Efficient algorithms to explore conformation spaces of flexible protein loops

Several applications in biology - e.g., incorporation of protein flexibility in ligand docking algorithms, interpretation of fuzzy X-ray crystallographic data, and homology modeling - require computing the internal parameters of a flexible fragment (usually, a loop) of a protein in order to connect its termini to the rest of the protein without causing any steric clash. One must often sample many such conformations in order to explore and adequately represent the conformational range of the studied loop. While sampling must be fast, it is made difficult by the fact that two conflicting constraints - kinematic closure and clash avoidance - must be satisfied concurrently. This paper describes two efficient and complementary sampling algorithms to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples broadly from this space, while the "deformation sampling" algorithm uses seed conformations as starting points to explore the conformation space around them at a finer grain. Computational results are presented for various loops ranging from 5 to 25 residues. More specific results also show that the combination of the sampling algorithms with a functional site prediction software (FEATURE) makes it possible to compute and recognize calcium-binding loop conformations. The sampling algorithms are implemented in a toolkit (LoopTK), which is available at https://simtk.org/home/looptk.     

Changes in the mechanical properties of the respiratory system during the development of interstitial lung edema

Background

Pulmonary edema induces changes in airway and lung tissues mechanical properties that can be measured by low-frequency forced oscillation technique (FOT). It is preceded by interstitial edema which is characterized by the accumulation of extravascular fluid in the interstitial space of the air-blood barrier. Our aim was to investigate the impact of the early stages of the development of interstitial edema on the mechanical properties of the respiratory system.

Methods

We studied 17 paralysed and mechanically ventilated closed-chest rats (325–375 g). Total input respiratory system impedance (Zrs) was derived from tracheal flow and pressure signals by applying forced oscillations with frequency components from 0.16 to 18.44 Hz distributed in two forcing signals. In 8 animals interstitial lung edema was induced by intravenous infusion of saline solution (0.75 ml/kg/min) for 4 hours; 9 control animals were studied with the same protocol but without infusion. Zrs was measured at the beginning and every 15 min until the end of the experiment.

Results

In the treated group the lung wet-to-dry weight ratio increased from 4.3 ± 0.72 to 5.23 ± 0.59, with no histological signs of alveolar flooding. Resistance (Rrs) increased in both groups over time, but to a greater extent in the treated group. Reactance (Xrs) did not change in the control group, while it decreased significantly at all frequencies but one in the treated. Significant changes in Rrs and Xrs were observed starting after ~135 min from the beginning of the infusion. By applying a constant phase model to partition airways and tissue mechanical properties, we observed a mild increase in airways resistance in both groups. A greater and significant increase in tissue damping (from 603.5 ± 100.3 to 714.5 ± 81.9 cmH₂O/L) and elastance (from 4160.2 ± 462.6 to 5018.2 ± 622.5 cmH₂O/L) was found only in the treated group.

Conclusion

These results suggest that interstitial edema has a small but significant impact on the mechanical features of lung tissues and that these changes begin at very early stages, before the beginning of accumulation of extravascular fluid into the alveoli.     

Hypoxia-induced modifications in plasma membranes and lipid microdomains in A549 cells and primary human alveolar cells

We evaluated the response to mild hypoxia exposure of A549 alveolar human cells and of a continuous alveolar cell line from human excised lungs (A30) exposed to 5% O(2) for 5 and 24 h. No signs of increased peroxidation and of early apoptosis were detected. After 24 h of hypoxia total cell proteins/DNA ratio decreased significantly by about 20%. Similarly, we found a decrease in membrane phospholipid and cholesterol content. The membrane fluidity assessed by fluorescence anisotropy measurements was unchanged. We also prepared the detergent resistant membrane fraction (DRM) to analyze the distribution of the two types of lipid microdomains, caveolae and lipid rafts. The DRM content of Cav-1, marker of caveolae, was decreased, while CD55, marker of lipid rafts, increased in both cell lines. Total content of these markers in the membranes was unchanged indicating remodelling of their distribution between detergent-resistant and detergent-soluble fraction of the cellular membrane. The changes in protein markers distribution did not imply changes in the corresponding mRNA, except in the case of Cav-1 for A30 line. In the latter case we found a parallel decrease in Cav-1 and in the corresponding mRNA. We conclude that an exposure to a mild degree of hypoxia triggers a significant remodelling of the lipid microdomains expression, confirming that they are highly dynamic structures providing a prompt signalling platform to changes of the pericellular microenvironment.     

Structural analysis of the Sulfolobus solfataricus MCM protein N-terminal domain

The Mini-Chromosome Maintenance (MCM) proteins are candidates of replicative DNA helicase in eukarya and archaea. Here we report a 2.8 Å crystal structure of the N-terminal domain (residues 1–268) of the Sulfolobus solfataricus MCM (Sso MCM) protein. The structure reveals single-hexameric ring-like architecture, at variance from the protein of Methanothermobacter thermoautotrophicus (Mth). Moreover, the central channel in Sso MCM seems significantly narrower than the Mth counterpart, which appears to more favorably accommodate single-stranded DNA than double-stranded DNA, as supported by DNA-binding assays. Structural analysis also highlights the essential role played by the zinc-binding domain in the interaction with nucleic acids and allows us to speculate that the Sso MCM N-ter domain may function as a molecular clamp to grasp the single-stranded DNA passing through the central channel. On this basis possible DNA unwinding mechanisms are discussed.     

Timescales and cultural process at 40,000 BP in the light of the Campanian Ignimbrite eruption, Western Eurasia

Significant new information shows that the Campanian Ignimbrite (CI) eruption from the Phlegrean Fields, southern Italy, was much larger than hitherto supposed and in fact one of the largest late Quaternary explosive events. The eruption can be dated to 40,000 calendar years ago, within the interval of the so-called Middle to Upper Paleolithic 'transition'. Its position can be precisely correlated with a number of other environmental events, including Heinrich Event 4 (HE4), the Laschamp excursion, and a particular cosmogenic nuclide peak. In view of this unique combination of factors, we studied the CI volcanic catastrophe with particular attention to its impact on climate and human ecosystems, including potential interference with ongoing processes of cultural evolution (biological evolution is best left aside for the moment). The contribution of this research is chronological and ecological. The CI volcanic event provides an unequalled means of correlating stratigraphic sequences across Western Eurasia, either directly or indirectly, and affords a unique opportunity to establish the age and climatic context of important archaeological sequences. Ecologically, the CI eruption inevitably interacted with the beginning of HE4 in terms of atmospheric feedback systems. Their combined forcing produced a sudden and at least hemispheric climatic deterioration; a 'volcanic winter' scenario cannot be ruled out. Paleolithic occupation was severely altered throughout the direct-impact zone of the eruption and likely along fringe areas in southern and southeastern Europe. The above observations call for a reconsideration of the processes and rhythms involved in the Middle to Upper Paleolithic 'transition'. A tentative model is suggested that links the exceptional environmental stress at 40,000 BP with processes already active in Paleolithic societies, leading to a period of accelerated change in cultural configurations. These eventually evolved into an Upper Paleolithic proper at a later date. The evidence to invoke allochthonous cultural input or invasionist scenarios is not considered compelling.     

Purification and characterization of a novel recombinant highly enantioselective short-chain NAD(H)-dependent alcohol dehydrogenase from Thermus thermophilus

The gene encoding a novel alcohol dehydrogenase (ADH) that belongs to the short-chain dehydrogenase/reductase (SDR) superfamily was identified in the extremely thermophilic, halotolerant gram-negative eubacterium Thermus thermophilus HB27. The T. thermophilus ADH gene (adh(Tt)) was heterologously overexpressed in Escherichia coli, and the protein (ADH(Tt)) was purified to homogeneity and characterized. ADH(Tt) is a tetrameric enzyme consisting of identical 26,961-Da subunits composed of 256 amino acids. The enzyme has remarkable thermophilicity and thermal stability, displaying activity at temperatures up to approximately 73 degrees C and a 30-min half-inactivation temperature of approximately 90 degrees C, as well as good tolerance to common organic solvents. ADH(Tt) has a strict requirement for NAD(H) as the coenzyme, a preference for reduction of aromatic ketones and alpha-keto esters, and poor activity on aromatic alcohols and aldehydes. This thermophilic enzyme catalyzes the following reactions with Prelog specificity: the reduction of acetophenone, 2,2,2-trifluoroacetophenone, alpha-tetralone, and alpha-methyl and alpha-ethyl benzoylformates to (S)-(-)-1-phenylethanol (>99% enantiomeric excess [ee]), (R)-alpha-(trifluoromethyl)benzyl alcohol (93% ee), (S)-alpha-tetralol (>99% ee), methyl (R)-(-)-mandelate (92% ee), and ethyl (R)-(-)-mandelate (95% ee), respectively, by way of an efficient in situ NADH-recycling system involving 2-propanol and a second thermophilic ADH. This study further supports the critical role of the D37 residue in discriminating NAD(H) from NADP(H) in members of the SDR superfamily.     

Design of Supervisors to Avoid Deadlock in Flexible Assembly Systems

Modern production systems exhibit a high degree of resource sharing that can lead to deadlock conditions. Deadlock arises when some parts remain indefinitely blocked because each of them requests access to a resource held by some other parts. One of the tasks of the control system lies in preventing such situations from occurring by proper resource management. This article addresses the deadlock problem for an important class of production facilities, that is, flexible assembly systems, that can perform both manufacturing or assembly operations. In particular, we develop an approach to deadlock avoidance based on a supervisory control that works by inhibiting or enabling the events involving resource allocation. The article proposes two supervisors characterized by easy implementation, efficiency, and flexibility in resource management. The analysis of some case studies, performed by discrete event simulation, confirms the effectiveness of the approach.     

Effects of intermediates on aggregation of native bovine serum albumin

Protein aggregation has been recognized to be a pathological indicator for several fatal diseases, such as Alzheimer's disease, transmissible spongiform encephalopathies, Creutzfeldt-Jacob disease, etc. Aggregation usually involves conformational changes of proteins that have acquired an intermediate beta-structure-rich conformation and can occur even at low protein concentration. Recent work in our laboratory has shown that bovine serum albumin (BSA), even at low-concentration, exhibits self-association properties related to conformational changes, so providing a very convenient model system to study this class of problems. Here we report data (obtained by different experimental techniques) on a mixture of BSA in native and intermediate (beta-structure-rich) form. Results show that the interaction between the two species is responsible for a decrease in the thermodynamic stability of the solution. This occurs without requiring noticeable conformational changes of the native protein. Results presented here can provide new insight on the "protein only" hypothesis proposed for the formation of plaques involved in several neurodegenerative diseases.     

Intrasexual and intersexual dimorphisms of the red salmon prosencephalon

Intrasexual as well as intersexual dimorphisms were found in the prosencephalon and mesencephalon of adult Oncorhynchus nerka (red/sockeye salmon). These dimorphisms are concerned with the position of the preoptic nucleus, nucleus lateralis tuberis, habenula, third ventricle, tectal ventricles, preoptic recess, recessus lateralis, horizontal commissure, posterior commissure, and toral commissure. The intrasexual dimorphism was characterized by either a rostral ("r"-pattern) or a caudal ("c"-pattern) position of the preoptic region as well as varying locations of other structures within the prosencephalon. As compared to "c"-pattern fish, the preoptic nucleus and nucleus lateralis tuberis were located more rostral, and the habenula was positioned further caudal, in "r"-type animals. The intersexual dimorphism was also characterized by different positions of the structures listed above. With the exception of the preoptic nucleus, all of these were located further rostral in "r"-pattern females than in type "r" males. In "c"-pattern females, they were positioned further caudal than in type "c" males. The number of neurons in the parvocellular and in the magnocellular portion of the preoptic region differed in the two genders with respect to "r"- as well as "c"-pattern fish. Males had more neurons than females in both the magno- and the parvocellular subdivisions of the preoptic region. In "r"- and "c"-pattern fish, the average size of magnocellular preoptic neurons was larger in females than in males. The observed intersexual variations may reflect gender-specific differences in the control of the pituitary. Functional correlates of intrasexual dimorphism are obscure.     

Interaction of processes on different length scales in a bioelastomer capable of performing energy conversion

This work concerns the aggregation properties of (Gly-Val-Gly-Val-Pro)(251) rec, a polypentapeptide reflecting a highly conserved repetitive unit of the bioelastomer, elastin. On raising the temperature of aqueous solutions above 25 degrees C, this polypeptide was already known to undergo concurrent conformational changes (hydrophobic folding), phase separation, and self-assembly with formation of aggregated three-stranded filaments composed of dynamic polypeptide helices, called beta-spirals. Aggregates obtained from the solution can be shaped into bands that acquire entropic elastic properties upon gamma-irradiation and can perform a variety of energy conversions. Previous studies have shown that aggregation is prompted by the (diverging) critical fluctuations of concentration occurring in the solution, in vicinity of its spinodal line. Here, we present combined circular dicroism (CD) and light scattering experiments, and independent fittings of experimental data to the theoretical spinodal and binodal (coexistence) lines. Results show the following logical and causal sequence of processes: (a) Smooth and progressive conformational changes promoted by concentration fluctuations occurring as temperature is raised "pull down" (in the temperature scale) the instability region of the solution. (b) This further promotes critical fluctuations. (c) The related locally high concentration prompts a further substantial conformational change ending in triple-helix formation and coacervation. (d) This intertwining of processes, covering different length scales (from that of individual peptides to the mesoscopic one of demixed regions), is related to the fact that solvent-induced interactions play a strong role over the entire scale span. These results concur with other recent ones in pointing out that process interactions over many length-scales probably reflect a frequent if not ubiquitous pattern in protein aggregation. This may be highly relevant to the desirable deep understanding of such phenomenon, whose interests cover many fields.