Acta Crystallographica Section D

Biological Crystallography

Volume 66, Part 11 (November 2010)


Neutrons in biology

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[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: (Fcalc, [varphi]calc) Fourier syntheses computed at different resolutions (top to bottom: 1, 1.5, 2 and 2.5 Å) and corresponding to four different cases (left to right): X-ray, neutron fully deuterated, neutron fully hydrogenated and neutron partially deuterated, in which the hydroxyl H (HH) of tyrosine shares its site with deuterium (DH) with an occupancy ratio of 0.6:0.4 (p. 1153).

editorial


 

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Acta Cryst. (2010). D66, 1121-1123  [ doi:10.1107/S0907444910039387 ]

Opportunities and challenges with the growth of neutron crystallography

P. Adams and P. Langan

Synopsis: A summary of the current state of neutron crystallography is given.

Online 20 October 2010


introduction


 

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Acta Cryst. (2010). D66, 1124-1125  [ doi:10.1107/S0907444910017646 ]

International Conference on Neutrons in Biology

R. Knott

Synopsis: A summary of the International Conference on Neutrons in Biology is presented.

Online 20 October 2010


research papers


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Acta Cryst. (2010). D66, 1126-1130  [ doi:10.1107/S0907444910034967 ]

Towards investigation of the inhibitor-recognition mechanisms of drug-target proteins by neutron crystallography

R. Kuroki, N. Okazaki, M. Adachi, T. Ohhara, K. Kurihara and T. Tamada

Synopsis: The crystal structures of drug-target proteins, such as human immunodeficiency virus protease and pancreatic elastase, in complex with transition-state analogue inhibitors have been determined by neutron diffraction.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1131-1138  [ doi:10.1107/S0907444910034013 ]

Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase)

J.C.-H. Chen, M. Mustyakimov, B. P. Schoenborn, P. Langan and M.-M. Blum

Synopsis: The structure and mechanism of diisopropyl fluorophosphatase (DFPase) have been studied using a variety of methods, including isotopic labelling, X-ray crystallography and neutron crystallography. The neutron structure of DFPase, mechanistic studies and subsequent rational design efforts are described.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1139-1143  [ doi:10.1107/S0907444910019785 ]

Sweet neutron crystallography

S. C. M. Teixeira, M. P. Blakeley, R. M. F. Leal, S. M. Gillespie, E. P. Mitchell and V. T. Forsyth

Synopsis: Neutron crystallography can make an important contribution to our understanding of the structural basis of sweetness, as illustrated by results on studies of the sweet protein thaumatin.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1144-1152  [ doi:10.1107/S0907444910025448 ]

Protonation states of histidine and other key residues in deoxy normal human adult hemoglobin by neutron protein crystallography

A. Kovalevsky, T. Chatake, N. Shibayama, S.-Y. Park, T. Ishikawa, M. Mustyakimov, S. Z. Fisher, P. Langan and Y. Morimoto

Synopsis: Using neutron diffraction analysis, the protonation states of 35 of 38 histidine residues were determined for the deoxy form of normal human adult hemoglobin. Distal and buried histidines may contribute to the increased affinity of the deoxy state for hydrogen ions and its decreased affinity for oxygen compared with the oxygenated form.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1153-1163  [ doi:10.1107/S0907444910026582 ]

Joint X-ray and neutron refinement with phenix.refine

P. V. Afonine, M. Mustyakimov, R. W. Grosse-Kunstleve, N. W. Moriarty, P. Langan and P. D. Adams

Synopsis: The implementation of crystallographic structure-refinement procedures that include both X-ray and neutron data (separate or jointly) in the PHENIX system is described.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1164-1171  [ doi:10.1107/S0907444910026107 ]

New computational tools for H/D determination in macromolecular structures from neutron data

D. Siliqi, R. Caliandro, B. Carrozzini, G. L. Cascarano and A. Mazzone

Synopsis: Two new computational tools have been developed for H/D determination in macromolecular structures from neutron data.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1172-1177  [ doi:10.1107/S0907444910032397 ]

Looking at hydrogen bonds in cellulose

Y. Nishiyama, P. Langan, M. Wada and V. T. Forsyth

Synopsis: A series of cellulose crystal allomorphs have been studied using high-resolution X-ray and neutron fibre diffraction to locate the positions of H atoms involved in hydrogen bonding.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1178-1183  [ doi:10.1107/S0907444910019700 ]

Enzymes for carbon sequestration: neutron crystallographic studies of carbonic anhydrase

S. Z. Fisher, A. Y. Kovalevsky, J. Domsic, M. Mustyakimov, D. N. Silverman, R. McKenna and P. Langan

Synopsis: The first neutron crystal structure of carbonic anhydrase is presented. The structure reveals interesting and unexpected features of the active site that affect catalysis.

Online 20 October 2010


 

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Acta Cryst. (2010). D66, 1184-1188  [ doi:10.1107/S0907444910029483 ]

In silico studies of crystalline cellulose and its degradation by enzymes

G. Bellesia, A. Asztalos, T. Shen, P. Langan, A. Redondo and S. Gnanakaran

Synopsis: The current state of in silico studies on cellulose is reviewed and commented on.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1189-1193  [ doi:10.1107/S0907444910020408 ]

SANS study of cellulose extracted from switchgrass

S. V. Pingali, V. S. Urban, W. T. Heller, J. McGaughey, H. M. O'Neill, M. Foston, D. A. Myles, A. J. Ragauskas and B. R. Evans

Synopsis: The multi-scale structures of cellulose extracted from native and dilute acid pretreated switchgrass, as well as that of microcrystalline cellulose (Avicel), were investigated using SANS.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1194-1197  [ doi:10.1107/S0907444910033020 ]

Neutron structure analysis using the IBARAKI biological crystal diffractometer (iBIX) at J-PARC

I. Tanaka, K. Kusaka, T. Hosoya, N. Niimura, T. Ohhara, K. Kurihara, T. Yamada, Y. Ohnishi, K. Tomoyori and T. Yokoyama

Synopsis: A new diffractometer (iBIX) at the next-generation neutron source at J-PARC has begun operation for protein crystallography. Preliminary structure analyses of organic crystals demonstrate that iBIX has high performance even at 120 kW operation.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1198-1205  [ doi:10.1107/S0907444910019797 ]

Neutron macromolecular crystallography with LADI-III

M. P. Blakeley, S. C. M. Teixeira, I. Petit-Haertlein, I. Hazemann, A. Mitschler, M. Haertlein, E. Howard and A. D. Podjarny

Synopsis: The LADI-III instrument for measuring neutron macromolecular crystallography diffraction data is described. The data collection of type-III perdeuterated antifreeze protein is given as an example.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1206-1212  [ doi:10.1107/S0907444910027198 ]

Macromolecular neutron crystallography at the Protein Crystallography Station (PCS)

A. Kovalevsky, Z. Fisher, H. Johnson, M. Mustyakimov, M. J. Waltman and P. Langan

Synopsis: The Protein Crystallography Station user facility at Los Alamos National Laboratory not only offers open access to a high-performance neutron beamline, but also actively supports and develops new methods in protein expression, deuteration, purification, robotic crystallization and the synthesis of substrates with stable isotopes and provides assistance with data-reduction and structure-refinement software and comprehensive neutron structure analysis.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1213-1217  [ doi:10.1107/S0907444910017658 ]

Small-angle neutron scattering and contrast variation: a powerful combination for studying biological structures

W. T. Heller

Synopsis: Small-angle neutron scattering with contrast variation is a powerful tool for probing complex biological macromolecular complexes.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1218-1223  [ doi:10.1107/S0907444910021323 ]

Decoration of microtubules in solution by the kinesin-14, Ncd

R. P. Hjelm, D. Bennett Stone, R. J. Fletterick and R. A. Mendelson

Synopsis: The binding of microtubules by the molecular motor Ncd in solution was investigated using small-angle neutron scattering. In the presence of an ATP analogue one of the two Ncd motor heads is cooperatively bound to a tubulin dimer.

Online 20 October 2010


 

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Acta Cryst. (2010). D66, 1224-1228  [ doi:10.1107/S0907444910021086 ]

The case for an empirical 'high-throughput' neutron scattering approach to protein dynamics

G. Zaccai

Synopsis: This article is a plea to neutron scatterers studying protein dynamics to move on from measuring a few model systems and arguing about the physics in order to address the diversity and specificity of proteins and provide much-needed data for the understanding of the essential role of dynamics in biological function and activity.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1229-1231  [ doi:10.1107/S0907444910022985 ]

Neutron scattering and protein dynamics

H. Frauenfelder and F. Mezei

Synopsis: Neutron scattering experiments with myoglobin over extended time and temperature ranges provide insight into protein dynamics.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1232-1236  [ doi:10.1107/S0907444910037856 ]

A neutron diffraction study of purple membranes under pressure

I. G. Rossand, G. Zaccai and G. Fragneto

Synopsis: Neutron diffraction from hydrated stacks of natural two-dimensional crystal patches of purple membrane from Halobacterium salinarum was studied as a function of pressure.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1237-1243  [ doi:10.1107/S090744491001766X ]

Investigations of surrogate cellular membranes using neutron reflectometry

M. Dubey, M. S. Jablin, H. Smith and J. Majewski

Synopsis: In this article, methods are presented for the creation and characterization of supported model membranes which can mimic many of the critical attributes of cell membranes. It is demonstrated that neutron reflectometry can characterize the structure, composition and organization of model membranes deposited on solid, nanoporous and polymer supports.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1244-1248  [ doi:10.1107/S0907444910017713 ]

Combined neutron and X-ray diffraction studies of DNA in crystals and solutions

R. M. F. Leal, S. Callow, P. Callow, M. P. Blakeley, C. J. Cardin, W. A. Denny, S. C. M. Teixeira, E. P. Mitchell and V. T. Forsyth

Synopsis: Neutron diffraction methods can be used to provide novel information on the structure and behaviour of nucleic acids as studied in single crystals, fibres and solutions.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1249-1256  [ doi:10.1107/S090744491002545X ]

Hemoglobin redux: combining neutron and X-ray diffraction with mass spectrometry to analyse the quaternary state of oxidized hemoglobins

T. C. Mueser, W. P. Griffith, A. Y. Kovalevsky, J. Guo, S. Seaver, P. Langan and B. L. Hanson

Synopsis: X-ray and neutron diffraction studies of cyanomethemoglobin are being used to evaluate the structural waters within the dimer-dimer interface involved in quaternary-state transitions.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1257-1261  [ doi:10.1107/S0907444910027915 ]

Using neutron protein crystallography to understand enzyme mechanisms

J. P. Glusker, H. L. Carrell, A. Y. Kovalevsky, L. Hanson, S. Z. Fisher, M. Mustyakimov, S. Mason, T. Forsyth and P. Langan

Synopsis: A description is given of the results of neutron diffraction studies of the structures of four different metal-ion complexes of deuterated D-xylose isomerase.

Online 20 October 2010


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Acta Cryst. (2010). D66, 1262-1268  [ doi:10.1107/S0907444910023140 ]

A history of neutrons in biology: the development of neutron protein crystallography at BNL and LANL

B. P. Schoenborn

Synopsis: Neutron scattering techniques provide valuable information on the structure of biological molecules and molecular systems, and hence provide insight into function.

Online 20 October 2010


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