluorescence microscopy and flow cytometry. After four rounds of optimized biological panning, phage recovery was 34-fold higher than that of the first round, and the specific phage clones bound to SKOV3 cells were significantly enriched. A total of 32 positive phage clones were preliminarily identified by ELISA from 54 randomly selected clones, and the positive rate was 59.3%. S36 was identified as the clone with best affinity to SKOV3 cells via fluorescence microscopy and flow cytometry. A representative clone of OSP2, S36 is expected to be an effective probe for diagnosis and treatment of ovarian cancer.

     

Molecular Rigidity in Dry and Hydrated Onion Cell Walls

Solid-state nuclear magnetic resonance relaxation experiments can provide information on the rigidity of individual molecules within a complex structure such as a cell wall, and thus show how each polymer can potentially contribute to the rigidity of the whole structure. We measured the proton magnetic relaxation parameters T2 (spin-spin) and T1p (spin-lattice) through the 13C-nuclear magnetic resonance spectra of dry and hydrated cell walls from onion (Allium cepa L.) bulbs. Dry cell walls behaved as rigid solids. The form of their T2 decay curves varied on a continuum between Gaussian, as in crystalline solids, and exponential, as in more mobile materials. The degree of molecular mobility that could be inferred from the T2 and T1p decay patterns was consistent with a crystalline state for cellulose and a glassy state for dry pectins. The theory of composite materials may be applied to explain the rigidity of dry onion cell walls in terms of their components. Hydration made little difference to the rigidity of cellulose and most of the xyloglucan shared this rigidity, but the pectic fraction became much more mobile. Therefore, the cellulose/xyloglucan microfibrils behaved as solid rods, and the most significant physical distinction within the hydrated cell wall was between the microfibrils and the predominantly pectic matrix. A minor xyloglucan fraction was much more mobile than the microfibrils and probably corresponded to cross-links between them. Away from the microfibrils, pectins expanded upon hydration into a nonhomogeneous, but much softer, almost-liquid gel. These data are consistent with a model for the stress-bearing hydrated cell wall in which pectins provide limited stiffness across the thickness of the wall, whereas the cross-linked microfibril network provides much greater rigidity in other directions.     

肌肽,一种神奇的小肽

阐述了国内外关于对肌肽生物学作用研究的最新进展和医学应用前景,详述了肌肽的抗自由基,抗氧化及抗衰老作用的实验依据及可能的作用机制。     

东北林蛙皮肤中一类新抗菌肽cDNA的克隆及成熟肽的预测

为进一步研究和开发高效广谱天然抗生素的抗菌肽,本文克隆东北林蛙(Rana dybowskii)的抗菌肽基因,并预测其成熟肽的有关性质。根据蛙属抗菌肽信号肽末端序列设计简并引物,以RT-PCR技术扩增皮肤中抗菌肽的cDNA,并进行克隆测序。用生物信息学软件分析cDNA序列特点,预测成熟肽的理化性质。研究发现一种长度为28个氨基酸残基的新抗菌肽dybowsin-1,该肽具有Rana box结构;与已发现的抗菌肽仅有35%的同源性;理论等电点在9.70-10.01之间;均呈阳离子性;从第3或4个氨基酸开始到第16个氨基酸形成α-螺旋结构,极性氨基酸位于螺旋轮的一侧,非极性氨基酸位于螺旋轮的另一侧;具有N-端疏水、C-端亲水的两亲性。一个个体表达5条cDNA序列编码3种不同的dybowsin-1分子,显示出该抗菌肽表达的多样性。序列分析显示,该抗菌肽可能由多基因座位编码。     

A Dynamic Hydrophobic Core and Surface Salt Bridges Thermostabilize a Designed Three-Helix Bundle

Thermostable proteins are advantageous in industrial applications, as pharmaceuticals or biosensors, and as templates for directed evolution. As protein-design methodologies improve, bioengineers are able to design proteins to perform a desired function. Although many rationally designed proteins end up being thermostable, how to intentionally design de novo, thermostable proteins is less clear. UVF is a de novo-designed protein based on the backbone structure of the Engrailed homeodomain (EnHD) and is highly thermostable (T_m > 99°C vs. 52°C for EnHD). Although most proteins generally have polar amino acids on their surfaces and hydrophobic amino acids buried in their cores, protein engineers followed this rule exactly when designing UVF. To investigate the contributions of the fully hydrophobic core versus the fully polar surface to UVF’s thermostability, we built two hybrid, chimeric proteins combining the sets of buried and surface residues from UVF and EnHD. Here, we determined a structural, dynamic, and thermodynamic explanation for UVF’s thermostability by performing 4 μs of all-atom, explicit-solvent molecular dynamics simulations at 25 and 100°C, Tanford-Kirkwood solvent accessibility Monte Carlo electrostatic calculations, and a thermodynamic analysis of 40 temperature runs by the weighted-histogram analysis method of heavy-atom, structure-based models of UVF, EnHD, and both chimeric proteins. Our models showed that UVF was highly dynamic because of its fully hydrophobic core, leading to a smaller loss of entropy upon folding. The charged residues on its surface made favorable electrostatic interactions that contributed enthalpically to its thermostability. In the chimeric proteins, both the hydrophobic core and charged surface independently imparted thermostability.     

Evaluation of Miniature Test for Bacteriuria Using Dehydrated Media and Nitrite Pads

A new dip-inoculum method for detecting bacteriuria which utilizes dehydrated media pads and a nitrite pad attached to a small plastic strip was evaluated in hospitalized patients. Discrepant interpretations were made by independent observers in 9.3% of the specimens with > 10(5) colonies per ml. The media pads failed to support growth of yeast and gave variable results with Staphylococcus epidermidis and non-group D streptococci. False-negative culture results commonly occurred if the patients were receiving antibiotics. The nitrite test occasionally remained positive for brief periods after the elimination of bacteriuria by antibiotics. Conditions and drugs (especially phenazopyridine) which discolor urine interfered with reading both the culture and nitrite tests. Although not suitable for hospital use, or for monitoring therapy, the test strip is probably as reliable as the calibrated loop-streak plate culture for office screening.