Protein structure dynamics by crosslinking mass spectrometry

Crosslinking mass spectrometry captures protein structures in solution. The crosslinks reveal spatial proximities as distance restraints, but do not easily reveal which of these restraints derive from the same protein conformation. This superposition can be reduced by photo-crosslinking, and adding information from protein structure models, or quantitative crosslinking reveals conformation-specific crosslinks. As a consequence, crosslinking MS has proven useful already in the context of multiple dynamic protein systems. We foresee a breakthrough in the resolution and scale of studying protein dynamics when crosslinks are used to guide deep-learning-based protein modelling. Advances in crosslinking MS, such as photoactivatable crosslinking and in-situ crosslinking, will then reveal protein conformation dynamics in the cellular context, at a pseudo-atomic resolution, and plausibly in a time-resolved manner.     

Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR

Most proteins are highly flexible and can adopt conformations that deviate from the energetically most favorable ground state. Structural information on these lowly populated, alternative conformations is often lacking, despite the functional importance of these states. Here, we study the pathway by which the Dcp1:Dcp2 mRNA decapping complex exchanges between an autoinhibited closed and an open conformation. We make use of methyl Carr–Purcell–Meiboom–Gill (CPMG) NMR relaxation dispersion (RD) experiments that report on the population of the sparsely populated open conformation as well as on the exchange rate between the two conformations. To obtain volumetric information on the open conformation as well as on the transition state structure we made use of RD measurements at elevated pressures. We found that the open Dcp1:Dcp2 conformation has a lower molecular volume than the closed conformation and that the transition state is close in volume to the closed state. In the presence of ATP the volume change upon opening of the complex increases and the volume of the transition state lies in-between the volumes of the closed and open state. These findings show that ATP has an effect on the volume changes that are associated with the opening-closing pathway of the complex. Our results highlight the strength of pressure dependent NMR methods to obtain insights into structural features of protein conformations that are not directly observable. As our work makes use of methyl groups as NMR probes we conclude that the applied methodology is also applicable to high molecular weight complexes.     

βVI Turns in peptides and proteins: A model peptide mimicry

To investigate the role of proline in defining β turn conformations within cyclic hexa- and pentapeptides we synthesized and determined the conformations of a series of L - and D -proline-containing peptides by means of 2D NMR spectroscopy and restrained molecular dynamics simulations. Due to cis/trans isomerism the L -proline peptides adopt at least two different conformations that are analyzed and compared to the structures of the corresponding D -proline peptides. The cis conformations of the compounds cyclo(-Pro-Ala-Ala-Pro-Ala-Ala-), cyclo(-Arg-Gly-Asp-Phe-Pro-Gly-), cyclo(-Arg-Gly-Asp-Phe-Pro-Ala-), cyclo(-Pro-Ala-Ala-Ala-Ala--), and cyclo(-Pro-Ala-Pro-Ala-Ala-) form uncommon βVI turns that mimic the turn geometries found in crystallographically refined protein structures at such a detailed level that even preferred side chain orientations are reproduced. The ratios of the cis/trans isomers are analyzed in terms of the steric demand of the proline-following residue. The conformational details derived from this study illustrate the importance of the examination of small model compounds derived from protein loop regions, especially if bioactive recognition sequences, such as RGD (Arg-Gly-Asp), are incorporated. © 1993 Wiley-Liss, Inc.     

Population Interactions and the Determinants of Population Size

Abstract The flux of individuals within populations is dependent upon six controlling processes: the intrinsic rate of increase of the plant, intraspecific competition for resources, interspecific competition, natural enemies, mutualisms and refuge effects such as the immigration of seeds from other populations. Although population interactions are generally believed to play a major role in determining the flux of individuals within populations, little attempt has been made to quantify the strength of these interactions and their role in the dynamics of populations. In this paper we examine the role of competition, herbivory and mutualistic interactions in determining the dynamics of a range of annual plant species. Firstly, it is shown that the dynamics of three weed species ( Bromus sterilis, Galium aparine, Papaver rhoeas ) in an experimental community in an arable cropping system of winter wheat are determined primarily by the rapid population growth of B. sterilis . Interactions between the species play a minor part in the dynamics of the system. Secondly, it is shown that current levels of grazing by overwintering populations of brent geese have a minor impact on the abundance of Salicornia europaea , but that increased grazing has the potential to reduce abundance and increase the instability of S. europaea populations. This is a consequence of the aggregative response of the geese, which results in an increasing proportion of the seeds of S. europaea being eaten as plant density increases. Thirdly, it is shown that there is a complex interaction between root pathogenic and arbuscular mycorrhizal fungi in natural field populations of Vulpia ciliata and that the benefit of mycorrhizal fungi to the plant is in providing protection against pathogens.     

Population dynamics of japanese serow in relation to social organization and habitat conditions. I. Stability of Japanese serow density in stable habitat conditions

The density of a Japanese serow (Capricornis crispus) population, which has been in stable habitat conditions and free from hunting and predation, was investigated by direct observation of serows at Kusoudomari (336 ha), Wakinosawa village, Aomori Prefecture, Japan, during 1977–89. The vegetation, composed of mature mixed forest ofThujopsis with deciduous trees (43.2%), secondary forest of deciduous trees (23.4%) and a plantation of coniferous trees (30.0%) showed little change during the study period. The serows were counted 17 times each winter for 14 consecutive years. The serow population maintained a stable density with a mean of 12.5 individuals km⁻² (SD=1.4) ranging from 8.6 to 14.6 km⁻². The ratio of the proportion of kids (<1 year old) to serows more than 1 year old decreased, but density did not decrease during the study period. Though extremely severe winters with heavy snowfall in 1984–86 caused a decline in serow density, the density recovered within a few years. It was considered that the stability of the serow density resulted mainly from the stable food supply and the lack of human disturbance, such as forest cutting in the habitat. Stable population density for a long period is probably related to the social organization of the serow.     

Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure

Summary A new method, a restrained Monte Carlo (rMC) calculation, is demonstrated for generating high-resolution structures of DNA oligonucleotides in solution from interproton distance restraints and bounds derived from complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect (NOE) spectral peak intensities. As in the case of restrained molecular dynamics (rMD) refinement of structures, the experimental distance restraints and bounds are incorporated as a pseudo-energy term (or penalty function) into the mathematical expression for the molecular energy. However, the use of generalized helical parameters, rather than Cartesian coordinates, to define DNA conformation increases efficiency by decreasing by an order of magnitude the number of parameters needed to describe a conformation and by simplifying the potential energy profile. The Metropolis Monte Carlo method is employed to simulate an annealing process. The rMC method was applied to experimental 2D NOE data from the octamer duplex d(GTA-TAATG)·d(CATTATAC). Using starting structures from different locations in conformational space (e.g. A-DNA and B-DNA), the rMC calculations readily converged, with a root-mean-square deviation (RMSD) of <0.3 Å between structures generated using different protocols and starting structures. Theoretical 2D NOE peak intensities were calculated for the rMC-generated structures using the complete relaxation matrix program CORMA, enabling a comparison with experimental intensities via residual indices. Simulation of the vicinal proton coupling constants was carried out for the structures generated, enabling a comparison with the experimental deoxyribose ring coupling constants, which were not utilized in the structure determination in the case of the rMC simulations. Agreement with experimental 2D NOE and scalar coupling data was good in all cases. The rMC structures are quite similar to that refined by a traditional restrained MD approach (RMSD<0.5 Å) despite the different force fields used and despite the fact that MD refinement was conducted with additional restraints imposed on the endocyclic torsion angles of deoxyriboses. The computational time required for the rMC and rMD calculations is about the same. A comparison of structural parameters is made and some limitations of both methods are discussed with regard to the average nature of the experimental restraints used in the refinement.Abbreviations MC Monte Carlo - rMC restrained Monte Carlo - MD molecular dynamics - rMD restrained molecular dynamics - DG distance geometry - EM energy minimization - 2D NOE two-dimensional nuclear Overhauser effect - DQF-COSY double-quantum-filtered correlation spectroscopy - RMSD root-mean-square deviation To whom correspondence should be addressed.     

罗非鱼对微型生态系统营养物水平的影响

本文总结了罗非鱼不同放养密度的微型生态系统中N、P浓度及P分布动态观测结果。在罗非鱼的影响下,微型生态系统中氨氮、颗粒磷和总磷浓度不同程度地高于对照组,而正磷酸盐浓度和沉积物磷的量显著地低于对照组。不同密度组某些指标的观测值虽有显著差异,但未见任何指标依罗非鱼放养密度而有规律地变动。微型生态系统中正磷酸盐浓度同浮游动、植物密度和初级生产力显著相关,氨氮浓度与浮游植物密度之间亦有显著的相关关系。然而,浮游植物密度与总磷浓度之间不存在营养级联假说所预见的下行影响,相反有前者决定于后者的上行影响的趋向。微型生态系统中P分布的变化可揭示罗非鱼促进系统中营养物循环,从而加速其富营养化的主要机制。     

Floral scent emission is the highest at the second night of anthesis in Lonicera japonica (Caprifoliaceae)

Floral color change in diverse plants has been thought to be a visual signal reflecting changes in floral rewards, promoting pollinator foraging efficiency as well as plant reproductive success. It remains unclear whether olfactory signals co-vary with floral color change. We investigated the production rhythms of floral scent and nectar associated with floral color change in Lonicera japonica. The flowers generally last 2–3 days. They are white on opening at night (N1) and become light yellow the following day (D1), yellow on the second night (N2), and golden on the second day of flowering (D2). Our measurements in the four stages indicated that nectar production decreased significantly from N1 and D1 to N2 and D2, tracking the floral color change. A total of 34 compounds were detected in floral scent and total scent emission was significantly higher in N2 than in the other three stages. The scent emission of three major compounds, Linalool, cis-3-Hexenyl tiglate, and Germacrene D was also significantly higher in N2, but the relative content of Linalool decreased gradually, cis-3-Hexenyl tiglate increased gradually, and the relative content of Germacrene D did not differ among the four measured stages. Greater scent emission by night than by day suggested a strong olfactory signal to attract nocturnal hawkmoths, the effective pollinators. However, floral scent rhythms in the four stages did not match the color change and nectar secretion, suggesting that floral color (visual) and scent (olfactory) in this species may play different roles in attracting or filtering various visitors.     

Stock and recruitment and inversely density-dependent growth of salmon, Salmo salar L., in a Scottish stream

For the 6 years for which detailed data are readily available, estimates of the survival of emergent fry of Atlantic salmon, Salmo salar L., to the first and second autumns at a site on the Shelligan Burn are consistent with the dome-shaped Ricker model with about 11 emergent fry m⁻² maximizing recruitment. The data are not satisfactorily fitted by the asymptotic Beverton and Holt model. A possible mechanism, which results from the observed inversely density-dependent growth, is discussed briefly.     

Seasonal population dynamics of Paraquimpevia tenevvima (Linstow) (Nematoda) in the European eel Anguilla anguilla (Linnaeus) in three localities of southwest England

Seasonal population dynamics of Puraquzmperia tenerrima (Linstow) in the European eel Anguillu anguillu (Linnaeus) have been investigated in three localities in Devon, southwest England. The nematode is common and exhibits very similar seasonal patterns in changes of prevalence and abundance in the three localities. The population increases over winter through to late spring or early summer as the recruitment of the new generation occurs throughout this period. Reproduction of the nematode starts in spring. A sharp decrease of prevalence and abundance accompanies or follows reproduction, and infection levels are very low in autumn and early winter. The dispersion pattern of the nematode varies with the infection levels from over-dispersion in spring and early summer to almost random dispersion in autumn and winter. It is suggested that P. tenerrimu is a common specific parasite of eels, especially in small streams or rivers and that insect larvae or species of crustaceans might serve as intermediate hosts for the nematode.