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Kovalevsky A, Fisher Z, Johnson H, Mustyakimov M, Waltman MJ, Langan P. Macromolecular neutron crystallography at the Protein Crystallography Station (PCS). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1206-12. [PMID: 21041938 PMCID: PMC2967422 DOI: 10.1107/s0907444910027198] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/08/2010] [Indexed: 11/10/2022]
Abstract
The Protein Crystallography Station (PCS) at Los Alamos Neutron Science Center is a high-performance beamline that forms the core of a capability for neutron macromolecular structure and function determination. Neutron diffraction is a powerful technique for locating H atoms and can therefore provide unique information about how biological macromolecules function and interact with each other and smaller molecules. Users of the PCS have access to neutron beam time, deuteration facilities, the expression of proteins and the synthesis of substrates with stable isotopes and also support for data reduction and structure analysis. The beamline exploits the pulsed nature of spallation neutrons and a large electronic detector in order to collect wavelength-resolved Laue patterns using all available neutrons in the white beam. The PCS user facility is described and highlights from the user program are presented.
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Affiliation(s)
- Andrey Kovalevsky
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Mueser TC, Griffith WP, Kovalevsky AY, Guo J, Seaver S, Langan P, Hanson BL. Hemoglobin redux: combining neutron and X-ray diffraction with mass spectrometry to analyse the quaternary state of oxidized hemoglobins. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1249-56. [PMID: 21041946 PMCID: PMC2967423 DOI: 10.1107/s090744491002545x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Accepted: 06/28/2010] [Indexed: 11/10/2022]
Abstract
Improvements in neutron diffraction instrumentation are affording the opportunity to re-examine the structures of vertebrate hemoglobins and to interrogate proton and solvent position changes between the different quaternary states of the protein. For hemoglobins of unknown primary sequence, structural studies of cyanomethemoglobin (CNmetHb) are being used to help to resolve sequence ambiguity in the mass spectra. These studies have also provided additional structural evidence for the involvement of oxidized hemoglobin in the process of erythrocyte senescence. X-ray crystal studies of Tibetan snow leopard CNmetHb have shown that this protein crystallizes in the B state, a structure with a more open dyad, which possibly has relevance to RBC band 3 protein binding and erythrocyte senescence. R-state equine CNmetHb crystal studies elaborate the solvent differences in the switch and hinge region compared with a human deoxyhemoglobin T-state neutron structure. Lastly, comparison of histidine protonation between the T and R state should enumerate the Bohr-effect protons.
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Affiliation(s)
- Timothy C Mueser
- Department of Chemistry, University of Toledo, Toledo, OH 43606, USA.
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Kovalevsky A, Chatake T, Shibayama N, Park SY, Ishikawa T, Mustyakimov M, Fisher SZ, Langan P, Morimoto Y. Protonation states of histidine and other key residues in deoxy normal human adult hemoglobin by neutron protein crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1144-52. [PMID: 21041929 PMCID: PMC2967419 DOI: 10.1107/s0907444910025448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 06/28/2010] [Indexed: 11/10/2022]
Abstract
The protonation states of the histidine residues key to the function of deoxy (T-state) human hemoglobin have been investigated using neutron protein crystallography. These residues can reversibly bind protons, thereby regulating the oxygen affinity of hemoglobin. By examining the OMIT F(o)-F(c) and 2F(o)-F(c) neutron scattering maps, the protonation states of 35 of the 38 His residues were directly determined. The remaining three residues were found to be disordered. Surprisingly, seven pairs of His residues from equivalent α or β chains, αHis20, αHis50, αHis58, αHis89, βHis63, βHis143 and βHis146, have different protonation states. The protonation of distal His residues in the α(1)β(1) heterodimer and the protonation of αHis103 in both subunits demonstrates that these residues may participate in buffering hydrogen ions and may influence the oxygen binding. The observed protonation states of His residues are compared with their ΔpK(a) between the deoxy and oxy states. Examination of inter-subunit interfaces provided evidence for interactions that are essential for the stability of the deoxy tertiary structure.
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Affiliation(s)
- Andrey Kovalevsky
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Kovalevsky AY, Fisher SZ, Seaver S, Mustyakimov M, Sukumar N, Langan P, Mueser TC, Hanson BL. Preliminary neutron and X-ray crystallographic studies of equine cyanomethemoglobin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:474-7. [PMID: 20383026 PMCID: PMC2852348 DOI: 10.1107/s1744309110007840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 03/01/2010] [Indexed: 11/10/2022]
Abstract
Room-temperature and 100 K X-ray and room-temperature neutron diffraction data have been measured from equine cyanomethemoglobin to 1.7 A resolution using a home source, to 1.6 A resolution on NE-CAT at the Advanced Photon Source and to 2.0 A resolution on the PCS at Los Alamos Neutron Science Center, respectively. The cyanomethemoglobin is in the R state and preliminary room-temperature electron and neutron scattering density maps clearly show the protonation states of potential Bohr groups. Interestingly, a water molecule that is in the vicinity of the heme group and coordinated to the distal histidine appears to be expelled from this site in the low-temperature structure.
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Affiliation(s)
- A. Y. Kovalevsky
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - S. Zoe Fisher
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Sean Seaver
- Department of Chemistry, University of Toledo, Toledo, OH 43606, USA
| | - Marat Mustyakimov
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Paul Langan
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Department of Chemistry, University of Toledo, Toledo, OH 43606, USA
| | - Timothy C. Mueser
- Department of Chemistry, University of Toledo, Toledo, OH 43606, USA
| | - B. Leif Hanson
- Department of Chemistry, University of Toledo, Toledo, OH 43606, USA
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Kovalevsky AY, Chatake T, Shibayama N, Park SY, Ishikawa T, Mustyakimov M, Fisher Z, Langan P, Morimoto Y. Direct determination of protonation states of histidine residues in a 2 A neutron structure of deoxy-human normal adult hemoglobin and implications for the Bohr effect. J Mol Biol 2010; 398:276-91. [PMID: 20230836 DOI: 10.1016/j.jmb.2010.03.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 03/06/2010] [Accepted: 03/09/2010] [Indexed: 11/26/2022]
Abstract
We have investigated the protonation states of histidine residues (potential Bohr groups) in the deoxy form (T state) of human hemoglobin by direct determination of hydrogen (deuterium) positions with the neutron protein crystallography technique. The reversible binding of protons is key to the allosteric regulation of human hemoglobin. The protonation states of 35 of the 38 His residues were directly determined from neutron scattering omit maps, with 3 of the remaining residues being disordered. Protonation states of 5 equivalent His residues--alpha His20, alpha His50, alpha His89, beta His143, and beta His146--differ between the symmetry-related globin subunits. The distal His residues, alpha His58 and beta His63, are protonated in the alpha 1 beta 1 heterodimer and are neutral in alpha 2 beta 2. Buried residue alpha His103 is found to be protonated in both subunits. These distal and buried residues have the potential to act as Bohr groups. The observed protonation states of His residues are compared to changes in their pK(a) values during the transition from the T to the R state and the results provide some new insights into our understanding of the molecular mechanism of the Bohr effect.
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Affiliation(s)
- Andrey Y Kovalevsky
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Novak WRP, Moulin AG, Blakeley MP, Schlichting I, Petsko GA, Ringe D. A preliminary neutron diffraction study of gamma-chymotrypsin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:317-20. [PMID: 19255494 PMCID: PMC2650460 DOI: 10.1107/s1744309109006630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Accepted: 02/23/2009] [Indexed: 05/27/2023]
Abstract
The crystal preparation and preliminary neutron diffraction analysis of gamma-chymotrypsin are presented. Large hydrogenated crystals of gamma-chymotrypsin were exchanged into deuterated buffer via vapor diffusion in a capillary and neutron Laue diffraction data were collected from the resulting crystal to 2.0 A resolution on the LADI-III diffractometer at the Institut Laue-Langevin (ILL) at room temperature. The neutron structure of a well studied protein such as gamma-chymotrypsin, which is also amenable to ultrahigh-resolution X-ray crystallography, represents the first step in developing a model system for the study of H atoms in protein crystals.
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Affiliation(s)
- Walter R. P. Novak
- Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | - Aaron G. Moulin
- Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | | | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gregory A. Petsko
- Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | - Dagmar Ringe
- Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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Blakeley MP, Langan P, Niimura N, Podjarny A. Neutron crystallography: opportunities, challenges, and limitations. Curr Opin Struct Biol 2008; 18:593-600. [PMID: 18656544 DOI: 10.1016/j.sbi.2008.06.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 06/26/2008] [Indexed: 10/21/2022]
Abstract
Neutron crystallography has had an important, but relatively small role in structural biology over the years. In this review of recently determined neutron structures, a theme emerges of a field currently expanding beyond its traditional boundaries, to address larger and more complex problems, with smaller samples and shorter data collection times, and employing more sophisticated structure determination and refinement methods. The origin of this transformation can be found in a number of advances including first, the development of neutron image-plates and quasi-Laue methods at nuclear reactor neutron sources and the development of time-of-flight Laue methods and electronic detectors at spallation neutron sources; second, new facilities and methods for sample perdeuteration and crystallization; third, new approaches and computational tools for structure determination.
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Langan P, Fisher Z, Kovalevsky A, Mustyakimov M, Sutcliffe Valone A, Unkefer C, Waltman MJ, Coates L, Adams PD, Afonine PV, Bennett B, Dealwis C, Schoenborn BP. Protein structures by spallation neutron crystallography. JOURNAL OF SYNCHROTRON RADIATION 2008; 15:215-218. [PMID: 18421142 PMCID: PMC2394804 DOI: 10.1107/s0909049508000824] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 01/11/2008] [Indexed: 05/26/2023]
Abstract
The Protein Crystallography Station at Los Alamos Neutron Science Center is a high-performance beamline that forms the core of a capability for neutron macromolecular structure and function determination. This capability also includes the Macromolecular Neutron Crystallography (MNC) consortium between Los Alamos (LANL) and Lawrence Berkeley National Laboratories for developing computational tools for neutron protein crystallography, a biological deuteration laboratory, the National Stable Isotope Production Facility, and an MNC drug design consortium between LANL and Case Western Reserve University.
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Affiliation(s)
- Paul Langan
- Bioscience Division, Los Alamos National Laboratory, NM 87545, USA.
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