{"id":7126,"date":"2026-10-23T15:07:57","date_gmt":"2026-10-23T15:07:57","guid":{"rendered":"https:\/\/www.waters.com\/blog\/?p=7126"},"modified":"2026-10-23T15:07:57","modified_gmt":"2026-10-23T15:07:57","slug":"from-hidden-assemblies-to-drug-target-insight-with-cdms-and-cryo-em","status":"publish","type":"post","link":"https:\/\/www.waters.com\/blog\/from-hidden-assemblies-to-drug-target-insight-with-cdms-and-cryo-em\/","title":{"rendered":"From Hidden Assemblies to Drug Target Insight with CDMS and Cryo-EM"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/pubs.acs.org\/jacsat\/article\/148\/38\/40889\/5255226\/Resolving-Hidden-Stoichiometries-in-Bacterial\">A recent <em>JACS<\/em> study<\/a> by Prof. Siavash Vahidi and collaborators at the University of Guelph (Canada) highlights how Charge Detection Mass Spectrometry (CDMS) can uncover hidden protein assemblies that conventional methods often miss. By guiding cryogenic electron microscopy (cryo-EM) toward structurally distinct populations, CDMS enabled a deeper understanding of the active architecture and substrate recognition mechanism of a validated tuberculosis drug target.<\/p>\n\n\n<style>.wp-block-kadence-spacer.kt-block-spacer-7126_ebc25c-dd .kt-block-spacer{height:60px;}.wp-block-kadence-spacer.kt-block-spacer-7126_ebc25c-dd .kt-divider{border-top-width:1px;height:1px;border-top-color:#eee;width:80%;border-top-style:solid;}<\/style>\n<div class=\"wp-block-kadence-spacer aligncenter kt-block-spacer-7126_ebc25c-dd\"><div class=\"kt-block-spacer kt-block-spacer-halign-center\"><hr class=\"kt-divider\"\/><\/div><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">The biological challenge<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Tuberculosis (TB) remains one of the world&#8217;s deadliest infectious diseases, claiming more than 1.2 million lives in 2024 alone. As drug-resistant strains continue to emerge, there is an urgent need for new therapeutic targets. One promising target is the bacterial proteasome activator Bpa, a protein found in <em>Mycobacterium tuberculosis<\/em> with no known human counterpart.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">However, understanding how Bpa recognizes and delivers substrates for degradation has proven challenging because it exists in multiple, closely related oligomeric assemblies that are difficult to distinguish using conventional analytical methods.<\/p>\n\n\n<style>.wp-block-kadence-spacer.kt-block-spacer-7126_7a764e-f3 .kt-block-spacer{height:60px;}.wp-block-kadence-spacer.kt-block-spacer-7126_7a764e-f3 .kt-divider{border-top-width:1px;height:1px;border-top-color:#eee;width:80%;border-top-style:solid;}<\/style>\n<div class=\"wp-block-kadence-spacer aligncenter kt-block-spacer-7126_7a764e-f3\"><div class=\"kt-block-spacer kt-block-spacer-halign-center\"><hr class=\"kt-divider\"\/><\/div><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">Why the complete picture remained elusive<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Multiple studies using X-ray crystallography, cryo-EM, SEC-MALS, and conventional native mass spectrometry described Bpa as forming a dodecameric ring. However, these approaches average together structurally similar species, making it difficult to distinguish closely related assemblies that differ only subtly in mass and size.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Because a potential 11-subunit ring differs from the dodecamer by less than 10% in mass, alternative oligomeric states could remain hidden in plain sight, obscuring a complete understanding of Bpa structure and function.<\/p>\n\n\n<style>.wp-block-kadence-spacer.kt-block-spacer-7126_ca7cff-45 .kt-block-spacer{height:60px;}.wp-block-kadence-spacer.kt-block-spacer-7126_ca7cff-45 .kt-divider{border-top-width:1px;height:1px;border-top-color:#eee;width:80%;border-top-style:solid;}<\/style>\n<div class=\"wp-block-kadence-spacer aligncenter kt-block-spacer-7126_ca7cff-45\"><div class=\"kt-block-spacer kt-block-spacer-halign-center\"><hr class=\"kt-divider\"\/><\/div><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">The CDMS finding that changed the story<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">CDMS revealed that apo Bpa exists as a mixture of previously unrecognized 11-subunit and 12-subunit rings and established a 12:2 binding stoichiometry between Bpa and HspR. It further showed that substrate binding favors the fully assembled dodecamer, providing critical evidence that guided subsequent cryo-EM analysis.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">These findings were made possible because CDMS directly measures both mass and charge for individual ions, allowing closely related assemblies to be separated even when they appear as a single population in conventional mass spectrometry.<\/p>\n\n\n<style>.wp-block-kadence-spacer.kt-block-spacer-7126_45e6d0-36 .kt-block-spacer{height:60px;}.wp-block-kadence-spacer.kt-block-spacer-7126_45e6d0-36 .kt-divider{border-top-width:1px;height:1px;border-top-color:#eee;width:80%;border-top-style:solid;}<\/style>\n<div class=\"wp-block-kadence-spacer aligncenter kt-block-spacer-7126_45e6d0-36\"><div class=\"kt-block-spacer kt-block-spacer-halign-center\"><hr class=\"kt-divider\"\/><\/div><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">cryo-EM turned the CDMS discovery into structural insight<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">cryo-EM transformed the CDMS discovery into structural insight by revealing how the native substrate HspR engages Bpa. Guided by CDMS data, researchers resolved both previously hidden 11-mer and established 12-mer Bpa assemblies and obtained a 3.9-\u00c5 structure of the Bpa:HspR complex.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">These structures showed that HspR preferentially associates with the fully assembled dodecamer and localized the region responsible for substrate recognition. Importantly, the undecameric assembly was not recovered in the initial cryo-EM analysis.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">It was the unexpected population identified by CDMS that prompted researchers to refine their classification and reconstruction strategy, enabling a more complete view of the system&#8217;s structural landscape.<\/p>\n\n\n<style>.wp-block-kadence-spacer.kt-block-spacer-7126_b1018c-e1 .kt-block-spacer{height:60px;}.wp-block-kadence-spacer.kt-block-spacer-7126_b1018c-e1 .kt-divider{border-top-width:1px;height:1px;border-top-color:#eee;width:80%;border-top-style:solid;}<\/style>\n<div class=\"wp-block-kadence-spacer aligncenter kt-block-spacer-7126_b1018c-e1\"><div class=\"kt-block-spacer kt-block-spacer-halign-center\"><hr class=\"kt-divider\"\/><\/div><\/div>\n\n\n\n<h2 class=\"wp-block-heading\">The key takeaway<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Hidden structural populations can hold the key to biological function. This study showed how CDMS revealed what conventional methods missed and how cryo-EM translated that discovery into structural understanding, providing new insight into a validated tuberculosis drug target.<\/p>\n\n\n<style>.wp-block-kadence-spacer.kt-block-spacer-7126_4af809-74 .kt-block-spacer{height:60px;}.wp-block-kadence-spacer.kt-block-spacer-7126_4af809-74 .kt-divider{border-top-width:1px;height:1px;border-top-color:#eee;width:80%;border-top-style:solid;}<\/style>\n<div class=\"wp-block-kadence-spacer aligncenter kt-block-spacer-7126_4af809-74\"><div class=\"kt-block-spacer kt-block-spacer-halign-center\"><hr class=\"kt-divider\"\/><\/div><\/div>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><a href=\"https:\/\/pubs.acs.org\/jacsat\/article\/doi\/10.1021\/jacs.6c09027\/5255226\/Resolving-Hidden-Stoichiometries-in-Bacterial\">Read the full article<\/a>, \u201c<\/strong>Resolving Hidden Stoichiometries in Bacterial Proteasome Activator (Bpa)-Substrate Complexes by Cryo-EM and Charge Detection Mass Spectrometry,\u201d to see how you can use CDMS and cryo-EM to advance your protein analysis.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>A recent JACS study by Prof. Siavash Vahidi and collaborators at the University of Guelph (Canada) highlights how Charge Detection Mass Spectrometry (CDMS) can uncover hidden protein assemblies that conventional methods often miss. By guiding cryogenic electron microscopy (cryo-EM) toward structurally distinct populations, CDMS enabled a deeper understanding of the active architecture and substrate recognition&#8230;<\/p>\n","protected":false},"author":165,"featured_media":7134,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_seopress_titles_title":"How CDMS and cryo-EM Reveal Hidden Protein Assemblies","_seopress_titles_desc":"Discover how charge detection mass spectrometry (CDMS) and cryo-EM revealed hidden Bpa protein assemblies and new insights into a tuberculosis drug target.","_seopress_robots_index":"","_seopress_robots_follow":"","_seopress_robots_imageindex":"","_seopress_robots_snippet":"","_seopress_robots_primary_cat":"","_seopress_robots_breadcrumbs":"","_seopress_robots_freeze_modified_date":"","_seopress_robots_custom_modified_date":"","_seopress_robots_canonical":"","_seopress_social_fb_title":"","_seopress_social_fb_desc":"","_seopress_social_fb_img":"","_seopress_social_fb_img_attachment_id":0,"_seopress_social_fb_img_width":0,"_seopress_social_fb_img_height":0,"_seopress_social_twitter_title":"","_seopress_social_twitter_desc":"","_seopress_social_twitter_img":"","_seopress_social_twitter_img_attachment_id":0,"_seopress_social_twitter_img_width":0,"_seopress_social_twitter_img_height":0,"_seopress_redirections_value":"","_seopress_redirections_enabled":"","_seopress_redirections_enabled_regex":"","_seopress_redirections_logged_status":"","_seopress_redirections_param":"","_seopress_redirections_type":0,"_seopress_analysis_target_kw":"","_seopress_news_disabled":"","_seopress_video_disabled":"","_seopress_video":[],"_seopress_pro_schemas_manual":[],"_seopress_pro_rich_snippets_disable_all":"","_seopress_pro_rich_snippets_disable":[],"_seopress_pro_schemas":[],"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_kad_post_transparent":"","_kad_post_title":"","_kad_post_layout":"","_kad_post_sidebar_id":"","_kad_post_content_style":"","_kad_post_vertical_padding":"","_kad_post_feature":"","_kad_post_feature_position":"","_kad_post_header":false,"_kad_post_footer":false,"_kad_post_classname":"","footnotes":""},"categories":[22],"tags":[781,705,158],"class_list":["post-7126","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-technology","tag-cdms","tag-charge-detection-mass-spectrometry","tag-protein-bioanalysis"],"acf":[],"taxonomy_info":{"category":[{"value":22,"label":"Technology"}],"post_tag":[{"value":781,"label":"CDMS"},{"value":705,"label":"charge detection mass spectrometry"},{"value":158,"label":"protein bioanalysis"}]},"featured_image_src_large":["https:\/\/www.waters.com\/blog\/wp-content\/uploads\/ins-protein-structure_full-res-presentation-logo-sm.png",600,592,false],"author_info":{"display_name":"Kate Yu","author_link":"https:\/\/www.waters.com\/blog\/author\/kyu\/"},"comment_info":"","category_info":[{"term_id":22,"name":"Technology","slug":"technology","term_group":0,"term_taxonomy_id":22,"taxonomy":"category","description":"Our expertise drives innovation, development, and\u00a0application of informatics and software that continue to enable leading pharmaceutical, environmental, food &amp; beverage and chemical materials organizations to accelerate decision-making, improve laboratory effectiveness, and get products to market faster.","parent":0,"count":127,"filter":"raw","term_order":"0","cat_ID":22,"category_count":127,"category_description":"Our expertise drives innovation, development, and\u00a0application of informatics and software that continue to enable leading pharmaceutical, environmental, food &amp; beverage and chemical materials organizations to accelerate decision-making, improve laboratory effectiveness, and get products to market faster.","cat_name":"Technology","category_nicename":"technology","category_parent":0}],"tag_info":[{"term_id":781,"name":"CDMS","slug":"cdms","term_group":0,"term_taxonomy_id":781,"taxonomy":"post_tag","description":"","parent":0,"count":7,"filter":"raw","term_order":"0"},{"term_id":705,"name":"charge detection mass spectrometry","slug":"charge-detection-mass-spectrometry","term_group":0,"term_taxonomy_id":705,"taxonomy":"post_tag","description":"","parent":0,"count":4,"filter":"raw","term_order":"0"},{"term_id":158,"name":"protein bioanalysis","slug":"protein-bioanalysis","term_group":0,"term_taxonomy_id":158,"taxonomy":"post_tag","description":"","parent":0,"count":7,"filter":"raw","term_order":"0"}],"_links":{"self":[{"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/posts\/7126","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/users\/165"}],"replies":[{"embeddable":true,"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/comments?post=7126"}],"version-history":[{"count":1,"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/posts\/7126\/revisions"}],"predecessor-version":[{"id":7127,"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/posts\/7126\/revisions\/7127"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/media\/7134"}],"wp:attachment":[{"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/media?parent=7126"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/categories?post=7126"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.waters.com\/blog\/wp-json\/wp\/v2\/tags?post=7126"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}