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1. Full Text Protein dynamics viewed by hydrogen exchange
by Skinner, John J and Lim, Woon K and Bédard, Sabrina and Black, Ben E and Englander, S. Walter
Protein Science, ISSN 0961-8368, 07/2012, Volume 21, Issue 7, pp. 996 - 1005
To examine the relationship between protein structural dynamics and measurable hydrogen exchange (HX) data, the detailed exchange behavior of most of the... 
static and dynamic | protein folding | hydrogen exchange | protein dynamics | Staphylococcal nuclease | Hydrogen exchange | Protein dynamics | Protein folding | Static and dynamic | PROTON-EXCHANGE | STABILITY | BIOCHEMISTRY & MOLECULAR BIOLOGY | STATE | PEPTIDE | CYTOCHROME-C | RATES | PATHWAY | FLUCTUATIONS | EQUILIBRIUM | Staphylococcus - enzymology | Hydrogen Bonding | Protein Structure, Secondary | Water - chemistry | Nuclear Magnetic Resonance, Biomolecular | Hydrogen - chemistry | Staphylococcus - chemistry | Micrococcal Nuclease - chemistry | Molecular Dynamics Simulation | Protein Folding | Solvents | Crystal structure
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2. Full Text Protein hydrogen exchange: Testing current models
by Skinner, John J and Lim, Woon K and Bédard, Sabrina and Black, Ben E and Englander, S. Walter
Protein Science, ISSN 0961-8368, 07/2012, Volume 21, Issue 7, pp. 987 - 995
To investigate the determinants of protein hydrogen exchange (HX), HX rates of most of the backbone amide hydrogens of Staphylococcal nuclease were measured by... 
static and dynamic | hydrogen exchange | electrostatics | Staphylococcal nuclease | protein folding | cleanex‐PM | EX1 | Protein folding | Cleanex-PM | Hydrogen exchange | Electrostatics | Static and dynamic | PEPTIDE GROUP | ENSEMBLE | BIOCHEMISTRY & MOLECULAR BIOLOGY | PROTECTION FACTORS | STATE | PREDICTION | ORIGIN | FOLDING PATHWAY | FLUCTUATIONS | DYNAMICS | cleanex-PM | Staphylococcus - enzymology | Models, Chemical | Nuclear Magnetic Resonance, Biomolecular | Static Electricity | Hydrogen - chemistry | Staphylococcus - chemistry | Micrococcal Nuclease - chemistry | Protein Folding
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3. Full Text Benchmarking all-atom simulations using hydrogen exchange
by John J. Skinner and Wookyung Yu and Elizabeth K. Gichana and Michael C. Baxa and James R. Hinshaw and Karl F. Freed and Tobin R. Sosnick and Univ. of Chicago, IL (United States)
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 11/2014, Volume 111, Issue 45, pp. 15975 - 15980
Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO,... 
Protons | Hydrogen | Protein folding | Ubiquitins | Force field | Molecular dynamics | Amides | Trajectories | Kinetics | Free energy | HX | Denatured states | Unfolded state | DENATURANT | MULTIDISCIPLINARY SCIENCES | denatured states | BOND FORMATION | FRET SPECTROSCOPY | molecular dynamics | FAST-FOLDING PROTEINS | EXCITED-STATES | UNFOLDED-STATE | unfolded state | RIBONUCLEASE-A | MODELS | LAMBDA-REPRESSOR | protein folding | MOLECULAR-DYNAMICS SIMULATIONS | Protein Structure, Tertiary | Deuterium Exchange Measurement | GTP-Binding Proteins - chemistry | Hydrogen Bonding | Protein Unfolding | Recombinant Proteins - chemistry | Hydrogen - chemistry | Physiological aspects | Protein research | Research | G proteins | ATOMIC AND MOLECULAR PHYSICS | Biological Sciences
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4. Full Text Hydrogen exchange methods to study protein folding
by Krishna, Mallela M.G and Hoang, Linh and Lin, Yan and Englander, S.Walter
Methods, ISSN 1046-2023, 2004, Volume 34, Issue 1, pp. 51 - 64
The measurement of amino acid-resolved hydrogen exchange (HX) has provided the most detailed information so far available on the structure and properties of... 
Cytochrome c | Foldon | Theory | Protein folding | Protein function | Native state hydrogen exchange | Hydrogen exchange | Pulse labeling | EX1 | hydrogen exchange | MECHANISM | LANDSCAPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | native state hydrogen exchange | protein function | pulse labeling | PROTONS | cytochrorne c | CYTOCHROME-C | NMR | RIBONUCLEASE-A | PATHWAY | KINETICS | DYNAMICS | INTERMEDIATE | protein folding | foldon | theory | Deuterium Exchange Measurement | Animals | Protein Structure, Secondary | Time Factors | Nuclear Magnetic Resonance, Biomolecular | Cytochrome c Group - chemistry | Hydrogen - chemistry | Protein Folding | Hydrogen-Ion Concentration
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5. Full Text Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry
by Wenbing Hu and Benjamin T. Walters and Zhong-Yuan Kan and Leland Mayne and Laura E. Rosen and Susan Marqusee and S. Walter Englander
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 5/2013, Volume 110, Issue 19, pp. 7684 - 7689
The kinetic folding of ribonuclease H was studied by hydrogen exchange (HX) pulse labeling with analysis by an advanced fragment separation mass spectrometry... 
Proteins | Molecules | Structural members | Protein folding | Hydrogen | Amides | Amino acids | Mass spectroscopy | Biochemistry | Kinetics | MOLTEN GLOBULE | OPTIONAL ERRORS | COLI RIBONUCLEASE-H | RESIDUAL STRUCTURE | MULTIDISCIPLINARY SCIENCES | UNFOLDED PROTEINS | INTERMEDIATE STATE | ATOMIC-RESOLUTION | ENERGY LANDSCAPE | NATIVE-STATE | RELAXATION DISPERSION | Escherichia coli - enzymology | Peptides - chemistry | Protein Denaturation | Ribonuclease H - chemistry | Amino Acids - chemistry | Software | Biophysics - methods | Hydrogen - chemistry | Mass Spectrometry - methods | Protein Folding | Hydrogen-Ion Concentration | Physiological aspects | Research | Health aspects | Mass spectrometry | Methods | Biological Sciences
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6. Full Text Symmetry and the geometric phase in ultracold hydrogen-exchange reactions
by Croft, J. F. E and Hazra, J and Balakrishnan, N and Kendrick, B. K and Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
The Journal of Chemical Physics, ISSN 0021-9606, 08/2017, Volume 147, Issue 7, p. 074302
Quantum reactive scattering calculations are reported for the ultracold hydrogen-exchange reaction and its non-reactive atom-exchange isotopic counterparts,... 
CHEMISTRY | DYNAMICS | CHEMISTRY, PHYSICAL | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | MOLECULES | Exchanging | Organic chemistry | Equivalence | Chemical reactions | Rotational states | Wave functions | Nuclear reactions | Symmetry | Physics - Chemical Physics | INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY | Berry phase | molecular collisions | Atomic and Nuclear Physics | Inorganic and Physical Chemistry | geometric phase | ultracold chemistry
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7. Full Text Measuring hydrogen exchange rates in invisible protein excited states
by Dong Long and Guillaume Bouvignies and Lewis E. Kay
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 6/2014, Volume 111, Issue 24, pp. 8820 - 8825
Hydrogen exchange rates have become a valuable probe for studying the relationship between dynamics and structure and for dissecting the mechanism by which... 
Proteins | Protons | Exchange rates | Chemical equilibrium | Solvents | Magnetization | Hydrogen | Protein folding | Amides | Nuclear magnetic resonance | Conformationally excited protein states | Amide exchange with solvent | CATALYSIS | ENERGY | BIOLOGICAL MACROMOLECULES | conformationally excited protein states | NMR-SPECTROSCOPY | MULTIDISCIPLINARY SCIENCES | NUCLEAR-MAGNETIC-RESONANCE | ATOMIC-RESOLUTION | SIDE-CHAINS | DYNAMICS | amide exchange with solvent | INTERMEDIATE | protein folding | CPMG RELAXATION DISPERSION | Protein Structure, Tertiary | Solvents - chemistry | Models, Molecular | Hydrogen - chemistry | Protein Folding | src Homology Domains | Animals | Nitrogen - chemistry | Chickens | Protein Denaturation | Nuclear Magnetic Resonance, Biomolecular | Protein Binding | Proto-Oncogene Proteins c-fyn - chemistry | Software | Kinetics | Proteins - chemistry | Hydrogen-Ion Concentration | Spectra | Analysis | Life Sciences | Biological Sciences
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8. Full Text Geometric phase effects in ultracold hydrogen exchange reaction
by Hazra, Jisha and Kendrick, Brian K and Balakrishnan, N and Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, 09/2016, Volume 49, Issue 19, p. 194004
The role of the geometric phase effect on chemical reaction dynamics is explored by examining the hydrogen exchange process in the fundamental H+HD reaction.... 
geometric phase effect | ultracold chemistry | molecular collisions | quantum reaction dynamics | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CONICAL INTERSECTION | SCATTERING CALCULATIONS | COOLED COPPER TRIMER | SIMPLEST CHEMICAL-REACTION | MOLECULAR-SYSTEMS | POTENTIAL-ENERGY SURFACE | DIFFERENTIAL CROSS-SECTIONS | OPTICS | H+H-2 REACTION | COLLISION ENERGIES | STATE TRANSITION-PROBABILITIES | ATOMIC AND MOLECULAR PHYSICS | Inorganic and Physical Chemistry | CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS | Astronomy and Astrophysics
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9. Full Text Protein hydrogen exchange mechanism: Local fluctuations
by Maity, Haripada and Lim, Woon Ki and Rumbley, Jon N and Englander, S. Walter
Protein Science, ISSN 0961-8368, 01/2003, Volume 12, Issue 1, pp. 153 - 160
Experiments were done to study the dynamic structural motions that determine protein hydrogen exchange (HX) behavior. The replacement of a solvent‐exposed... 
Cytochrome c | hydrogen exchange | glycine mutations | pWT, pseudowild type | GdmCl, guanidinium chloride | HX, hydrogen exchange | local fluctuation | Cyt c, cytochrome c | Hydrogen exchange | Local fluctuation | Glycine mutations | AMIDE PROTON-EXCHANGE | STABILITY | BIOCHEMISTRY & MOLECULAR BIOLOGY | LYSOZYME | STATE | CONFORMATION | NUCLEIC-ACIDS | CYTOCHROME-C | RATES | DYNAMICS | PANCREATIC TRYPSIN-INHIBITOR | cytochrome c
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10. Full Text Monitoring Hydrogen Exchange During Protein Folding by Fast Pressure Jump NMR Spectroscopy
by Alderson, T. Reid and Charlier, Cyril and Torchia, Dennis A and Anfinrud, Philip and Bax, Ad
Journal of the American Chemical Society, ISSN 0002-7863, 08/2017, Volume 139, Issue 32, pp. 11036 - 11039
A method is introduced that permits direct observation of the rates at which backbone amide hydrogens become protected from solvent exchange after rapidly... 
BETA-HAIRPIN | RIBONUCLEASE-A | MECHANISM | PATHWAY | UBIQUITIN | DYNAMICS | STATE | DENATURATION | STAPHYLOCOCCAL NUCLEASE | CHEMISTRY, MULTIDISCIPLINARY | INSIGHTS | Ubiquitin | Nuclear magnetic resonance spectroscopy | Usage | Research | Isostatic pressing
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11. Full Text Conformer-specific characterization of nonnative protein states using hydrogen exchange and top-down mass spectrometry
by Guanbo Wang and Rinat R. Abzalimov and Cedric E. Bobst and Igor A. Kaltashov
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 12/2013, Volume 110, Issue 50, pp. 20087 - 20092
Characterization of structure and dynamics of nonnative protein states is important for understanding molecular mechanisms of processes as diverse as folding,... 
Proteins | Deuterium | Aggregation | Hydrogen | Ubiquitins | Ions | Mass spectroscopy | Amides | Biochemistry | Alcohols | Nonnative state | Protein dynamics | Conformational dynamics | Protein conformation | NMR-SPECTROSCOPY | MULTIDISCIPLINARY SCIENCES | protein dynamics | protein conformation | HYDROGEN/DEUTERIUM EXCHANGE | ESI-MS | IONS | HUMAN UBIQUITIN | nonnative state | A-STATE | conformational dynamics | ELECTRON-CAPTURE DISSOCIATION | ENERGY LANDSCAPE PERSPECTIVE | GAS-PHASE | DYNAMICS | Magnetic Resonance Spectroscopy | Ubiquitin - chemistry | Protein Conformation | Proteins - chemistry | Tandem Mass Spectrometry - methods | Deuterium Exchange Measurement - methods | Hydrogen-Ion Concentration | Research | Properties | Mass spectrometry | Methods | Protein-protein interactions | Biological Sciences
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12. Full Text Revealing unknown protein structures using computational conformational sampling guided by experimental hydrogen-exchange data
by Devaurs, Didier and Antunes, Dinler A and Kavraki, Lydia E
International Journal of Molecular Sciences, ISSN 1661-6596, 11/2018, Volume 19, Issue 11, p. 3406
Both experimental and computational methods are available to gather information about a protein's conformational space and interpret changes in protein... 
Hydrogen exchange | Protein conformational sampling | Nuclear magnetic resonance | Mass spectrometry | Protein structure | ENSEMBLE | protein conformational sampling | hydrogen exchange | BIOCHEMISTRY & MOLECULAR BIOLOGY | RESOLUTION | nuclear magnetic resonance | CHEMISTRY, MULTIDISCIPLINARY | COMPLEMENT COMPONENT C3 | INTERLEUKIN-8 | protein structure | NMR | FLUCTUATIONS | DYNAMICS | mass spectrometry | NATIVE-STATE | Models, Molecular | Protein Conformation | Deuterium Exchange Measurement | Humans | Interleukin-8 - chemistry | Complement C3b - chemistry
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13. Full Text The hydrogen exchange core and protein folding
by LI, RENHAO and WOODWARD, CLARE
PRS, ISSN 0961-8368, 8/1999, Volume 8, Issue 8, pp. 1571 - 1590
A database of hydrogen‐deuterium exchange results has been compiled for proteins for which there are published rates of out‐exchange in the native state,... 
NMR | protein folding | hydrogen exchange | slow exchange core | COLI RIBONUCLEASE HI | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSITION-STATE | SRC SH3 DOMAIN | DENATURED STATE | BETA-SHEET PROTEIN | PARTIALLY FOLDED STATE | MOLTEN GLOBULE INTERMEDIATE | PANCREATIC TRYPSIN-INHIBITOR | EGG-WHITE LYSOZYME | MOLECULAR-DYNAMICS SIMULATIONS | Deuterium - chemistry | Animals | Protein Structure, Secondary | Cattle | Hydrogen - chemistry | Protein Folding | Hydrogen exchange | Slow exchange core | Protein folding
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