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Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.

ABSTRACT: Contacts with neighboring molecules in protein crystals inevitably restrict the internal motions of intrinsically flexible proteins. The resultant clear electron densities permit model building, as crystallographic snapshot structures. Although these still images are informative, they could provide biased pictures of the protein motions. If the mobile parts are located at a site lacking direct contacts in rationally designed crystals, then the amplitude of the movements can be experimentally analyzed. We propose a fusion protein method, to create crystal contact-free space (CCFS) in protein crystals and to place the mobile parts in the CCFS. Conventional model building fails when large amplitude motions exist. In this study, the mobile parts appear as smeared electron densities in the CCFS, by suitable processing of the X-ray diffraction data. We applied the CCFS method to a highly mobile presequence peptide bound to the mitochondrial import receptor, Tom20, and a catalytically relevant flexible segment in the oligosaccharyltransferase, AglB. These two examples demonstrated the general applicability of the CCFS method to the analysis of the spatial distribution of motions within protein molecules.

SUBMITTER: Matsuoka R

PROVIDER: S-EPMC4815401 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.

Matsuoka Rei R Shimada Atsushi A Komuro Yasuaki Y Sugita Yuji Y Kohda Daisuke D

Protein science : a publication of the Protein Society 20160113 3

Contacts with neighboring molecules in protein crystals inevitably restrict the internal motions of intrinsically flexible proteins. The resultant clear electron densities permit model building, as crystallographic snapshot structures. Although these still images are informative, they could provide biased pictures of the protein motions. If the mobile parts are located at a site lacking direct contacts in rationally designed crystals, then the amplitude of the movements can be experimentally ana ...[more]

PMID: 26694222

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Project description:BackgroundA spatial and temporal study of the distribution of facility-based deliveries can identify areas of low and high facility usage and help devise more targeted interventions to improve delivery outcomes. Developing countries like Bangladesh face considerable challenges in reducing the maternal mortality ratio to the targets set by the Sustainable Development Goals. Recent studies have already identified that the progress of reducing maternal mortality has stalled. Giving birth in a health facility is one way to reduce maternal mortality.MethodsFacility delivery data from a demographic surveillance site was analyzed at both village and Bari (comprising several households with same paternal origins) level to understand spatial and temporal heterogeneity. Global spatial autocorrelation was detected using Moran's I index while local spatial clusters were detected using the local Getis G i * statistics. In addition, space-time scanning using a discrete Poisson approach facilitated the identification of space-time clusters. The likelihood of delivering at a facility when located inside a cluster was calculated using log-likelihood ratios.ResultsThe three cluster detection approaches detected significant spatial and temporal heterogeneity in the distribution of facility deliveries in the study area. The hot and cold spots indicated contiguous and relocation type diffusion and increased in number over the years. Space-time scanning revealed that when a parturient woman is located in a Bari inside the cluster, the likelihood of delivering at a health facility increases by twenty-seven times.ConclusionsSpatiotemporal studies to understand delivery patterns are quite rare. However, in resource constraint countries like Bangladesh, detecting hot and cold spot areas can aid in the detection of diffusion centers, which can be targeted to expand regions with high facility deliveries. Places and periods with reduced health facility usages can be identified using various cluster detection techniques, to assess the barriers and facilitators in promoting health facility deliveries.

Dataset Information

Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.

Publications

Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.

Similar Datasets

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