Macromolecular docking restrained by a small angle X-ray scattering profile

While many structures of single protein components are becoming available, structural characterization of their complexes remains challenging. Methods for modeling assembly structures from individual components frequently suffer from large errors, due to protein flexibility and inaccurate scoring functions. However, when additional information is available, it may be possible to reduce the errors and compute near-native complex structures. One such type of information is a small angle X-ray scattering (SAXS) profile that can be collected in a high-throughput fashion from a small amount of sample in solution. Here, we present an efficient method for protein–protein docking with a SAXS profile (FoXSDock): generation of complex models by rigid global docking with PatchDock, filtering of the models based on the SAXS profile, clustering of the models, and refining the interface by flexible docking with FireDock. FoXSDock is benchmarked on 124 protein complexes with simulated SAXS profiles, as well as on 6 complexes with experimentally determined SAXS profiles. When induced fit is less than 1.5 Å interface C_α RMSD and the fraction residues of missing from the component structures is less than 3%, FoXSDock can find a model close to the native structure within the top 10 predictions in 77% of the cases; in comparison, docking alone succeeds in only 34% of the cases. Thus, the integrative approach significantly improves on molecular docking alone. The improvement arises from an increased resolution of rigid docking sampling and more accurate scoring.     

Monolayer–multilayer transitions in a lung surfactant model: IR reflection–absorption spectroscopy and atomic force microscopy

A hydrophobic pulmonary surfactant protein, SP-C, has been implicated in surface-associated activities thought to facilitate the work of breathing. Model surfactant films composed of lipids and SP-C display a reversible transition from a monolayer to surface-associated multilayers upon compression and expansion at the air/water (A/W) interface. The molecular-level mechanics of this process are not yet fully understood. The current work uses atomic force microscopy on Langmuir–Blodgett films to verify the formation of multilayers in a dipalmitoylphosphatidylcholine, dipalmitoylphosphatidylglycerol, cholesterol, and SP-C model system. Isotherms of SP-C-containing films are consistent with exclusion and essentially complete respreading during compression and expansion, respectively. Multilayer formation was not detected in the absence of SP-C. Most notable are the results from IR reflection–absorption spectroscopy (IRRAS) conducted at the A/W interface, where the position and intensity of the Amide I band of SP-C reveal that the predominantly helical structure changes its orientation in monolayers versus multilayers. IRRAS measurements indicate that the helix tilt angle changed from approximately 80° in monolayers to a transmembrane orientation in multilayers. The results constitute the first quantitative measure of helix orientation in mixed monolayer/multilamellar domains at the A/W interface and provide insight into the molecular mechanism for SP-C-facilitated respreading of surfactant.     

Surface energy components of a dye-ligand immobilized pHEMA membranes: effects of their molecular attracting forces for non-covalent interactions with IgG and HSA in aqueous media

In the present paper, we report the study of the adsorption behaviour of human immunoglobulin G (IgG), human serum albumin (HSA) and polyethylenimine (PEI) onto surfaces of Procion Green HE-4BD (PG) immobilized poly(hydroxyethylmethacrylate) (pHEMA) membranes. The adsorption behaviour of the IgG and HSA onto surfaces of the PG–PEI complexed membrane was also studied. Surface wettability and hydrophilicity of all the membranes were investigated by static contact angle measurements. The measurements of the contact angle to various test liquids, i.e., water, glycerol, formamide, diiodomethane (DIM) and ethylene glycol on the investigated membranes were made by sessile drop method. In accordance to the Young equation, the smaller the surface tension of the test liquid, the smaller becomes the contact angles measured on all the investigated membranes surfaces. The highest contact angles were obtained with water, whereas ethylene glycol gave the lowest contact angles for all the tested membranes. Component and parameters of the surface free energy of all the investigated membranes were calculated from measured contact angle values using two methods (the geometric mean by Fowkes and acid–base by van Oss). HSA adsorption was enhanced after complexation of PEI with the immobilized dye-ligand. The adsorption of proteins and PEI significantly changed both the contact angles and component of surface free energies of the investigated membranes.     

SOFAST-HMQC Experiments for Recording Two-dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds

Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein ¹H–¹⁵N correlation spectra in a few seconds of acquisition time using a new SOFAST-HMQC experiment (Schanda and Brutscher (2005) J. Am. Chem. Soc. 127, 8014). Here, we investigate in detail the performance of SOFAST-HMQC to record ¹H–¹⁵N and ¹H−¹³C correlation spectra of proteins of different size and at different magnetic field strengths. Compared to standard ¹H–¹⁵N correlation experiments SOFAST-HMQC provides a significant gain in sensitivity, especially for fast repetition rates. Guidelines are provided on how to set up SOFAST-HMQC experiments for a given protein sample. In addition, an alternative pulse scheme, IPAP-SOFAST-HMQC is presented that allows application on NMR spectrometers equipped with cryogenic probes, and fast measurement of one-bond ¹H–¹³C and ¹H–¹⁵N scalar and residual dipolar coupling constants.     

Residual backbone and side-chain <Superscript>13</Superscript>C and <Superscript>15</Superscript>N resonance assignments of the intrinsic transmembrane light-harvesting 2 protein complex by solid-state Magic Angle Spinning NMR spectroscopy

This study reports the sequence specific chemical shifts assignments for 76 residues of the 94 residues containing monomeric unit of the photosynthetic light-harvesting 2 transmembrane protein complex from Rhodopseudomonas acidophila strain 10050, using Magic Angle Spinning (MAS) NMR in combination with extensive and selective biosynthetic isotope labeling methods. The sequence specific chemical shifts assignment is an essential step for structure determination by MAS NMR. Assignments have been performed on the basis of 2-dimensional proton-driven spin diffusion ¹³C–¹³C correlation experiments with mixing times of 20 and 500 ms and band selective ¹³C–¹⁵N correlation spectroscopy on a series of site-specific biosynthetically labeled samples. The decreased line width and the reduced number of correlation signals of the selectively labeled samples with respect to the uniformly labeled samples enable to resolve the narrowly distributed correlation signals of the backbone carbons and nitrogens involved in the long -helical transmembrane segments. Inter-space correlations between nearby residues and between residues and the labeled BChl a cofactors, provided by the ¹³C–¹³C correlation experiments using a 500 ms spin diffusion period, are used to arrive at sequence specific chemical shift assignments for many residues in the protein complex. In this way it is demonstrated that MAS NMR methods combined with site-specific biosynthetic isotope labeling can be used for sequence specific assignment of the NMR response of transmembrane proteins.     

New anatomical method of grain angles measurement using confocal microscopy and image cross-correlation

Some tropical trees with indistinct growth rings have a distinct interlocked grain that reveals their internal growth rhythm. To determine their growth rhythm, it is necessary to accurately measure the wood grain angle. The usual methods for grain angle measurement are radial splitting using wood disks, which occasionally provides inaccurate data, and serial tangential sectioning, which requires preparation and analysis of many sections. The present report proposes an easier but accurate method to measure grain angle using a single xylem transverse section. A confocal microscope was used to obtain two optical sections of different depths from a transverse section of a 7-year-old Hopea odorata Roxb. The tangential lag between the optical images was then calculated using image cross-correlation and transformed into grain angle. Radially consecutive sampling revealed distinct radial fluctuations in the grain angle. The fluctuation data were compared to data obtained by radial splitting and serial tangential sectioning. There was a strong correlation between grain angle using the three methods. In the region close to the cambium, however, the present method revealed an abrupt change in the grain angle, although radial splitting showed a smooth undulation throughout the radius. Using the present method, the analysis of a radial range of 5 cm required a single transverse section compared to 1,000 tangential sections 50-m thick. In conclusion, the present method using a single transverse section, confocal microscopy, and image cross-correlation analysis provides more accurate data than radial splitting, and is less time-consuming than serial tangential sectioning.     

Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria

Chlorosomes of green photosynthetic bacteria constitute the most efficient light harvesting complexes found in nature. In addition, the chlorosome is the only known photosynthetic system where the majority of pigments (BChl) is not organized in pigment-protein complexes but instead is assembled into aggregates. Because of the unusual organization, the chlorosome structure has not been resolved and only models, in which BChl pigments were organized into large rods, were proposed on the basis of freeze-fracture electron microscopy and spectroscopic constraints. We have obtained the first high-resolution images of chlorosomes from the green sulfur bacterium Chlorobium tepidum by cryoelectron microscopy. Cryoelectron microscopy images revealed dense striations approximately 20 A apart. X-ray scattering from chlorosomes exhibited a feature with the same approximately 20 A spacing. No evidence for the rod models was obtained. The observed spacing and tilt-series cryoelectron microscopy projections are compatible with a lamellar model, in which BChl molecules aggregate into semicrystalline lateral arrays. The diffraction data further indicate that arrays are built from BChl dimers. The arrays form undulating lamellae, which, in turn, are held together by interdigitated esterifying alcohol tails, carotenoids, and lipids. The lamellar model is consistent with earlier spectroscopic data and provides insight into chlorosome self-assembly.     

内蒙古荒漠草原地表反照率变化特征

基于2008年全年内蒙古荒漠草原的气象观测数据对荒漠草原地表反照率的变化特征分析发现,内蒙古荒漠草原的地表反照率在晴天呈早晚高、正午前后低的U形变化特征,降水引起的土壤含水量变化将导致地表反照率减小,云对地表反照率的影响比较复杂。荒漠草原地表反照率的月平均日变化类似于晴天条件下的日变化,大多数月份呈现早晚高正午前后低的U形变化趋势,仅在1-2月份及11-12月份呈现V形。地表反照率的季节变化较为明显。在生长季,由于存在植被覆盖使得地表反照率较低;而在冬季,地表反照率较高,特别是1\,2月份,其月均值分别为0.56和0.48,甚至高于沙漠。9月份地表反照率月均值达到最小值0.230, 7、8\,9月份地表反照率接近,分别为0.236、0.232和0.230。而且在生长季,荒漠草原的地表反照率高于退化草地、农田及麦田,低于沙漠的地表反照率,但是荒漠草原的地表反照率除7-10月份明显低于沙漠地表反照率外(相差大于0.02),生长季的其它月份与沙漠相差不大。晴天地表反照率随太阳高度角的增大而减小,当太阳高度角大于40°时,地表反照率趋于稳定,其与太阳高度角呈指数关系。土壤含水量的增大会导致地表反照率的减小,地表反照率与土壤含水量呈指数或线性关系。根据地表反照率与这两个因子之间的单因子关系式,建立了内蒙古荒漠草原晴天地表反照率随太阳高度角与土壤含水量变化的双因子参数化公式,而且太阳高度角和土壤含水量两者共同解释了地表反照率变化的68%左右。该公式可以较好地模拟内蒙古荒漠草原晴天地表反照率的变化。该公式是否可以进一步耦合到天气或气候模式中,还需要借助更多代表性的观测资料的验证,但是本研究无疑对陆面模式中地表反照率更准确的参数化及模拟提供了参考依据。     

Light Activation of Rhodopsin: Insights from Molecular Dynamics Simulations Guided by Solid-State NMR Distance Restraints

Structural restraints provided by solid-state NMR measurements of the metarhodopsin II intermediate are combined with molecular dynamics simulations to help visualize structural changes in the light activation of rhodopsin. Since the timescale for the formation of the metarhodopsin II intermediate (> 1 ms) is beyond that readily accessible by molecular dynamics, we use NMR distance restraints derived from ¹³C dipolar recoupling measurements to guide the simulations. The simulations yield a working model for how photoisomerization of the 11-cis retinylidene chromophore bound within the interior of rhodopsin is coupled to transmembrane helix motion and receptor activation. The mechanism of activation that emerges is that multiple switches on the extracellular (or intradiscal) side of rhodopsin trigger structural changes that converge to disrupt the ionic lock between helices H3 and H6 on the intracellular side of the receptor.