A new approach for extracting information from protein dynamics

Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from network science. Most studies build protein dynamics networks from correlation measures, an approach that only works under very specific conditions, instead of the more robust inverse approach. Thus, we apply the inverse approach to the dynamics of protein dihedral angles, a system of internal coordinates, to avoid structural alignment. Using the well-characterized adhesion protein, FimH, we show that our method identifies networks that are physically interpretable, robust, and relevant to the allosteric pathway sites. We further use our approach to detect dynamical differences, despite structural similarity, for Siglec-8 in the immune system, and the SARS-CoV-2 spike protein. Our study demonstrates that using the inverse approach to extract a network from protein dynamics yields important biophysical insights.     

Essential dynamics of the cold denaturation: pressure and temperature effects in yeast frataxin

The cold denaturation of globular proteins is a process that can be caused by increasing pressure or decreasing the temperature. Currently, the action mechanism of this process has not been clearly understood, raising an interesting debate on the matter. We have studied the process of cold denaturation using molecular dynamics simulations of the frataxin system Yfh1, which has a dynamic experimental characterization of unfolding at low and high temperatures. The frataxin model here studied allows a comparative analysis using experimental data. Furthermore, we monitored the cold denaturation process of frataxin and also investigated the effect under the high‐pressure regime. For a better understanding of the dynamics and structural properties of the cold denaturation, we also analyzed the MD trajectories using essentials dynamic. The results indicate that changes in the structure of water by the effect of pressure and low temperatures destabilize the hydrophobic interaction modifying the solvation and the system volume leading to protein denaturation. Proteins 2016; 85:125–136. © 2016 Wiley Periodicals, Inc.     

Long-term change in growth, mortality and regeneration of trees in Denny Wood, an old-growth wood-pasture in the New Forest (UK)

Long-term changes in stand composition and structure were recorded in Denny Wood (New Forest, UK) by means of a permanent transect covering 2 ha. Denny is an ancient, mixed deciduous wood-pasture dominated by beech (Fagus sylvatica), pedunculate oak (Quercus robur) and holly (Ilex aquifolium) whose canopy trees ranged in age from approximately 70 years to over 300 years when the study began in 1956. Individual trees, shrubs and saplings were mapped and measured at irregular intervals until 1996.

During the 40 years of observations, storms and drought disrupted the stand. Considerable volumes of dead wood accumulated, and canopy gaps extended to 30% of the transect area. Small trees and saplings were severely damaged by ponies and grey squirrels. Regeneration ceased after 1964, due principally to heavy grazing and browsing by deer and ponies. Despite the disturbances, most mortality was due to competitive exclusion within well-stocked parts of the stand.

Historical records from the 17th century onwards demonstrate a long-term change from oak dominance with groups of beech before 1800 to beech dominance in the late 20th century. The stand through which the transect now runs was enclosed in 1870, and this allowed beech to regenerate abundantly, but in the nearby unenclosed part of Denny Wood holly regenerated more abundantly than beech.

The patterns of growth, mortality and regeneration are compared with natural temperate deciduous woodland. The long-term relationship between beech and oak is likely to involve periodic oak regeneration after major disturbances, interspersed with steady increases in the proportion of beech. The implications for managing and monitoring the “Ancient and Ornamental Woods” of the New Forest are considered.     

The effect of temperature on membrane hydraulic conductivity

The objective of this study was to use the temperature dependence of water permeability to suggest the physical mechanisms of water transport across membranes of osmotically slowly responding cells and to demonstrate that insight into water transport mechanisms in these cells may be gained from easily performed experiments using an electronic particle counter. Osmotic responses of V-79W Chinese hamster fibroblast cells were measured in hypertonic solutions at various temperatures and the membrane hydraulic conductivity was determined. The results were fit with the general Arrhenius equation with two free parameters, and also fit with two specific membrane models each having only one free parameter. Data from the literature including that for human bone marrow stem cells, hamster pancreatic islets, and bovine articular cartilage chondrocytes were also examined. The results indicated that the membrane models could be used in conjunction with measured permeability data at different temperatures to investigate the method of water movement across various cell membranes. This approach for slower responding cells challenges the current concept that the presence of aqueous pores is always accompanied by an osmotic water permeability value, P(f)>0.01 cm/s. The possibility of water transport through aqueous pores in lower-permeability cells is proposed.     

Tree regeneration and future dynamics of the laurel forest on Tenerife,Canary Islands

Abstract. We studied two sites in the laurel forest of Tenerife to predict future changes in canopy composition. We used two projection methods: Horn's ‘Markovian Projection’, which utilizes information on juveniles in the vicinity of canopy trees, and a 'Stand Projection’, which ignores such information. We performed these projections both including and excluding a-sexual regeneration. Although all of our projections predict a change in species composition, inclusion of a-sexual reproduction decreased the magnitude of successional change. The persistence of Prunus lusitanica and Ilex canariensis appears to be highly dependent on a-sexual regeneration. Both the Markov- and stand projections predict a slight convergence in species composition between the two sites when only sexual regeneration is considered, and also a higher dominance of the shade-tolerant species Laurus azorica. When a-sexual regeneration is also considered, some divergence is shown, with less projected change in the stand projection than in the Markov projection. In spite of some differences between the models, general patterns such as an increase of shade-tolerant species (Laurus azorica and Prunus lusitanica) and a decrease of shade-intolerant species (Erica arborea, Erica scoparia and Myrica faya) are consistent.     

Environment outweighs the effects of fishing in regulating demersal community structure in an exploited marine ecosystem

Global climate change has already caused bottom temperatures of coastal marine ecosystems to increase worldwide. These ecosystems face many pressures, of which fishing is one of the most important. While consequences of global warming on commercial species are studied extensively, the importance of the increase in bottom temperature and of variation in fishing effort is more rarely considered together in these exploited ecosystems. Using a 17 year time series from an international bottom trawl survey, we investigated covariations of an entire demersal ecosystem (101 taxa) with the environment in the Celtic Sea. Our results showed that over the past two decades, biotic communities in the Celtic Sea were likely controlled more by environmental variables than fisheries, probably due to its long history of exploitation. At the scale of the entire zone, relations between taxa and the environment remained stable over the years, but at a local scale, in the center of the Celtic Sea, dynamics were probably driven by interannual variation in temperature. Fishing was an important factor structuring species assemblages at the beginning of the time series (2000) but decreased in importance after 2009. This was most likely caused by a change in spatial distribution of fishing effort, following a change in targeted taxa from nephrops to deeper water anglerfish that did not covary with fishing effort. Increasing bottom temperatures could induce additional changes in the coming years, notably in the cold‐water commercial species cod, hake, nephrops, and American plaice. We showed that analyzing covariation is an effective way to screen a large number of taxa and highlight those that may be most susceptible to future simultaneous increases in temperature and changes in exploitation pattern by fisheries. This information can be particularly relevant for ecosystem assessments.     

Molecular dynamics simulations of phenylimidazole inhibitor complexes of cytochrome P450 cam

Molecular dynamics simulations have been performed on three phenylimidazole inhibitor complexes ofP450 _cam, utilizing the X-ray structures and the AMBER suite of programs. Compared to their corresponding optimized X-ray structures, very similar features were observed for the 1-phenylimidazole (1-PI) and 2-phenylimidazole (2-PI) complexes during a 100 ps MD simulation. The 1-PI inhibitor binds as a Type II complex with the imidazole nitrogen as a ligand of the heme iron. Analysis of the inhibitor-enzyme interctions during the MD simulations reveals that electrostatic interactions of the imidazole with the heme and van der Waals interactions of the phenyl ring with nearby hydrophobic residues are dominant. By contrast, 2-PI binds as a Type I inhibitor in the substrate binding pocket, but not as a ligand of the iron. The interactions of this inhibitor are qualitatively different from that of the Type II 1-PI, being mainly electrostatic/H-bonding interactions with a bound water and polar residues. Although the third compound, 4-PI, in common with 1-PI, also binds as a Type II inhibitor, with one nitrogen of the imidazole as a ligand to the iron, the MD average binding orientation deviates significantly from the X-ray structure. The most important changes observed include: (1) the rotation of the imidazole ring of this inhibitor by about 90° to enhance electrostatic interactions of the imidazole NH group with the carbonyl group of LEU244, and (2) the rotation of the carbonyl group of ASP251 to form a H-bond with VAL254. An analysis of the H-bonding network surrounding this substrate in the optimized crystal structure revealed that there is no H-bonding partner either for the free polar NH group in the imidazole ring of 4-phenylimidazole or for the polar carbonyl group of the nearby ASP251 residue. The deviation of the dynamically averaged inhibitor-enzyme structure of the 4-PI complex from the optimized crystal structure can therefore be rationalized as a consequence of the optimization of the electrostatic interactions among the polar groups.     

The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine pancreatic trypsin inhibitor dynamics in water as a test case for solvent influences.

In this paper the NMR secondary chemical shifts, that are estimated from a set of 3D-structures, are compared with the observed ones to appraise the behaviour of a known x-ray diffraction structure (of the bovine pancreatic trypsin inhibitor protein) when various molecular dynamics are applied. The results of a 200 ps molecular dynamics under various conditions are analysed and different ways to modify the molecular dynamics are considered. With the purpose of avoiding the time-consuming explicit representation of the solvent (water) molecules, an attempt was made to understand the role of the solvent and to develop an implicit representation, which may be refined. A simulation of hydrophobic effects in an aqueous environment is also proposed which seems to provide a better approximation of the observed solution structure of the protein.     

Multiscale modeling of cellular actin filaments: from atomistic molecular to coarse-grained dynamics

In this article, we present a computational multiscale model for the characterization of subcellular proteins. The model is encoded inside a simulation tool that builds coarse-grained (CG) force fields from atomistic simulations. Equilibrium molecular dynamics simulations on an all-atom model of the actin filament are performed. Then, using the statistical distribution of the distances between pairs of selected groups of atoms at the output of the MD simulations, the force field is parameterized using the Boltzmann inversion approach. This CG force field is further used to characterize the dynamics of the protein via Brownian dynamics simulations. This combination of methods into a single computational tool flow enables the simulation of actin filaments with length up to 400 nm, extending the time and length scales compared to state-of-the-art approaches. Moreover, the proposed multiscale modeling approach allows to investigate the relationship between atomistic structure and changes on the overall dynamics and mechanics of the filament and can be easily (i) extended to the characterization of other subcellular structures and (ii) used to investigate the cellular effects of molecular alterations due to pathological conditions.     

A New Amide Proton R 1ρ Experiment Permits Accurate Characterization of Microsecond Time-scale Conformational Exchange

A new off-resonance spin-lock experiment to record relaxation dispersion profiles of amide protons is presented. The sensitivity-enhanced HSQC-type sequence is designed to minimize the interference from cross-relaxation effects and ensure that the dispersion profiles in the absence of μs-ms time-scale dynamics are flat. Toward this end (i) the proton background is eliminated by sample deuteration (Ishima et al., 1998), (ii) ¹H spin lock is applied to two-spin modes 2(H_xSin ϑ + H_zCos ϑ) N_z, and (iii) the tilt angle ϑ ≈ 35° is maintained throughout the series of measurements (Desvaux et al. Mol. Phys., 86 (1995) 1059). The relaxation dispersion profiles recorded in this manner sample a wide range of effective rf field strengths (up to and in excess of 20 kHz) which makes them particularly suitable for studies of motions on the time scale ≤100 μs. The new experiment has been tested on the Ca²⁺-loaded regulatory domain of cardiac troponin C. Many residues show pronounced dispersions with remarkably similar correlation times of 30 μs. Furthermore, these residues are localized in the regions that have been previously implicated in conformational changes (Spyracopoulos et al. Biochemistry, 36 (1997) 12138) Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.