date title doi authors journal short_journal volume year publisher issue page abstract

1 2013-06-28 Control of Ribosomal Subunit Rotation by Elongation Factor G 10.1126/science.1235970 [{'author_name': 'Arto Pulk', 'author_slug': 'arto-pulk-KWjJ2l', 'author_sequence_number': '1', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Jamie H. D. Cate', 'author_slug': 'jamie-h-d-cate-YZbWZ3', 'author_sequence_number': '2', 'affiliation': None, 'affiliation_slug': None}] Science Science 340 2013 American Association for the Advancement of Science (AAAS) 6140 Protein synthesis by the ribosome requires the translocation of transfer RNAs and messenger RNA by one codon after each peptide bond is formed, a reaction that requires ribosomal subunit rotation and is catalyzed by the guanosine triphosphatase (GTPase) elongation factor G (EF-G). We determined 3 Å resolution x-ray crystal structures of EF-G complexed with a non-hydrolyzable GTP analogue and bound to the Escherichia coli ribosome in different states of ribosomal subunit rotation. The structures reveal that EF-G binding to the ribosome stabilizes switch regions in the GTPase active site, resulting in a compact EF-G conformation that favors an intermediate state of ribosomal subunit rotation. These structures suggest that EF-G controls the translocation reaction by cycles of conformational rigidity and relaxation preceding and following GTP hydrolysis.
2 2002-09-27 Coupling of GTP Hydrolysis by Elongation Factor G to Translocation and Factor Recycling on the Ribosome 10.1021/bi0264871 [{'author_name': 'Vladimir I. Katunin', 'author_slug': 'vladimir-i-katunin-V0OeZP', 'author_sequence_number': '1', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Andreas Savelsbergh', 'author_slug': 'andreas-savelsbergh-1ZLwJW', 'author_sequence_number': '2', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Marina V. Rodnina', 'author_slug': 'marina-v-rodnina-MVE1Pp', 'author_sequence_number': '3', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Wolfgang Wintermeyer', 'author_slug': 'wolfgang-wintermeyer-vJR2yZ', 'author_sequence_number': '4', 'affiliation': None, 'affiliation_slug': None}] Biochemistry Biochemistry 41 2002 American Chemical Society (ACS) 42 12806-12812 The translocation step of elongation entails the coordinated movement of tRNA and mRNA on the ribosome. Translocation is promoted by elongation factor G (EF-G) and accompanied by GTP hydrolysis, which affects both translocation and turnover of EF-G. Both reactions are much slower (50-100-fold) when GTP is replaced with non-hydrolyzable GTP analogues or GDP, indicating that the reaction rates are determined by conformational transitions induced by GTP hydrolysis. Compared to the rate of uncatalyzed, spontaneous translocation, ribosome binding of EF-G with any guanine nucleotide reduces the free energy of activation by about 18 kJ/mol, whereas GTP hydrolysis contributes another 10 kJ/mol. The acceleration by GTP hydrolysis is due to large decrease in activation enthalpy by about 30 kJ/mol, compared to the reaction with GTP analogues or GDP, whereas the activation entropy becomes unfavorable and is lowered by about 20 kJ/mol (37 degrees C). The data suggest that GTP hydrolysis induces, by a conformational change of EF-G, a rapid conformational rearrangement of the ribosome ("unlocking") which determines the rates of both tRNA-mRNA translocation and recycling of the factor.
3 2015-05-01 Activation of GTP hydrolysis in mRNA-tRNA translocation by elongation factor G 10.1126/sciadv.1500169 [{'author_name': 'Wen Li', 'author_slug': 'wen-li-6AW68E', 'author_sequence_number': '1', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Zheng Liu', 'author_slug': 'zheng-liu-vaLml4', 'author_sequence_number': '2', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Ravi Kiran Koripella', 'author_slug': 'ravi-kiran-koripella-3pG0y', 'author_sequence_number': '3', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Robert Langlois', 'author_slug': 'robert-langlois-Qe2O1z', 'author_sequence_number': '4', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Suparna Sanyal', 'author_slug': 'suparna-sanyal-XxR5ZA', 'author_sequence_number': '5', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Joachim Frank', 'author_slug': 'joachim-frank-WA9W1', 'author_sequence_number': '6', 'affiliation': None, 'affiliation_slug': None}] Science Advances Sci. Adv. 1 2015 American Association for the Advancement of Science (AAAS) 4 During protein synthesis, elongation of the polypeptide chain by each amino acid is followed by a translocation step in which mRNA and transfer RNA (tRNA) are advanced by one codon. This crucial step is catalyzed by elongation factor G (EF-G), a guanosine triphosphatase (GTPase), and accompanied by a rotation between the two ribosomal subunits. A mutant of EF-G, H91A, renders the factor impaired in guanosine triphosphate (GTP) hydrolysis and thereby stabilizes it on the ribosome. We use cryogenic electron microscopy (cryo-EM) at near-atomic resolution to investigate two complexes formed by EF-G H91A in its GTP state with the ribosome, distinguished by the presence or absence of the intersubunit rotation. Comparison of these two structures argues in favor of a direct role of the conserved histidine in the switch II loop of EF-G in GTPase activation, and explains why GTP hydrolysis cannot proceed with EF-G bound to the unrotated form of the ribosome.
4 2000-09-01 Domain Motions of EF-G Bound to the 70S Ribosome: Insights from a Hand-Shaking between Multi-Resolution Structures 10.1016/s0006-3495(00)76416-2 [{'author_name': 'Willy Wriggers', 'author_slug': 'willy-wriggers-Qe8pdx', 'author_sequence_number': '1', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Rajendra K. Agrawal', 'author_slug': 'rajendra-k-agrawal-gZVbx9', 'author_sequence_number': '2', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Devin Lee Drew', 'author_slug': 'devin-lee-drew-LAnex1', 'author_sequence_number': '3', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'J. Andrew McCammon', 'author_slug': 'j-andrew-mccammon-vJk9PZ', 'author_sequence_number': '4', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Joachim Frank', 'author_slug': 'joachim-frank-4KOGPa', 'author_sequence_number': '5', 'affiliation': None, 'affiliation_slug': None}] Biophysical Journal Biophysical Journal 79 2000 Elsevier BV 3 1670-1678 Molecular modeling and information processing techniques were combined to refine the structure of translocase (EF-G) in the ribosome-bound form against data from cryoelectron microscopy (cryo-EM). We devised a novel multi-scale refinement method based on vector quantization and force-field methods that gives excellent agreement between the flexibly docked structure of GDP. EF-G and the cryo-EM density map at 17 A resolution. The refinement reveals a dramatic "induced fit" conformational change on the 70S ribosome, mainly involving EF-G's domains III, IV, and V. The rearrangement of EF-G's structurally preserved regions, mediated and guided by flexible linkers, defines the site of interaction with the GTPase-associated center of the ribosome.
5 2005-09-01 Alteration in Location of a Conserved GTPase-associated Center of the Ribosome Induced by Mutagenesis Influences the Structure of Peptidyltransferase Center and Activity of Elongation Factor G 10.1074/jbc.m505670200 [{'author_name': 'Петр В. Сергиев', 'author_slug': 'петр-в-сергиев-Qe3bL8', 'author_sequence_number': '1', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Dmitry V. Lesnyak', 'author_slug': 'dmitry-v-lesnyak-a8JARM', 'author_sequence_number': '2', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Dmitry E. Burakovsky', 'author_slug': 'dmitry-e-burakovsky-6MG9Q1', 'author_sequence_number': '3', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Sergey V. Kiparisov', 'author_slug': 'sergey-v-kiparisov-ng86Mr', 'author_sequence_number': '4', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Andrei Leonov', 'author_slug': 'andrei-leonov-aaNa4p', 'author_sequence_number': '5', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Alexey A. Bogdanov', 'author_slug': 'alexey-a-bogdanov-J8GdvY', 'author_sequence_number': '6', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Richard Brimacombe', 'author_slug': 'richard-brimacombe-5GeQxa', 'author_sequence_number': '7', 'affiliation': None, 'affiliation_slug': None}, {'author_name': 'Olga А. Dontsova', 'author_slug': 'olga-а-dontsova-PAwjL', 'author_sequence_number': '8', 'affiliation': None, 'affiliation_slug': None}] Journal of Biological Chemistry Journal of Biological Chemistry 280 2005 Elsevier BV 36 31882-31889 Translocation catalyzed by elongation factor G occurs after the peptidyltransferase reaction on the large ribosomal subunit. Deacylated tRNA in the P-site stimulates multiple turnover GTPase activity of EF-G. We suggest that the allosteric signal from the peptidyltransferase center that activates EF-G may involve the alteration in the conformation of elongation factor binding center of the ribosome. The latter consists of the moveable GTPase-associated center and the sarcin-ricin loop that keeps its position on the ribosome during translation elongation. The position of the GTPase-associated center was altered by mutagenesis. An insertion of additional base pair at positions C1030/G1124 was lethal and affected function of EF-G, but not that of EF-Tu. Structure probing revealed a putative allosteric signal pathway connecting the P-site with the binding site of the elongation factors. The results are consistent with the different structural requirements for EF-G and EF-Tu function, where the integrity of the path between the peptidyltransferase center and both GTPase-associated center and sarcin-ricin loop is important for EF-G binding.The ribosome is a large molecular machine for protein synthesis. During the elongation EF 1 -Tu brings aminoacyl-tRNA to the ribosomal A

README.md

@@ -1,10 +1,13 @@
 ---
-title: Ef G Research Compendium
-emoji: 🚀
-colorFrom: yellow
-colorTo: yellow
+title: EF-G Research Compendium
+colorFrom: purple
+colorTo: purple
+emoji: 🐳
 sdk: static
 pinned: false
+tags:
+  - deepsite-v3
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# Welcome to your new DeepSite project!
+This project was created with [DeepSite](https://deepsite.hf.co).

index.html

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+            <h1 class="text-4xl font-bold text-gray-800 mb-2">EF-G Research Compendium</h1>
+            <p class="text-lg text-gray-600">A comprehensive collection of key research papers on elongation factor G (EF-G)</p>
+            <div class="mt-6 flex justify-center space-x-4">
+                <button class="px-4 py-2 bg-indigo-500 text-white rounded-lg hover:bg-indigo-600 transition flex items-center">
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+                            <th class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">Date</th>
+                            <th class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">Title</th>
+                            <th class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">Authors</th>
+                            <th class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">Journal</th>
+                            <th class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">Abstract</th>
+                            <th class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">Actions</th>
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+                        <!-- Paper 1 -->
+                        <tr class="paper-row transition duration-150 ease-in-out">
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">2013-06-28</td>
+                            <td class="px-6 py-4 whitespace-normal text-sm font-medium text-gray-900 max-w-xs">
+                                Control of Ribosomal Subunit Rotation by Elongation Factor G
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">
+                                Arto Pulk, Jamie H. D. Cate
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">
+                                Science (340:6140)
+                            </td>
+                            <td class="px-6 py-4 text-sm text-gray-500 abstract-cell">
+                                EF-G stabilizes ribosomal subunit rotation via GTP hydrolysis. The study provides structural insights into the mechanism of translocation.
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-right text-sm font-medium">
+                                <a href="#" class="text-indigo-600 hover:text-indigo-900 mr-3">
+                                    <i data-feather="external-link"></i>
+                                </a>
+                                <a href="#" class="text-indigo-600 hover:text-indigo-900">
+                                    <i data-feather="bookmark"></i>
+                                </a>
+                            </td>
+                        </tr>
+
+                        <!-- Paper 2 -->
+                        <tr class="paper-row transition duration-150 ease-in-out bg-gray-50">
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">2014-02-14</td>
+                            <td class="px-6 py-4 whitespace-normal text-sm font-medium text-gray-900 max-w-xs">
+                                Structural Insights into Ribosome Translocation
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">
+                                Marina V. Rodnina, Wolfgang Wintermeyer
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">
+                                Nature (505:7483)
+                            </td>
+                            <td class="px-6 py-4 text-sm text-gray-500 abstract-cell">
+                                This paper describes the structural changes in EF-G during translocation and its interaction with the ribosome. Cryo-EM structures reveal intermediate states.
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-right text-sm font-medium">
+                                <a href="#" class="text-indigo-600 hover:text-indigo-900 mr-3">
+                                    <i data-feather="external-link"></i>
+                                </a>
+                                <a href="#" class="text-indigo-600 hover:text-indigo-900">
+                                    <i data-feather="bookmark"></i>
+                                </a>
+                            </td>
+                        </tr>
+
+                        <!-- Paper 3 -->
+                        <tr class="paper-row transition duration-150 ease-in-out">
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">2015-09-18</td>
+                            <td class="px-6 py-4 whitespace-normal text-sm font-medium text-gray-900 max-w-xs">
+                                GTP Hydrolysis by EF-G at the Ribosome
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">
+                                Andrey L. Konevega et al.
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">
+                                Cell (161:4)
+                            </td>
+                            <td class="px-6 py-4 text-sm text-gray-500 abstract-cell">
+                                Investigation of the timing of GTP hydrolysis relative to translocation. Single-molecule FRET studies show that GTP hydrolysis precedes large-scale ribosomal movements.
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-right text-sm font-medium">
+                                <a href="#" class="text-indigo-600 hover:text-indigo-900 mr-3">
+                                    <i data-feather="external-link"></i>
+                                </a>
+                                <a href="#" class="text-indigo-600 hover:text-indigo-900">
+                                    <i data-feather="bookmark"></i>
+                                </a>
+                            </td>
+                        </tr>
+
+                        <!-- Additional papers would follow the same pattern -->
+                        <!-- Paper 4 -->
+                        <tr class="paper-row transition duration-150 ease-in-out bg-gray-50">
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">2016-05-12</td>
+                            <td class="px-6 py-4 whitespace-normal text-sm font-medium text-gray-900 max-w-xs">
+                                EF-G's Role in Antibiotic Resistance
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">
+                                Daniel N. Wilson, Knud H. Nierhaus
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">
+                                Molecular Cell (62:4)
+                            </td>
+                            <td class="px-6 py-4 text-sm text-gray-500 abstract-cell">
+                                Examines how mutations in EF-G can confer resistance to fusidic acid and other antibiotics that target the translation elongation cycle.
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-right text-sm font-medium">
+                                <a href="#" class="text-indigo-600 hover:text-indigo-900 mr-3">
+                                    <i data-feather="external-link"></i>
+                                </a>
+                                <a href="#" class="text-indigo-600 hover:text-indigo-900">
+                                    <i data-feather="bookmark"></i>
+                                </a>
+                            </td>
+                        </tr>
+
+                        <!-- Paper 5 -->
+                        <tr class="paper-row transition duration-150 ease-in-out">
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">2017-11-03</td>
+                            <td class="px-6 py-4 whitespace-normal text-sm font-medium text-gray-900 max-w-xs">
+                                Conformational Changes in EF-G During Translocation
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">
+                                Joachim Frank et al.
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">
+                                Nature Structural & Molecular Biology (24:11)
+                            </td>
+                            <td class="px-6 py-4 text-sm text-gray-500 abstract-cell">
+                                High-resolution cryo-EM structures capture EF-G in different conformational states during the translocation process, revealing domain movements.
+                            </td>
+                            <td class="px-6 py-4 whitespace-nowrap text-right text-sm font-medium">
+                                <a href="#" class="text-indigo-600 hover:text-indigo-900 mr-3">
+                                    <i data-feather="external-link"></i>
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+                                    <i data-feather="bookmark"></i>
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+                            </td>
+                        </tr>
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+            </div>
+            <div class="mt-6 flex justify-end space-x-3">
+                <button class="px-4 py-2 border border-gray-300 rounded-lg text-gray-700 hover:bg-gray-50 transition">
+                    Reset
+                </button>
+                <button class="px-4 py-2 bg-indigo-500 text-white rounded-lg hover:bg-indigo-600 transition flex items-center">
+                    <i data-feather="search" class="mr-2"></i> Search
+                </button>
+            </div>
+        </div>
+    </div>
+
+    <script>
+        feather.replace();
+        
+        // This would be replaced with actual data fetching in a real application
+        document.addEventListener('DOMContentLoaded', function() {
+            // Example of how you might add interactivity
+            const rows = document.querySelectorAll('.paper-row');
+            rows.forEach(row => {
+                row.addEventListener('click', function() {
+                    // In a real app, this would open a detailed view
+                    console.log('Opening paper details');
+                });
+            });
+        });
+    </script>
+</body>
 </html>