{"id":34310,"date":"2017-02-08T16:25:14","date_gmt":"2017-02-09T00:25:14","guid":{"rendered":"http:\/\/lifeboat.com\/blog\/2017\/02\/comparative-study-of-the-collective-dynamics-of-proteins-and-inorganic-nanoparticles"},"modified":"2017-04-24T18:53:16","modified_gmt":"2017-04-25T01:53:16","slug":"comparative-study-of-the-collective-dynamics-of-proteins-and-inorganic-nanoparticles","status":"publish","type":"post","link":"https:\/\/lifeboat.com\/blog\/2017\/02\/comparative-study-of-the-collective-dynamics-of-proteins-and-inorganic-nanoparticles","title":{"rendered":"Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles"},"content":{"rendered":"<p><a class=\"aligncenter blog-photo\" href=\"https:\/\/lifeboat.com\/blog.images\/comparative-study-of-the-collective-dynamics-of-proteins-and-inorganic-nanoparticles.jpg\"><\/a><\/p>\n<p>Interesting read for those interested in inorganic protein (NP) states from a solid to a liquid as the research proves inorganic NPs are in a \u2018glassy\u2019 state while transitioning from a solid to a liquid form.<\/p>\n<hr>\n<p>Molecular <i>dynamics<\/i> simulations of ubiquitin in water\/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a <i>dynamics<\/i> similar to \u2018surface-melted\u2019 inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a \u2018glassy\u2019 state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of <i>string <\/i>-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations (\u2018colored\u2019 or \u2018pink\u2019 noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes. On the other hand, we find the <i>dynamics<\/i> of ubiquitin to be even more like a polycrystalline material in which the \u03b1-helix and \u03b2-sheet regions of the protein are similar to crystal grains so that the <i>string <\/i>-like collective atomic motion is concentrated in regions between the \u03b1-helix and \u03b2-sheet domains.<\/p>\n<p><!-- Link: <a href=\"http:\/\/www.nature.com\/articles\/srep41671\">http:\/\/www.nature.com\/articles\/srep41671<\/a> --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Interesting read for those interested in inorganic protein (NP) states from a solid to a liquid as the research proves inorganic NPs are in a \u2018glassy\u2019 state while transitioning from a solid to a liquid form. Molecular dynamics simulations of ubiquitin in water\/glycerol solutions are used to test the suggestion by Karplus and coworkers that [\u2026]<\/p>\n","protected":false},"author":395,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,48],"tags":[],"class_list":["post-34310","post","type-post","status-publish","format-standard","hentry","category-nanotechnology","category-particle-physics"],"_links":{"self":[{"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/posts\/34310","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/users\/395"}],"replies":[{"embeddable":true,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/comments?post=34310"}],"version-history":[{"count":3,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/posts\/34310\/revisions"}],"predecessor-version":[{"id":48991,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/posts\/34310\/revisions\/48991"}],"wp:attachment":[{"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/media?parent=34310"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/categories?post=34310"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/lifeboat.com\/blog\/wp-json\/wp\/v2\/tags?post=34310"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}