The structure of a highly conserved complex between a 58-nucleotide domain of large subunit ribosomal RNA and the RNA-binding domain of ribosomal protein L11 has been solved at 2.8 angstrom ...resolution. It reveals a precisely folded RNA structure that is stabilized by extensive tertiary contacts and contains an unusually large core of stacked bases. A bulge loop base from one hairpin of the RNA is intercalated into the distorted major groove of another helix; the protein locks this tertiary interaction into place by binding to the intercalated base from the minor groove side. This direct interaction with a key ribosomal RNA tertiary interaction suggests that part of the role of L11 is to stabilize an unusual RNA fold within the ribosome.
A glutamic acid was buried in the hydrophobic core of staphylococcal nuclease by replacement of Val-66. Its pK
a was measured with equilibrium thermodynamic methods. It was 4.3 units higher than the ...pK
a of Glu in water. This increase was comparable to the ΔpK
a of 4.9 units measured previously for a lysine buried at the same location. According to the Born formalism these ΔpK
a are energetically equivalent to the transfer of a charged group from water to a medium of dielectric constant of 12. In contrast, the static dielectric constants of dry protein powders range from 2 to 4. In the crystallographic structure of the V66E mutant, a chain of water molecules was seen that hydrates the buried Glu-66 and links it with bulk solvent. The buried water molecules have never previously been detected in >20 structures of nuclease. The structure and the measured energetics constitute compelling and unprecedented experimental evidence that solvent penetration can contribute significantly to the high apparent polarizability inside proteins. To improve structure-based calculations of electrostatic effects with continuum methods, it will be necessary to learn to account quantitatively for the contributions by solvent penetration to dielectric effects in the protein interior.
The technique of small angle solution scattering has been revolutionized in the last two decades. Exponential increases in computing power, parallel algorithm development, and the development of ...synchrotron, free-electron X-ray sources, and neutron sources, have combined to allow new classes of studies for biological specimens. These include time-resolved experiments in which functional motions of proteins are monitored on a picosecond timescale, and the first steps towards determining actual electron density fluctuations within particles. In addition, more traditional experiments involving the determination of size and shape, and contrast matching that isolate substructures such as nucleic acid, have become much more straightforward to carry out, and simultaneously require much less material. These new capabilities have sparked an upsurge of interest in solution scattering on the part of investigators in related disciplines. Thus, this book seeks to guide structural biologists to understand the basics of small angle solution scattering in both the X-ray and neutron case, to appreciate its strengths, and to be cognizant of its limitations. It is also directed at those who have a general interest in its potential. The book focuses on three areas: theory, practical aspects and applications, and the potential of developing areas. It is an introduction and guide to the field but not a comprehensive treatment of all the potential applications.
Next-generation synchrotron radiation sources, such as X-ray free-electron lasers, energy recovery linacs, and ultra-low-emittance storage rings, are catalyzing novel methods of biomolecular ...microcrystallography and solution scattering. These methods are described and future trends are predicted. Importantly, there is a growing realization that serial microcrystallography and certain cutting-edge solution scattering experiments can be performed at existing storage ring sources by utilizing new technology. In this sense, next-generation sources are serving two distinct functions, namely, provision of new capabilities that require the newer sources and inspiration of new methods that can be performed at existing sources.
Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to ...rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electron laser sources.
The use of portable gas chromatography–mass spectrometry (GC-MS) is an important capability that has been available commercially for almost 25 years. These systems have been used within a variety of ...different industries, including their extensive use by environmental scientists for the analysis of hazardous air pollutants. Recently, these systems were deployed to conventional military forces for use in theater to detect and identify toxic chemicals including chemical warfare agents (CWAs). The challenges of deploying such complex analytical instruments to these military users are unique. Among other things, these organizations have considerable and variable mission strains, complex and difficult logistics and coordination needs, and variability in user backgrounds. This review outlines the value portable GC-MS systems offer to these warfighters in theater, discusses some important aspects of the design of portable systems that makes their deployment to this type of end user possible, and proposes methods that can be used to overcome challenges to successful deployment of portable GC-MS to non-scientists working within hostile environments.
Accessibility has conventionally been measured and evaluated ignoring user perceptions in favor of focusing on travel time and distance to a number of pre-determined destinations. Acknowledging this ...gap, we recently developed a scale for perceived accessibility PAC (Lättman, Friman, & Olsson 2016b) aimed at capturing the individual perspective of accessibility with a certain travel mode. In this paper, we 1) further develop the PAC measure of perceived accessibility in order to capture how easy it is to live a satisfactory life with the help of the transport system, 2) compare levels of perceived accessibility between residential areas and main travel modes, and 3) compare residents’ perceived accessibility to the objective accessibility level for the same residential area. Data from 2711 residents of Malmö, Sweden show that perceived accessibility is consistently different from objective accessibility across 13 residential areas, with minor differences in levels of perceived accessibility between areas. Surprisingly, bicycle users rate their accessibility significantly higher than those who mainly use the car or public transport for daily travel, contrary to objective accessibility assumptions. These differences point at the importance of including perceived accessibility as a complementary tool when planning for and evaluating transport systems.
The structure of a 58 nucleotide ribosomal RNA fragment buries several phosphate groups of a hairpin loop within a large tertiary core. During refinement of an X-ray crystal structure containing this ...RNA, a potassium ion was found to be contacted by six oxygen atoms from the buried phosphate groups; the ion is contained completely within the solvent-accessible surface of the RNA. The electrostatic potential at the ion chelation site is unusually large, and more than compensates for the substantial energetic penalties associated with partial dehydration of the ion and displacement of delocalized ions. The very large predicted binding free energy, ∼−30
kcal/mol, implies that the site must be occupied for the RNA to fold. These findings agree with previous studies of the ion-dependent folding of tertiary structure in this RNA, which concluded that a monovalent ion was bound in a partially dehydrated environment where Mg
2+ could not easily compete for binding. By compensating the unfavorable free energy of buried phosphate groups with a chelated ion, the RNA is able to create a larger and more complex tertiary fold than would be possible otherwise.
Service quality in public transport is proposed as a key determinant of perceived accessibility, the ease to live the life one wants with the help of the transport system, as low service quality may ...be a barrier for use, decreasing the ease to participate in daily activities. The first aim was to validate the direct relationship between public transport quality and perceived accessibility. Secondly, we analyzed the mediating role of safety perceptions to better explain the link between service quality and perceived accessibility. Public transport travelers (n = 4944) from five northern European cities were surveyed. Results from PLS-SEM modeling show that service quality has a significant and direct relationship with perceived accessibility, especially regarding functionality. An indirect relationship through travel safety perceptions was also observed, highlighting information and comfort as main drivers. High car use, low public transport use, increasing age, and being a woman were also associated with greater perceived accessibility. City comparisons yielded a number of significant differences. Our results contribute to the research literature by highlighting the importance of service quality in public transport for perceptions of accessibility in daily travel. In particular, we argue that functionality is the core attribute to focus on, and that attributes related to travel safety perceptions should be carefully considered when planning for sustainable transport.
•A configurational approach unveiled the complexity of travel satisfaction.•Travel satisfaction is achieved by different configurations of quality attributes.•Safety has an inherent part in ...experiencing high travel satisfaction.•Context play a key role in how users of public transport experience service quality.
Previous findings have established that satisfaction with public transport service quality attributes (reliability/functionality, information, courtesy/simplicity, comfort, safety) relate to overall travel satisfaction. Recent studies propose that the importance of these attributes for travel satisfaction varies in different contexts and call for new approaches for enhancing the understanding of these relationships. We address this call by using a configurational perspective and applying fuzzy set Qualitative Comparative Analysis (fsQCA), to explore how satisfaction with service quality attributes relate to high travel satisfaction. By analyzing user survey data before and after an intervention in public transport services in a Swedish city, we: 1) find that high travel satisfaction occurs in the interaction between service quality attributes; 2) identify different configurations of satisfaction with service quality attributes leading to high travel satisfaction; and 3) show how context alters overall travel satisfaction. We conclude that using a configurational approach is useful for understanding the complexity of travel satisfaction.
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