Principles of Protein X-ray Crystallography

Drenth, Jan

doi:10.1007/978-1-4757-2335-9

Cited by 401 publications

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“…1 Because the wavelength of visible or infrared light is much longer than usual molecular sizes, the techniques do not capture every structural detail and provide a lower resolution than the X-ray crystallography. 2 However, an increased conformational and enantiomer sensitivity can be achieved with some polarized methods, particularly with those using different absorption or scattering of circularly polarized light on optically active (chiral) systems. Thus the optical rotatory dispersion (ORD) or circular dichroism (CD) became standard analytical tools in chemistry and molecular biology.…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics with restrictions derived from optical spectra

2008

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The information about molecular structure coded in the optical spectra must often be deciphered by complicated computational procedures. A combination of spectral modeling with the molecular dynamic simulations makes the process simpler, by implicit accounting for the inhomogeneous band broadening and Boltzmann averaging of many conformations. Ideally, geometries of studied systems can be deduced by a direct confrontation of such modeling with the experiment. In this work, the comparison is enhanced by restrictions to molecular dynamics propagations based on the Raman and Raman optical activity spectra. The methodology is introduced and tested on model systems comprising idealized H 2 O 2 , H 2 O 3 molecules, and the alanine zwitterion. An additional gradient term based on the spectral overlap smoothed by Fourier transformation is constructed and added to the molecular energy during the molecular dynamics run. For systems with one prevalent conformation the method did allow to enrich the Boltzmann ensemble by a spectroscopically favored structure. For systems with multiconformational equilibria families preferential conformations can be selected. An alternative algorithm based on the comparison of the averaged spectra with the reference enabling iterative updates of the conformer probabilities provided even more distinct distributions in shorter times. It also accounts for multiconformer equilibria and provided realistic spectra and conformer distribution for the alanine.

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Section: Introductionmentioning

confidence: 99%

Molecular dynamics with restrictions derived from optical spectra

2008

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“…Unlike crystals of small molecules, macromolecular crystals have an open structure with an interconnected network of large channels ®lled with a solution in equilibrium with the mother solution from which the crystal grew (Drenth, 1994). Some of these solvent molecules are bound to the macromolecule and contribute to stabilize the crystal building, but others are actually part of the bulk solution.…”

Section: Introductionmentioning

confidence: 99%

Soaking: the effect of osmotic shock on tetragonal lysozyme crystals

Lopéz-Jaramillo

Moraleda

González-Ramírez

et al. 2002

Acta Crystallogr D Biol Crystallogr

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Protein crystals crack when they are soaked in a solution with ionic strength suf®ciently different from the environment in which they grew. It is demonstrated for the case of tetragonal lysozyme that the forces involved and the mechanisms that lead to the formation of cracks are different for hypertonic and hypotonic soaking. Tetragonal lysozyme crystals are very sensitive to hypotonic shocks and, after a certain waiting time, cracks always appear with a characteristic pattern perpendicular to the crystallographic c axis. Conversely, a hypertonic shock is better withstood: cracks do not display any deterministic pattern, are only visible at higher differences in ionic strength and after a certain time a phenomenon of crystal reconstruction occurs and the cracks vanish. At the lattice level, the unit-cell volume expands in hypotonic shock and shrinks under hypertonic conditions. However, the compression of the unit cell is anisotropic: the c axis is compressed to a minimum, beyond which it expands despite the unit-cell volume continuing to shrink. This behaviour is a direct consequence of the positive charge that the crystals bear and the existence of channels along the crystallographic c axis. Both features are responsible for the Gibbs±Donnan effect which limits the free exchange of ions and affects the movement of water inside the channels and bound to the protein.

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“…Therefore, to solve the phase problem, a MAD experiment was conducted using a Á 1 -KSTD1 crystal soaked in a solution containing Na 2 PtCl 4 . Since the crystal initially grew from a solution containing ammonium sulfate, which may compete with the protein to bind the platinum ions (Drenth, 2007), the ammonium sulfate was removed from the crystal by washing and soaking the crystal in 0.4 M NaH 2 PO 4 /1.6 M K 2 HPO 4 . This latter condition was inspired by another successful crystallization condition for Á 1 -KSTD1 (Fig.…”

Section: Resultsmentioning

confidence: 99%

Purification, crystallization and preliminary X-ray crystallographic analysis of 3-ketosteroid Δ¹-dehydrogenase fromRhodococcus erythropolisSQ1

Rohman

Oosterwijk

Dijkstra

2012

Acta Crystallogr F Struct Biol Cryst Commun

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3-Ketosteroid Á 1 -dehydrogenase plays a crucial role in the early steps of steroid degradation by introducing a double bond between the C1 and C2 atoms of the A-ring of its 3-ketosteroid substrates. The 3-ketosteroid Á 1 -dehydrogenase from Rhodococcus erythropolis SQ1, a 56 kDa flavoprotein, was crystallized using the sitting-drop vapour-diffusion method at room temperature. The crystals grew in various buffers over a wide pH range (from pH 5.5 to 10.5), but the best crystallization condition consisted of 2%(v/v) PEG 400, 0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate. A native crystal diffracted X-rays to 2.0 Å resolution. It belonged to the primitive orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 107.4, b = 131.6, c = 363.2 Å , and contained eight molecules in the asymmetric unit. The initial structure of the enzyme was solved using multiwavelength anomalous dispersion (MAD) data collected from a Pt-derivatized crystal.

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Principles of Protein X-ray Crystallography

Cited by 401 publications

References 0 publications

Molecular dynamics with restrictions derived from optical spectra

Molecular dynamics with restrictions derived from optical spectra

Soaking: the effect of osmotic shock on tetragonal lysozyme crystals

Purification, crystallization and preliminary X-ray crystallographic analysis of 3-ketosteroid Δ¹-dehydrogenase fromRhodococcus erythropolisSQ1

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Principles of Protein X-ray Crystallography

Cited by 401 publications

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Molecular dynamics with restrictions derived from optical spectra

Molecular dynamics with restrictions derived from optical spectra

Soaking: the effect of osmotic shock on tetragonal lysozyme crystals

Purification, crystallization and preliminary X-ray crystallographic analysis of 3-ketosteroid Δ1-dehydrogenase fromRhodococcus erythropolisSQ1

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Purification, crystallization and preliminary X-ray crystallographic analysis of 3-ketosteroid Δ¹-dehydrogenase fromRhodococcus erythropolisSQ1