|
| 1 | + |
| 2 | +@article{smitProbingUniversalProtein2021e, |
| 3 | + title = {Probing {{Universal Protein Dynamics Using Hydrogen}}\textendash{{Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy}}}, |
| 4 | + author = {Smit, Jochem H. and Krishnamurthy, Srinath and Srinivasu, Bindu Y. and Parakra, Rinky and Karamanou, Spyridoula and Economou, Anastassios}, |
| 5 | + year = {2021}, |
| 6 | + month = sep, |
| 7 | + journal = {Analytical Chemistry}, |
| 8 | + volume = {93}, |
| 9 | + number = {38}, |
| 10 | + pages = {12840--12847}, |
| 11 | + publisher = {{American Chemical Society}}, |
| 12 | + issn = {0003-2700}, |
| 13 | + doi = {10.1021/acs.analchem.1c02155}, |
| 14 | + abstract = {Hydrogen\textendash deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to monitor protein intrinsic dynamics. The technique provides high-resolution information on how protein intrinsic dynamics are altered in response to biological signals, such as ligand binding, oligomerization, or allosteric networks. However, identification, interpretation, and visualization of such events from HDX-MS data sets is challenging as these data sets consist of many individual data points collected across peptides, time points, and experimental conditions. Here, we present PyHDX, an open-source Python package and webserver, that allows the user to batch extract the universal quantity Gibbs free energy at residue levels over multiple protein conditions and homologues. The output is directly visualized on a linear map or 3D structures or is exported as .csv files or PyMOL scripts.}, |
| 15 | + file = {C\:\\Users\\jhsmi\\Zotero\\storage\\Z784VN47\\Smit_et_al_2021_Probing_Universal_Protein_Dynamics_Using_Hydrogen–Deuterium_Exchange_Mass.pdf;C\:\\Users\\jhsmi\\Zotero\\storage\\D6XSB5YX\\acs.analchem.html} |
| 16 | +} |
| 17 | + |
| 18 | + |
| 19 | + |
| 20 | +@article{baiPrimaryStructureEffects1993, |
| 21 | + title = {Primary Structure Effects on Peptide Group Hydrogen Exchange}, |
| 22 | + author = {Bai, Yawen and Milne, John S. and Mayne, Leland and Englander, S. Walter}, |
| 23 | + year = {1993}, |
| 24 | + journal = {Proteins: Structure, Function, and Bioinformatics}, |
| 25 | + volume = {17}, |
| 26 | + number = {1}, |
| 27 | + pages = {75--86}, |
| 28 | + issn = {1097-0134}, |
| 29 | + doi = {10.1002/prot.340170110}, |
| 30 | + abstract = {The rate of exchange of peptide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, all 20 naturally occurring amino acids were studied using dipeptide models. Both inductive and steric blocking effects are apparent. The additivity of nearest-neighbor blocking and inductive effects was tested in oligo-and polypeptides and, suprisingly, confirmed. Reference rates for alanine-containing peptides were determined and effects of temperature considered. These results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured aligo- and polypeptides. The application of this approach to protein studies is discussed. \textcopyright{} 1993 Wiley-Liss, Inc.}, |
| 31 | + copyright = {Copyright \textcopyright{} 1993 Wiley-Liss, Inc.}, |
| 32 | + langid = {english}, |
| 33 | + keywords = {hydrogen exchange,inductive effects,protein structure,side chain effects,steric hindrance}, |
| 34 | + annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.340170110}, |
| 35 | + file = {C\:\\Users\\jhsmi\\Zotero\\storage\\RRY8NFFS\\Bai_et_al_1993_Primary_structure_effects_on_peptide_group_hydrogen_exchange.pdf;C\:\\Users\\jhsmi\\Zotero\\storage\\PURS556T\\prot.html} |
| 36 | +} |
| 37 | + |
| 38 | +@article{connellyIsotopeEffectsPeptide1993, |
| 39 | + title = {Isotope Effects in Peptide Group Hydrogen Exchange}, |
| 40 | + author = {Connelly, Gregory P. and Bai, Yawen and Jeng, Mei-Fen and Englander, S. Walter}, |
| 41 | + year = {1993}, |
| 42 | + month = sep, |
| 43 | + journal = {Proteins: Structure, Function, and Genetics}, |
| 44 | + volume = {17}, |
| 45 | + number = {1}, |
| 46 | + pages = {87--92}, |
| 47 | + issn = {0887-3585, 1097-0134}, |
| 48 | + doi = {10.1002/prot.340170111}, |
| 49 | + abstract = {Kinetic and equilibrium isotope effects in peptide group hydrogen exchange reactions were evaluated. Unlike many other reactions, kinetic isotope effects in amide hydrogen exchange are small because exchange pathways are not limited b y bondbreaking steps. Rate constants for the acid-catalyzed exchange of peptide group NH,ND, and NT in H,O are essentially identical, but a solvent isotope effect doubles the rate in D20. Rate constants for base-catalyzed exchange in H 2 0 decrease slowly in the order NH{$>$}ND{$>$}NT.The alkaline rate constant in D 2 0 is very close to that in H20 when account is taken of the glass electrode p H artifact and the difference in solvent ionization constant. Small equilibrium isotope effects lead to an excess equilibrium accumulation of the heavier isotopes b y the peptide group. Results obtained are expressed in terms of rate constants for the random coil polypeptide, poly-DL-alanine, to provide reference rates for protein hydrogen exchange studies as described in Bai et al. [preceding paper in this issue]. 0 1993 Wiley-Liss, Inc.}, |
| 50 | + langid = {english}, |
| 51 | + file = {C\:\\Users\\jhsmi\\Zotero\\storage\\KWBW3HXS\\Connelly_et_al_1993_Isotope_effects_in_peptide_group_hydrogen_exchange.pdf} |
| 52 | +} |
| 53 | + |
| 54 | +@article{moriMeasurementWaterAmide1997, |
| 55 | + title = {{Measurement of water\textendash amide proton exchange rates in the denatured state of staphylococcal nuclease by a magnetization transfer technique}}, |
| 56 | + author = {Mori, Susumu and van Zijl, Peter C. M. and Shortle, David}, |
| 57 | + year = {1997}, |
| 58 | + journal = {Proteins: Structure, Function, and Bioinformatics}, |
| 59 | + volume = {28}, |
| 60 | + number = {3}, |
| 61 | + pages = {325--332}, |
| 62 | + issn = {1097-0134}, |
| 63 | + doi = {10.1002/(SICI)1097-0134(199707)28:3<325::AID-PROT3>3.0.CO;2-B}, |
| 64 | + abstract = {The rates of hydrogen exchange were measured in a ``physiological'' denatured state of staphylococcal nuclease using a NMR magnetization transfer experiment suitable for the measurement of exchange rates faster than 0.5 s-1. The results are compared with predicted exchange rates (kex) for the random coil state (Bai et al., Proteins 17:75\textendash 86, 1993). No protection factors ({$\cdot$} predicted rate/measured rate) larger than 2.4 were observed, consistent with other NMR data which strongly suggest only small amounts of residual secondary structure in this denatured state. Systematically low protection factors (0.51 {$\cdot$} 0.23) were found for Asp and Glu residues, while high protection factors were observed for Gly (1.60 {$\cdot$} 0.60). We conclude that the predicted exchange rates (kex) may have an uncertainty of 2- to 3-fold. Thus, for denatured proteins only protection factors with a value of 5 or larger can be assigned structural significance. These results also demonstrate that multidimensional magnetization transfer NMR techniques are powerful tools in this research field due to its ability to measure rapidly exchanging protons ({$\cdot$}05 s-1) with high accuracy. Proteins 28:325\textendash 332, 1997. \textcopyright{} 1997 Wiley-Liss, Inc.}, |
| 65 | + copyright = {Copyright \textcopyright{} 1997 Wiley-Liss, Inc.}, |
| 66 | + langid = {french}, |
| 67 | + keywords = {denatured state,hydrogen exchange,magnetization transfer,NMR,staphylococcal nuclease}, |
| 68 | + annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/\%28SICI\%291097-0134\%28199707\%2928\%3A3\%3C325\%3A\%3AAID-PROT3\%3E3.0.CO\%3B2-B}, |
| 69 | + file = {C\:\\Users\\jhsmi\\Zotero\\storage\\K8G77DG6\\Mori_et_al_1997_Measurement_of_water–amide_proton_exchange_rates_in_the_denatured_state_of.pdf;C\:\\Users\\jhsmi\\Zotero\\storage\\5ZYF7EZ8\\(SICI)1097-0134(199707)283325AID-PROT33.0.html} |
| 70 | +} |
| 71 | + |
| 72 | +@article{nguyenReferenceParametersProtein2018, |
| 73 | + title = {Reference {{Parameters}} for {{Protein Hydrogen Exchange Rates}}}, |
| 74 | + author = {Nguyen, David and Mayne, Leland and Phillips, Michael C. and Walter Englander, S.}, |
| 75 | + year = {2018}, |
| 76 | + month = sep, |
| 77 | + journal = {Journal of the American Society for Mass Spectrometry}, |
| 78 | + volume = {29}, |
| 79 | + number = {9}, |
| 80 | + pages = {1936--1939}, |
| 81 | + publisher = {{American Chemical Society}}, |
| 82 | + issn = {1044-0305}, |
| 83 | + doi = {10.1021/jasms.8b05911}, |
| 84 | + abstract = {The analysis of many hydrogen exchange (HX) experiments depends on knowledge of exchange rates expected for the unstructured protein under the same conditions. We present here some minor adjustments to previously calibrated values and a stringent test of their accuracy.}, |
| 85 | + file = {C\:\\Users\\jhsmi\\Zotero\\storage\\EWESLH4X\\Nguyen_et_al_2018_Reference_Parameters_for_Protein_Hydrogen_Exchange_Rates.pdf;C\:\\Users\\jhsmi\\Zotero\\storage\\EWJKBBWG\\jasms.html} |
| 86 | +} |
| 87 | + |
| 88 | + |
| 89 | +@article{sehnalMolViewerModern2021, |
| 90 | + title = {Mol* {{Viewer}}: Modern Web App for {{3D}} Visualization and Analysis of Large Biomolecular Structures}, |
| 91 | + shorttitle = {Mol* {{Viewer}}}, |
| 92 | + author = {Sehnal, David and Bittrich, Sebastian and Deshpande, Mandar and Svobodov{\'a}, Radka and Berka, Karel and Bazgier, V{\'a}clav and Velankar, Sameer and Burley, Stephen K and Ko{\v c}a, Jaroslav and Rose, Alexander S}, |
| 93 | + year = {2021}, |
| 94 | + month = jul, |
| 95 | + journal = {Nucleic Acids Research}, |
| 96 | + volume = {49}, |
| 97 | + number = {W1}, |
| 98 | + pages = {W431-W437}, |
| 99 | + issn = {0305-1048}, |
| 100 | + doi = {10.1093/nar/gkab314}, |
| 101 | + abstract = {Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.}, |
| 102 | + file = {C\:\\Users\\jhsmi\\Zotero\\storage\\CU5CXZ3Q\\Sehnal_et_al_2021_Mol_Viewer.pdf;C\:\\Users\\jhsmi\\Zotero\\storage\\YWIT9X2M\\6270780.html} |
| 103 | +} |
| 104 | + |
| 105 | + |
| 106 | + |
| 107 | +@article{krishnamurthyNexusIntrinsicDynamics2021d, |
| 108 | + title = {A Nexus of Intrinsic Dynamics Underlies Translocase Priming}, |
| 109 | + author = {Krishnamurthy, Srinath and Eleftheriadis, Nikolaos and Karathanou, Konstantina and Smit, Jochem H. and Portaliou, Athina G. and Chatzi, Katerina E. and Karamanou, Spyridoula and Bondar, Ana-Nicoleta and Gouridis, Giorgos and Economou, Anastassios}, |
| 110 | + year = {2021}, |
| 111 | + month = aug, |
| 112 | + journal = {Structure}, |
| 113 | + volume = {29}, |
| 114 | + number = {8}, |
| 115 | + pages = {846-858.e7}, |
| 116 | + publisher = {{Elsevier}}, |
| 117 | + issn = {0969-2126}, |
| 118 | + doi = {10.1016/j.str.2021.03.015}, |
| 119 | + langid = {english}, |
| 120 | + pmid = {33852897}, |
| 121 | + keywords = {graph analysis,HDX-MS,intrinsic dynamics,MD simulation,protein secretion,SecA,SecYEG channel,signal peptide,smFRET,translocase}, |
| 122 | + file = {C\:\\Users\\jhsmi\\Zotero\\storage\\9TLKKGAE\\Krishnamurthy_et_al_2021_A_nexus_of_intrinsic_dynamics_underlies_translocase_priming.pdf;C\:\\Users\\jhsmi\\Zotero\\storage\\FRK4LRP4\\S0969-2126(21)00113-1.html} |
| 123 | +} |
| 124 | + |
| 125 | +@article{krishnamurthyPreproteinsCoupleIntrinsic2022, |
| 126 | + title = {Preproteins Couple the Intrinsic Dynamics of {{SecA}} to Its {{ATPase}} Cycle to Translocate via a Catch and Release Mechanism}, |
| 127 | + author = {Krishnamurthy, Srinath and Sardis, Marios-Frantzeskos and Eleftheriadis, Nikolaos and Chatzi, Katerina E. and Smit, Jochem H. and Karathanou, Konstantina and Gouridis, Giorgos and Portaliou, Athina G. and Bondar, Ana-Nicoleta and Karamanou, Spyridoula and Economou, Anastassios}, |
| 128 | + year = {2022}, |
| 129 | + month = feb, |
| 130 | + journal = {Cell Reports}, |
| 131 | + volume = {38}, |
| 132 | + number = {6}, |
| 133 | + publisher = {{Elsevier}}, |
| 134 | + issn = {2211-1247}, |
| 135 | + doi = {10.1016/j.celrep.2022.110346}, |
| 136 | + langid = {english}, |
| 137 | + pmid = {35139375}, |
| 138 | + keywords = {enzyme activation,HDX-MS,intrinsic dynamics,molecular dynamics,protein secretion,SecA,secretory clients,SecYEG channel,signal peptide,smFRET,translocase}, |
| 139 | + file = {C\:\\Users\\jhsmi\\Zotero\\storage\\N97WS2HX\\Krishnamurthy_et_al_2022_Preproteins_couple_the_intrinsic_dynamics_of_SecA_to_its_ATPase_cycle_to.pdf;C\:\\Users\\jhsmi\\Zotero\\storage\\XSWRBKUT\\S2211-1247(22)00062-6.html} |
| 140 | +} |
| 141 | + |
| 142 | +@article{yuanStructuralDynamicsFunctional2021, |
| 143 | + title = {Structural {{Dynamics}} of the {{Functional Nonameric Type III Translocase Export Gate}}}, |
| 144 | + author = {Yuan, Biao and Portaliou, Athina G. and Parakra, Rinky and Smit, Jochem H. and Wald, Jiri and Li, Yichen and Srinivasu, Bindu and Loos, Maria S. and Dhupar, Harveer Singh and Fahrenkamp, Dirk and Kalodimos, Charalampos G. and {Duong van Hoa}, Franck and Cordes, Thorben and Karamanou, Spyridoula and Marlovits, Thomas C. and Economou, Anastassios}, |
| 145 | + year = {2021}, |
| 146 | + month = oct, |
| 147 | + journal = {Journal of Molecular Biology}, |
| 148 | + volume = {433}, |
| 149 | + number = {21}, |
| 150 | + pages = {167188}, |
| 151 | + issn = {0022-2836}, |
| 152 | + doi = {10.1016/j.jmb.2021.167188}, |
| 153 | + abstract = {Type III protein secretion is widespread in Gram-negative pathogens. It comprises the injectisome with a surface-exposed needle and an inner membrane translocase. The translocase contains the SctRSTU export channel enveloped by the export gate subunit SctV that binds chaperone/exported clients and forms a putative ante-chamber. We probed the assembly, function, structure and dynamics of SctV from enteropathogenic E. coli (EPEC). In both EPEC and E. coli lab strains, SctV forms peripheral oligomeric clusters that are detergent-extracted as homo-nonamers. Membrane-embedded SctV9 is necessary and sufficient to act as a receptor for different chaperone/exported protein pairs with distinct C-domain binding sites that are essential for secretion. Negative staining electron microscopy revealed that peptidisc-reconstituted His-SctV9 forms a tripartite particle of {$\sim$}22~nm with a N-terminal domain connected by a short linker to a C-domain ring structure with a {$\sim$}5~nm-wide inner opening. The isolated C-domain ring was resolved with cryo-EM at 3.1~\AA{} and structurally compared to other SctV homologues. Its four sub-domains undergo a three-stage ``pinching'' motion. Hydrogen-deuterium exchange mass spectrometry revealed this to involve dynamic and rigid hinges and a hyper-flexible sub-domain that flips out of the ring periphery and binds chaperones on and between adjacent protomers. These motions are coincident with local conformational changes at the pore surface and ring entry mouth that may also be modulated by the ATPase inner stalk. We propose that the intrinsic dynamics of the SctV protomer are modulated by chaperones and the ATPase and could affect allosterically the other subunits of the nonameric ring during secretion.}, |
| 154 | + langid = {english}, |
| 155 | + keywords = {EPEC,export apparatus,protein dynamics,SctV-C structure,type III secretion}, |
| 156 | + file = {C\:\\Users\\jhsmi\\Zotero\\storage\\SEV44PWH\\Yuan_et_al_2021_Structural_Dynamics_of_the_Functional_Nonameric_Type_III_Translocase_Export_Gate.pdf;C\:\\Users\\jhsmi\\Zotero\\storage\\SIK4SIXX\\1-s2.0-S0022283621004216-mmc6.pdf} |
| 157 | +} |
| 158 | + |
| 159 | + |
| 160 | + |
| 161 | + |
| 162 | + |
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