{"id":31,"date":"2020-01-24T17:28:28","date_gmt":"2020-01-24T17:28:28","guid":{"rendered":"https:\/\/neelsb.com\/myblog\/?p=31"},"modified":"2025-08-16T22:14:06","modified_gmt":"2025-08-16T16:44:06","slug":"folding","status":"publish","type":"post","link":"https:\/\/neelsb.com\/myblog\/2020\/01\/24\/folding\/","title":{"rendered":"Structure of an intermediate state during protein unfolding"},"content":{"rendered":"\n
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Cover art (Designed by Anupam Patra) featured on 21st Jan 2020 issue of Biophysical Journal<\/a> (Left). Dr. Harshesh Bhatt and Dr. Akshay Kumar Ganguly (Right)<\/figcaption><\/figure>\n\n\n\n

<\/a>Proteins are unique molecules; they read the code of life in genes, and their own codes are also hidden in genes.\u00a0 Therefore, they are called the architects, pillars, and workhorses of life. \u00a0A vast majority of proteins require a well-defined three-dimensional shape and flexibility for their specific and regulated function inside the cell. The hierarchy of protein structure starts with primary structure, consisting of individual amino acid residues, which then organizes itself into helices or sheets to form secondary structures<\/a>. The great Prof. G. N. Ramachandran<\/a> was the first to codify the geometry of the secondary structural elements in the form of backbone torsion angles. The iconic plot is called the Ramachandran Plot<\/a>. Proteins further fold these secondary structural elements into tertiary and quaternary structures.<\/p>\n\n\n\n

The process of formation of these structures, called Protein Folding, starts immediately at their birthplace, called Ribosomes, and most proteins emerge as perfectly folded native structures at the end of their complete synthesis. However, there are a few that require helper protein molecules called chaperones to correctly shape them. Different kinds of protein have different lifespans, and at the end of it, they are degraded to individual units with the help of another set of protein molecules, the process called Protein Unfolding. Both folding and unfolding processes are very specific, rapid, and follow a well-defined path. The Levinthal Paradox,<\/em><\/a> described by Prof. Cyrus Levinthal, concluded that had it been a random search process among all possible conformations, it would take an astronomical age to fold a protein. Any aberration in folding-unfolding processes leads to dysregulation and sometimes formation of the aggregated state, resulting in disease conditions such as Alzheimer\u2019s and Parkinson\u2019s disease.<\/p>\n\n\n\n

Prof. Christian B. Anfinsen<\/a> had used ribonuclease A as a model and showed that the primary sequence of the protein under a particular set of environmental conditions (temperature, solvent concentration, and composition, etc.) at which folding occurs, dictates the formation of the native structure, which is a unique, stable, and kinetically accessible minimum of the free energy. Several studies have demonstrated that proteins unfold under different physical and chemical conditions in a test tube and refold back to their native conformation upon removal of such conditions. This helped the experimentalists to follow folding-unfolding pathways at a high spatial and time resolution and understand mechanisms. The Landscape funnel model<\/a> of protein folding is currently a widely accepted model that describes a protein\u2019s journey through the crests and troughs of internal free energy and degrees of freedom to reach the folded state from a rapidly exchanging ensemble. Proteins also take a trek through the funnel during their unfolding.<\/p>\n\n\n\n

The key to understanding protein (un)folding mechanism, which is still a challenge, is high-resolution structural characterisation of all states along the funnel. In this regard, solution-state NMR spectroscopy is unparalleled in providing atomic-resolution structural and dynamics information of all the states, folded, unfolded, and intermediates, including invisibles, along the funnel. In this work, we have used a canonical RNA recognition motif (RRM) from the ETR3 protein (involved in muscular dystrophy disease) to understand the unfolding mechanism of RRM-containing protein. This is important as a similar motif in TDP-43 protein aggregates, eventually leading to neuromuscular disease conditions due to the formation of non-native structural elements. We determined the atomic-resolution structure and dynamics of folded native state (at the bottom of the funnel) and an unfolding intermediate at the middle of the funnel, and performed structural and dynamics characterisation of the unfolded ensemble rapidly dancing at the top of the funnel. Our data indicates that the intermediate state has a folded-like structure but is swollen and dynamic. It allows the solvent to access its core more easily than the folded structure. The edges of secondary structural elements are the initiation sites of unfolding. Although the unfolded state is very dynamic and lacks any structural elements, it still shows a bias for certain structural propensities, which appear to keep a memory of their folded state.<\/p>\n\n\n\n

We believe that the atomic-resolution characterisation of the unfolding pathway of a canonical RNA recognition motif is likely to help understand the unfolding events in other RRMs involved in disease-causing conditions upon misfolding.<\/p>\n\n\n\n

The study might also help understand those systems where protein is refolded from the purified inclusion bodies. In those cases, there could be the presence of a minor population of folded-like but not fully folded native structure.<\/p>\n\n\n\n

The work was primarily done by Dr. Harshesh Bhatt and Dr. Akshay Kumar Ganguly, and the FCS work was performed in collaboration with Dr. Sobhan Sen<\/a>, School of Physical Sciences, Jawaharlal Nehru University<\/a> (JNU<\/a>), New Delhi. The cover art was designed by Mr. Anupam Patra, a Ph.D. student.<\/p>\n\n\n\n

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(\u092a\u093e\u0928\u0940) \u0915\u094b \u092e\u0942\u0932 \u0938\u0902\u0930\u091a\u0928\u093e \u0915\u0940 \u0924\u0941\u0932\u0928\u093e \u092e\u0947\u0902 \u0905\u0927\u093f\u0915 \u0906\u0938\u093e\u0928\u0940 \u0938\u0947 \u091c\u093e \u092a\u093e\u0924\u0947 \u0939\u0948\u0902\u0964 \u092e\u093e\u0927\u094d\u092f\u092e\u093f\u0915 \u0906\u0915\u0943\u0924\u093f \u0915\u0947 \u0938\u0902\u0930\u091a\u0928\u093e\u0924\u094d\u092e\u0915 \u0924\u0924\u094d\u0935\u094b\u0902 \u0915\u0947 \u0915\u093f\u0928\u093e\u0930\u0947 \u092a\u094d\u0930\u094b\u091f\u0940\u0928 \u0915\u0947 \u0916\u0941\u0932\u0928\u0947 \u0915\u0947 \u0906\u0930\u092e\u094d\u092d\u093f\u0915 \u0938\u094d\u0925\u0932 \u0939\u0948\u0902\u0964 \u0939\u093e\u0932\u093e\u0902\u0915\u093f \u092a\u0942\u0930\u094d\u0923\u0924\u0903 \u0916\u0941\u0932\u0947 \u0939\u0941\u0906 \u0906\u0915\u0943\u0924\u093f \u0938\u092e\u0942\u0939 \u092c\u0939\u0941\u0924 \u0939\u0940 \u0917\u0924\u093f\u0936\u0940\u0932 \u0939\u0948 \u0914\u0930 \u0909\u0938\u092e\u0947 \u0915\u093f\u0938\u0940 \u092d\u0940 \u0938\u0902\u0930\u091a\u0928\u093e\u0924\u094d\u092e\u0915 \u0924\u0924\u094d\u0935\u094b\u0902 \u0915\u0940 \u0915\u092e\u0940 \u0939\u0948, \u092b\u093f\u0930 \u092d\u0940 \u092f\u0939 \u0915\u0941\u091b \u0935\u093f\u0936\u0947\u0937 \u0938\u0902\u0930\u091a\u0928\u093e\u0924\u094d\u092e\u0915 \u0938\u094d\u0925\u093f\u0924\u093f\u0913\u0902 \u0915\u0947 \u0932\u093f\u090f \u092a\u0942\u0930\u094d\u0935\u093e\u0917\u094d\u0930\u0939 \u0926\u093f\u0916\u093e\u0924\u0940 \u0939\u0948, \u091c\u094b \u0909\u0928\u0915\u0947 \u092e\u0942\u0932 \u0938\u0902\u0930\u091a\u0928\u093e \u0915\u0940 \u0938\u094d\u092e\u0943\u0924\u093f \u0930\u0916\u0928\u0947 \u091c\u0948\u0938\u093e \u092a\u094d\u0930\u0924\u0940\u0924 \u0939\u094b\u0924\u093e \u0939\u0948\u0964<\/p>\n\n\n\n

\u0939\u092e \u092e\u093e\u0928\u0924\u0947 \u0939\u0948\u0902 \u0915\u093f \u0939\u092e\u093e\u0930\u0947 \u0926\u094d\u0935\u093e\u0930\u093e \u0935\u0930\u094d\u0923\u093f\u0924 \u092a\u0930\u092e\u093e\u0923\u0941-\u0938\u094d\u0924\u0930 \u0915\u0940 \u091c\u093e\u0928\u0915\u093e\u0930\u0940 \u0938\u0947 \u0935\u093f\u092d\u093f\u0928\u094d\u0928 \u0930\u094b\u0917\u094b\u0902 \u092e\u0947\u0902 \u0936\u093e\u092e\u093f\u0932 \u0905\u0928\u094d\u092f \u0906\u0930. \u0906\u0930. \u090f\u092e. \u0915\u0947 \u0938\u0902\u0930\u091a\u0928\u093e \u0916\u0941\u0932\u0928\u0947 \u0915\u0940 \u0918\u091f\u0928\u093e\u0913\u0902 \u0915\u094b \u0938\u092e\u091d\u0928\u0947 \u092e\u0947\u0902 \u092e\u0926\u0926 \u092e\u093f\u0932\u0947\u0917\u0940 |<\/p>\n\n\n\n

\u092f\u0939 \u0905\u0927\u094d\u092f\u092f\u0928 \u0909\u0928 \u092a\u094d\u0930\u0923\u093e\u0932\u093f\u092f\u094b\u0902 \u0915\u094b \u0938\u092e\u091d\u0928\u0947 \u092e\u0947\u0902 \u092d\u0940 \u092e\u0926\u0926 \u0915\u0930 \u0938\u0915\u0924\u093e \u0939\u0948 \u091c\u0939\u093e\u0902 \u092a\u094d\u0930\u094b\u091f\u0940\u0928 \u0925\u0915\u094d\u0915\u0947\u0926\u093e\u0930 \u0905\u0935\u0938\u094d\u0925\u093e \u0938\u0947 \u0935\u093e\u092a\u0938 \u092e\u0942\u0932 \u0938\u0902\u0930\u091a\u0928\u093e \u092e\u0947\u0902 \u0932\u093e\u092f\u093e \u091c\u093e\u0924\u093e \u0939\u0948\u0964 \u0907\u0928 \u092e\u093e\u092e\u0932\u094b\u0902 \u092e\u0947\u0902 \u092e\u0942\u0932 \u0938\u0902\u0930\u091a\u0928\u093e \u091c\u0948\u0938\u0940 \u092e\u093e\u092e\u0942\u0932\u0940 \u0906\u092c\u093e\u0926\u0940 \u0915\u0940 \u092d\u0940 \u092e\u094c\u091c\u0942\u0926\u0917\u0940 \u0939\u094b \u0938\u0915\u0924\u0940 \u0939\u0948, \u091c\u094b \u092a\u0942\u0930\u0940 \u0924\u0930\u0939 \u0938\u0947 \u092e\u0942\u0932 \u0938\u0902\u0930\u091a\u0928\u093e \u092e\u0947\u0902 \u0928\u093e \u0939\u094b\u0902\u0964<\/p>\n\n\n\n

\u092f\u0939 \u0936\u094b\u0927 \u092e\u0941\u0916\u094d\u092f\u0924\u0903 \u0921\u093e. \u0939\u0930\u094d\u0937\u0947\u0936 \u092d\u091f\u094d\u091f \u0914\u0930 \u0921\u093e. \u0905\u0915\u094d\u0937\u092f \u0915\u0941\u092e\u093e\u0930 \u0917\u093e\u0902\u0917\u0941\u0932\u0940 \u0926\u094d\u0935\u093e\u0930\u093e \u0915\u093f\u092f\u093e \u0917\u092f\u093e \u0914\u0930 FCS \u0915\u093e\u0930\u094d\u092f \u091c\u0935\u093e\u0939\u0930\u0932\u093e\u0932 \u0928\u0947\u0939\u0930\u0942 \u0935\u093f\u0936\u094d\u0935\u0935\u093f\u0926\u094d\u092f\u093e\u0932\u092f<\/a> (\u091c\u0947. \u090f\u0928. \u092f\u0942.)<\/a> \u0915\u0947 \u092d\u094c\u0924\u093f\u0915 \u0935\u093f\u091c\u094d\u091e\u093e\u0928 \u0915\u0947 \u0921\u093e.<\/a> \u0938\u094b\u092d\u0928 \u0938\u0947\u0928<\/a> \u0915\u0947 \u0938\u0939\u092d\u093e\u0917\u093f\u0924\u093e \u0938\u0947 \u0915\u0940 \u0917\u0908 | \u092e\u0941\u0916\u094d\u092f \u092a\u0943\u0937\u094d\u0920 \u0906\u0935\u0930\u0923 \u0915\u094b \u0936\u094d\u0930\u0940 \u0905\u0928\u0941\u092a\u092e \u092a\u093e\u0924\u094d\u0930\u093e, \u0935\u0930\u094d\u0924\u092e\u093e\u0928 \u092a\u0940.\u090f\u091a.\u0921\u0940. \u091b\u093e\u0924\u094d\u0930, \u0928\u0947 \u092c\u0928\u093e\u092f\u093e \u0939\u0948\u0964<\/p>\n\n\n\n

References<\/strong><\/p>\n\n\n\n

    \n
  1. Dill K.A. and Chan H.S. (1997) From Levinthal to pathways to funnels. Nat. Struct. Biol.<\/a><\/em> 4<\/strong>: 10-19<\/li>\n\n\n\n
  2. Bhatt H, Ganguly AK, Sharma S, Kushwaha GS, Khan MF, Sen S and Bhavesh NS (2020) Structure of an unfolding intermediate of an RRM domain of ETR-3 reveals its native-like fold. Biophys. J. <\/a><\/em>118<\/strong>, 352-365.<\/li>\n\n\n\n
  3. Structure co-ordinates<\/strong>: Protein Data Bank (PDB) accession numbers 2MY7<\/a> and 2MY8<\/a>. Sequence-specific resonance assignments<\/strong>: BioMagResBank (BMRB) IDs: 19316<\/a> and 19685<\/a>.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    Proteins are unique molecules; they read the code of life in genes, and their own codes are also hidden in genes.\u00a0 Therefore, they are called the architects, pillars, and workhorses of life. \u00a0A vast majority of proteins require a well-defined three-dimensional shape and flexibility for their specific and regulated function inside the cell. The hierarchy … Continue reading Structure of an intermediate state during protein unfolding<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"pagelayer_contact_templates":[],"_pagelayer_content":"","footnotes":""},"categories":[3],"tags":[15,11,25,12],"class_list":["post-31","post","type-post","status-publish","format-standard","hentry","category-science","tag-nmr-spectroscopy","tag-protein","tag-protein-folding","tag-structure"],"_links":{"self":[{"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/posts\/31","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/comments?post=31"}],"version-history":[{"count":10,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/posts\/31\/revisions"}],"predecessor-version":[{"id":93,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/posts\/31\/revisions\/93"}],"wp:attachment":[{"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/media?parent=31"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/categories?post=31"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/tags?post=31"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}