No abstract

SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state.

This paper reports a computational method, the quantized elastic deformational model, that can reliably describe the conformational flexibility of a protein in the absence of the amino acid sequence and atomic coordinates. The essence of this method lies in the fact that, in modeling the functionally important conformational changes such as domain movements, it is possible to abandon the traditional concepts of protein structure (bonds, angles, dihedrals, etc.) and treat the protein as an elastic object. The shape and mass distribution of the object are described by the electron density maps, at various resolutions, from methods such as x-ray diffraction or cryo-electron microscopy. The amplitudes and directionality of the elastic deformational modes of a protein, whose patterns match the biologically relevant conformational changes, can then be derived solely based on the electron density map. The method yields an accurate description of protein dynamics over a wide range of resolutions even as low as 15-20 Å at which there is nearly no visually distinguishable internal structures. Therefore, this method dramatically enhances the capability of studying protein motions in structural biology. It is also expected to have ample applications in related fields such as bioinformatics, structural genomics, and proteomics, in which one's ability to extract functional information from the not-so-well-defined structural models is vitally important.conformational flexibility ͉ elastic deformation ͉ large conformational change ͉ elastic network ͉ normal mode analysis C omputational simulations of protein dynamics (1, 2) play an important role in deciphering protein functions in modern structural biology. To date, all the procedures for describing the motions of a protein require the knowledge of the atomic coordinates-i.e., the precise locations of the atoms. However, as the field of structural biology moves into an era of supermolecular complexes and membrane-bound proteins, there have been an increasing number of cases in which one can only obtain fuzzy images of the molecules by means of, for example, cryoelectron microscopy (cryo-EM). The knowledge of structures in these cases is not much more than the rough shapes of the molecules. Therefore, a challenging question is whether one can describe the motions of a protein, at least the gross features, based on its fuzzy image. The success of such a method would not only advance one's ability to model protein motions to a completely new level in structure biology, but it will also profoundly inf luence broader fields such as bioinformatics, structural genomics, and proteomics, in which one's ability to extract functional information from the not-so-well-defined structural models is vitally important.In the light of such a challenge, we developed a computational method, the quantized elastic deformational model (QEDM), by combining and extending several existing methods that were developed for related, but different, purposes. The results clearly demonstrate that, without the...

BackgroundCardiovascular disease (CVD) is one of the leading causes of death worldwide. Our study aimed to investigate the prevalence of two conditions, angina and stroke, and relevant risk factors among older adults in six low- and middle- income countries(LMICs).MethodsThe data was from World Health Organization (WHO) Study on global AGEing and adult Health (SAGE) Wave 1 in China, Ghana, India, Mexico, Russian Federation and South Africa. Presence of CVD was based on self-report of angina and stroke. Multivariate logistic regression was performed to examine the relationship between CVD and selected variables, including age, sex, urban/rural setting, household wealth, and risk factors such as smoking, alcohol drinking, fruit/vegetable intake, physical activity and BMI.ResultsThe age standardized prevalence of angina ranged from 9.5 % (South Africa) to 47.5 % (Russian Federation), and for stoke from 2.0% (India) to 6.1 % (Russia). Hypertension was associated with angina in China, India and Russian Federation after adjustment for age, sex, urban/rural setting, education and marital status (OR ranging from 1.3 [1.1-1.6] in India to 3.8 [2.9-5.0] in Russian Federation), furthermore it was a risk factor of stroke in five countries except Mexico. Low or moderate physical activity were also associated with angina in China, and were also strongly associated with stroke in all countries except Ghana and India. Obesity had a stronger association with angina in Russian Federation and China(ORs were 1.5[1.1-2.0] and 1.2 [1.0-1.5] respectively), and increased the risk of stroke in China. Smoking was associated with angina in India and South Africa(ORs were 1.6[1.0-2.4] and 2.1 [1.2-3.6] respectively ), and was also a risk factor of stroke in South Africa. We observed a stronger association between frequent heavy drinking and stroke in India. Household income was associated with reduced odds of angina in China, India and Russian Federation, however higher household income was a risk factor of angina in South Africa.ConclusionWhile the specific mix of risk factors contribute to disease prevalence in different ways in these six countries – they should all be targeted in multi-sectoral efforts to reduce the high burden of CVD in today’s society.