{"id":462,"date":"2019-03-01T18:34:35","date_gmt":"2019-03-01T18:34:35","guid":{"rendered":"http:\/\/clemson.world\/research\/?p=462"},"modified":"2019-03-12T19:13:00","modified_gmt":"2019-03-12T19:13:00","slug":"stroke-treatment","status":"publish","type":"post","link":"https:\/\/clemson.world\/research\/stroke-treatment\/","title":{"rendered":"New Dimension in Stroke Treatment"},"content":{"rendered":"

\"\"<\/span><\/p>\n

In an extension of\u00a0research<\/a><\/span>\u00a0published a month ago in\u00a0Nature Methods<\/span><\/a>,<\/span> a novel hybrid approach performed by researchers from Clemson University\u2019s\u00a0department of physics and astronomy<\/span><\/a>\u00a0<\/span>and\u00a0Stony Brook University<\/a><\/span>\u00a0has revealed a 3-D structure of a protein fragment that could serve as a drug target in treating stroke patients.<\/span><\/p>\n

The protein called \u201cpostsynaptic density protein of 95 kDa (PSD-95)\u201d is positioned on neurons in the brain that are receiving chemical messages \u2013 neurotransmitters \u2013 from adjacent neurons. By recruiting receptors and other helper proteins,\u00a0PSD-95<\/a><\/span>\u00a0works to maintain the integrity of neural connections over time, thereby facilitating neural communication, learning and memory.<\/span><\/p>\n

<\/div>\n

PSD-95 consists of five parts, or domains, that each play a different role in the protein\u2019s overall function. Two of these domains, called PDZ-1 and PDZ-2, have been shown to influence symptoms associated with ischemic stroke, such as paralysis or speech impairment.<\/span><\/p>\n

\u201cOne of the ideas that has been postulated in the literature is to create a multivalent drug that targets both PDZ domains because they\u2019re very similar in nature. If you can block the PDZ domains from binding particular proteins or enzymes, you can reduce the debilitating effects of a stroke,\u201d said\u00a0Hugo Sanabria<\/a><\/span>, lead author on the study.<\/span><\/p>\n

The challenge, however, is that it\u2019s nearly impossible to design a drug inhibitor without first knowing the exact structure of the PDZ domains of PSD-95. It would be like driving across the country without having a map of the United States.<\/span><\/p>\n

\u201cThe biological functions of biomolecules are determined by their structures, so we need detailed structural and dynamic insights of PDZ-1 and -2 to help better understand their functional roles and aid in the design of novel inhibitors,\u201d said\u00a0Feng Ding<\/a><\/span>, Sanabria\u2019s colleague here at Clemson.<\/span><\/p>\n

A handful of approaches exists to render the structure of biomolecules. But in the case of PSD-95, each approach \u2013 NMR spectroscopy, X-ray crystallography and F\u00f6rster resonance energy transfer (FRET) \u2013 delivered a different structural model. The researchers\u2019 collaborator at Stony Brook University, associate professor\u00a0Mark Bowen<\/span><\/a>\u00a0in the\u00a0department of physiology and biophysics<\/a><\/span>, established a partnership with Sanabria on this project after he uncovered one of the inconsistent structural models of the PSD-95 fragment.<\/span><\/p>\n

Sanabria\u2019s lab addressed this discrepancy by first modeling the PSD-95 fragment using FRET, an approach that identifies possible configurations of biomolecules. Under this method, Sanabria attached two light-sensitive molecules, called chromophores, at two differing positions on the PSD-95 fragment. He then uncovered the distance between the chromophores by visualizing the fragment under a microscope. This was repeated multiple times from different attaching points.<\/span><\/p>\n

\u201cFor the modeling aspect, FRET gives you distances between chromophores, but that\u2019s not enough to fill all of the geometrical restraints of the molecule, so we have to rely on something else, some other methodology. That\u2019s where Professor Ding comes into play,\u201d Sanabria said.<\/span><\/p>\n

Ding leads a\u00a0computational biophysics lab<\/span><\/a>\u00a0at Clemson University where he uses computer software to gauge how biomolecules look, move and function. His approach to modeling utilizes a computer simulation known as discrete molecular dynamics (DMD) that maps the landscape of a biomolecule, predicting the trajectories of proteins as they fold and interact with other molecules. The subsequent simulation can be played back like a movie, helping researchers visualize protein behaviors over time.<\/span><\/p>\n

\u201cIf you do traditional molecular simulations, typically you\u2019re going to sample a very tiny region of the space, particularly for larger molecules, so you\u2019re not going to have a good overview of how the entire molecule will look even in physiological conditions,\u201d Sanabria said. \u201cDiscrete molecular dynamics is a much faster and less computationally expensive way to accurately and rapidly sample the conformational space of proteins.\u201d<\/span><\/p>\n

To do it, Sanabria first obtained a set of distances by measuring PSD-95 with FRET. In that experiment, Sanabria had 10 samples of the PSD-95 fragment that each\u00a0were rendering different distances and three common shapes \u2013 or conformations \u2013 of PSD-95 were observed. Yet, without a DMD simulation, there was no way for the researchers to know which distance corresponded to which conformation of the fragment. So they input each possible distance against each possible shape and let the simulation do the rest.<\/span><\/p>\n

\u201cOnce we did the first simulation, we saw that there were three main states that PDZ-1 and -2 were taking. One showed very close contact between the two, one showed a set of intermediate contact and one had no contact whatsoever,\u201d Ding said.<\/span><\/p>\n

<\/div>\n

The researchers then ran a DMD simulation again without considering the FRET distances to confirm that the three observed states exist in nature and are not simply a fluke imposed by the FRET distances. They further probed the structures by looking at the way that individual amino acids, which constitute the PDZ domains, bond to one another. From these analyses, Ding, Bowen and Sanabria were able to confirm that the PDZ domains take on two out of the three observed states in the DMD simulation \u2013 that with some contact and that with no contact whatsoever.<\/span><\/p>\n

\u201cNow, we have two potential targets for engineering new drugs that will be more efficient than the ones that are currently available,\u201d Sanabria said. \u201cThe outlook for stroke patients is promising.\u201d<\/span><\/p>\n

Without discrete molecular dynamics, which can capture conformational changes that occur on the microsecond timescale, these two states would have been missed as they were in past studies.<\/span><\/p>\n

\u201cMost of the people doing FRET-guided structural modeling are working with a rigid molecule, like DNA. If you have a rigid molecule, it\u2019s easy to model \u2013 you have only a single state to capture. You can assign the FRET distances and there\u2019s really no problem,\u201d Sanabria said. \u201cIn this case, we surpassed this approach in many ways.\u201d<\/span><\/p>\n

In future studies, the team is looking to analyze the potential for the PSD-95 fragment to auto-inhibit itself based on the fragment\u2019s own structure.<\/span><\/p>\n

The team\u2019s\u00a0paper<\/a>, titled \u201cIdentifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95,\u201d was published in September in\u00a0Nature Communications<\/a>. The work reported in this release was supported by the National Institute of Mental Health and National Science Foundation under award No.\u00a02R01MH081923-11A1<\/span><\/a>. The researchers are wholly responsible for the content of this study, of which the funder had no input.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

In an extension of\u00a0research\u00a0published a month ago in\u00a0Nature Methods, a novel hybrid approach performed by researchers from Clemson University\u2019s\u00a0department of physics and astronomy\u00a0and\u00a0Stony Brook University\u00a0has revealed a 3-D structure of a protein fragment that could serve as a drug target in treating stroke patients. The protein called \u201cpostsynaptic density protein of 95 kDa (PSD-95)\u201d is […]<\/p>\n","protected":false},"author":13,"featured_media":509,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[153],"tags":[116,134,135,133,132,131,130,129],"coauthors":[136],"class_list":["post-462","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-researchupdates","tag-2019-research-updates","tag-feng-ding","tag-fret","tag-hugo-sanabria","tag-molecule-structure","tag-protein","tag-stony-brook","tag-stroke-treatment"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"https:\/\/clemson.world\/research\/wp-content\/uploads\/sites\/2\/2019\/03\/Xray.jpg","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p9IEky-7s","_links":{"self":[{"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/posts\/462","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/comments?post=462"}],"version-history":[{"count":0,"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/posts\/462\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/media\/509"}],"wp:attachment":[{"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/media?parent=462"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/categories?post=462"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/tags?post=462"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/clemson.world\/research\/wp-json\/wp\/v2\/coauthors?post=462"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}