Comparison of conformational characteristics in structurally similar protein pairs.

Although it is known that three-dimensional structure is well conserved during the evolutionary development of proteins, there have been few studies that consider other parameters apart from divergence of the main-chain coordinates. In this study, we align the structures of 90 pairs of homologous proteins having sequence identities ranging from 5 to 100%. Their structures are compared as a function of sequence identity, including not only consideration of C alpha coordinates but also accessibility, Ooi numbers, secondary structure, and side-chain angles. We discuss how these properties change as the sequences become less similar. This will be of practical use in homology modeling, especially for modeling very distantly related or analogous proteins. We also consider how the average size and number of insertions and deletions vary as sequences diverge. This study presents further quantitative evidence that structure is remarkably well conserved in detail, as well as at the topological level, even when the sequences do not show similarity that is significant statistically.     

Representing an ensemble of NMR-derived protein structures by a single structure.

The usefulness of representing an ensemble of NMR-derived protein structures by a single structure has been investigated. Two stereochemical properties have been used to assess how a single structure relates to the ensemble from which it was derived, namely the distribution of phi psi torsion angles and the distribution of chi 1 torsion angles. The results show that the minimized average structure derived from the ensemble (a total of 11 ensembles from the Brookhaven Protein Data Bank were analyzed) does not always correspond well with this ensemble, particularly for those ensembles generated with a smaller number of experimentally derived restraints per residue. An alternative method that selects the member of the ensemble which is closest to the "average" of the ensemble has been investigated (a total of 23 ensembles from the Brookhaven Protein Data Bank were analyzed). Although this method selected a structure that on the whole corresponded more closely to the ensemble than did the minimized average structure, this is still not a totally reliable means of selecting a single structure to represent the ensemble. This suggests that it is advisable to study the ensemble as a whole. A study has also been made of the practice of selecting the "best" rather than the most representative member of the ensemble. This too suggests that the ensemble should be studied as a whole. A study of the conformational space occupied by the ensemble also suggests the need to consider the ensemble as a whole, particularly for those ensembles generated with a smaller number of experimentally derived restraints per residue.     

Controlling the secondary-structure-forming tendencies of proteins by a backbone torsion-energy term

We examined a new backbone torsion-energy term proposed by us in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, namely the backbone dihedral angles φ and ψ. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both φ and ψ can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase or decrease the α-helix-forming-tendencies by lowering or raising the torsion-energy surface in the α-helix region and likewise increase or decrease the β-sheet-forming tendencies by lowering or raising the surface in the β-sheet region in the Ramachandran space. We applied this torsion-energy modification method to six force fields, AMBER parm94, AMBER parm96, AMBER parm99, CHARMM27, OPLS-AA and OPLS-AA/L, and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming tendencies by performing folding simulations of α-helical and β-hairpin peptides.     

A screening method to analyse the sensitivity of a lower limb multibody kinematic model

The study presents a screening method used to identify the influential parameters of a lower limb model including ligaments, at low numerical cost. Concerning multibody kinematics optimisation, the ligament parameters (isometric length) were found the most influential ones in a previous study. The screening method tested if they remain influential with minimised length variations. The most important parameters for tibiofemoral kinematics were the skin markers, segment lengths and joint parameters, including two ligaments. This was confirmed by a quantitative sensitivity analysis. The screening method has the potential to be used as a stand-alone procedure for a sensitivity analysis.     

Changes in human skeletal muscle architecture and function induced by extended spaceflight

The aim of this study was to quantitatively describe the relationships between joint angles and muscle architecture (lengths (L_f) and angles (Θ_f) of fascicles) of human triceps surae [medial (MG) and lateral (LG) gastrocnemius and soleus (SOL) muscles] in vivo for three men-cosmonaut after long-duration spaceflight. Sagittal sonographs of MG, LG, SOL were taken at ankle was positioned at 15° (dorsiflexion), 0° (neutral position), +15°, and +30° (plantarflexion), with the knee at 90° at rest and after a long-duration spaceflight. At each position, longitudinal ultrasonic images of the MG and LG and SOL were obtained while the cosmonauts was relaxed from which fascicle lengths and angles with respect to the aponeuroses were determined. After space flight plantarflexor force declined significantly (26%; p < 0.001). The internal architecture of the GM, and LG, and SOL muscle was significantly altered. In the passive condition, L_f changed from 45, 53, and 39 mm (knee, 0°, ankle, −15°) to 26, 33, and 28 mm (knee, 90° ankle, 30°) for MG, LG, and SOL, respectively. Different lengths and angles of fascicles, and their changes by contraction, might be related to differences in force-producing capabilities of the muscles and elastic characteristics of tendons and aponeuroses. The three heads of the triceps surae muscle substantially differ in architecture, which probably reflects their functional roles. Differences in fiber length and pennation angle that were observed among the muscles and could be associated with differences in force production and in elastic properties of musculo-tendinous complex and aponeuroses.     

Hepatitis A virus attachment to agri-food surfaces using immunological, virological and thermodynamic assays

AIMS: This study was designed to investigate the ability of hepatitis A virus (HAV) to attach to various food contact surfaces. METHODS AND RESULTS: HAV attachment was demonstrated after elution of attached viruses from solid surfaces by an immunofluorescent method using anti-HAV-specific antibodies and confocal microscopy. Attachment and survival of HAV on stainless steel, copper, polythene and polyvinyl chloride (PVC) at 20 and 4 degrees C after 2 and 4 h were quantified by plaque assay. HAV was shown to attach almost instantaneously to all four surfaces tested. Attachment of HAV depended on initial viral concentration and was slightly greater at 4 degrees C. The total surface energy (gammaTOT), nonpolar Lifshitz-Van der Waals (gammaLW) and polar short range (gammaSR) hydrogen-bonding components for HAV and each surface as well as total free energy of the system were determined by contact angle measurements using an extended Young equation [Young (1805) Philosophical Transactions of The Royal Society (London) 95, 65-87). The calculation of these parameters predicted the favourable conditions for attachment of HAV to all four surfaces tested. CONCLUSION: HAV particles attach to stainless steel, copper, polythene and PVC at 20 and 4 degrees C and the total free energy of the interaction is optimal for this attachment. SIGNIFICANCE AND IMPACT OF THE STUDY: Comprehension of viral attachment to the solid surfaces will permit to successfully disinfect these surfaces and to establish a better surveillance programme for control of viral food-borne illnesses.     

Segment and joint angles of hind limb during bipedal and quadrupedal walking of the bonobo (Pan paniscus)

We describe segment angles (trunk, thigh, shank, and foot) and joint angles (hip, knee, and ankle) for the hind limbs of bonobos walking bipedally ("bent-hip bent-knee walking," 17 sequences) and quadrupedally (33 sequences). Data were based on video recordings (50 Hz) of nine subjects in a lateral view, walking at voluntary speed. The major differences between bipedal and quadrupedal walking are found in the trunk, thigh, and hip angles. During bipedal walking, the trunk is approximately 33-41 degrees more erect than during quadrupedal locomotion, although it is considerably more bent forward than in normal human locomotion. Moreover, during bipedal walking, the hip has a smaller range of motion (by 12 degrees ) and is more extended (by 20-35 degrees ) than during quadrupedal walking. In general, angle profiles in bonobos are much more variable than in humans. Intralimb phase relationships of subsequent joint angles show that hip-knee coordination is similar for bipedal and quadrupedal walking, and resembles the human pattern. The coordination between knee and ankle differs much more from the human pattern. Based on joint angles observed throughout stance phase and on the estimation of functional leg length, an efficient inverted pendulum mechanism is not expected in bonobos.     

Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates

Angular potentials play an important role in the refinement of protein structures through angle-dependent restraints (e.g., those determined by cross-correlated relaxations, residual dipolar couplings, and hydrogen bonds). Analytic derivatives of such angular potentials with respect to the dihedral angles of proteins would be useful for optimizing such restraints and other types of angular potentials (i.e., such as we are now introducing into protein structure prediction) but have not been described. In this article, analytic derivatives are calculated for four types of angular potentials and integrated with the efficient recursive derivative calculation methods of Gō and coworkers. The formulas are implemented in publicly available software and illustrated by refining a low-resolution protein structure with idealized vector-angle, dipolar-coupling, and hydrogen-bond restraints. The method is now being used routinely to optimize hydrogen-bonding potentials in ROSETTA.     

Supramolecular exciton chirality of carotenoid aggregates

The conventional organic chemistry concept of chirality relates to single molecules. This article deals with cases in which exciton chirality is generated by the interaction of associated carotenoids. The handed property responsible for exciton signals in these systems is due to the alignment of neighboring molecules held together by secondary chemical forces. Their mutual positions are characterized by the overlay angle. Experimental manifestation is obtained by spectroscopic studies on carotenoid aggregates. Compared to molecular spectra, both UV/visible and circular dichroism spectroscopic observations reveal modified absorption bands and induced Cotton effects of opposite sign (exciton couplets), respectively. A new term, "supramolecular exciton chirality," is suggested for these phenomena, allowing the detection of weak chemical interactions not readily accessible for experimental studies, although highly important in the mechanism of biological processes.     

On the NMR structure determination of a 44n RNA pseudoknot: Assignment strategies and derivation of torsion angle restraints

The complete T- and pseudoknotted acceptor arm of the tRNA-like structure of turnip yellow mosaic virus (TYMV) genomic RNA has been studied by NMR spectroscopy. Resonance assignment and the gathering of restraints of the 44-mer are impeded by spectral complexity as well as by line broadening. The latter is caused by local dynamical effects in the pseudoknot domain in the molecule. These specific problems could be solved by using different field strengths and selectively ¹³C/¹⁵ labeled samples. Experiments for assigning the sugar spin systems were adjusted to satisfy the requirements of this system. Furthermore, the quality of the structure could be improved by determining the backbone torsion angles , and , using new approaches that were tailored for use in large RNA molecules.