Extension of molecular replacement: a new search strategy based on Patterson correlation refinement

Brünger, A.T.

doi:10.1107/s0108767389009633

Cited by 313 publications

(120 citation statements)

References 18 publications

Supporting

Mentioning

119

Contrasting

Order By: Relevance

“…The hydrogen bonds and salt bridges were calculated using either WHATIF (Vriend, 1990) or XPLOR (Brunger, 1990a). Accessible surfaces were calculate using modified RESAREA and SURFACE programs of the CCP4 suite (1994).…”

Section: Methodsmentioning

confidence: 99%

Crystal structure of recombinant triosephosphate isomerase from bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three‐dimensional structures points to the importance of hydrophobic interactions

et al. 1995

View full text Add to dashboard Cite

The structure of the thermostable triosephosphate isomerase (TIM) from Bacillus stearothermophilus complexed with the competitive inhibitor 2-phosphoglycolate was determined by X-ray crystallography to a resolution of 2.8 A. The structure was solved by molecular replacement using XPLOR. Twofold averaging and solvent flattening was applied to improve the quality of the map. Active sites in both the subunits are occupied by the inhibitor and the flexible loop adopts the "closed" conformation in either subunit. The crystallographic R-factor is 17.6% with good geometry. The two subunits have an RMS deviation of 0.29 A for 248 C" atoms and have average temperature factors of 18.9 and 15.9 A*, respectively. In both subunits, the active site Lys 10 adopts an unusual $,$ combination.A comparison between the six known thermophilic and mesophilic TIM structures was conducted in order to understand the higher stability of B. stearothermophilus TIM. Although the ratio Arg/(Arg+Lys) is higher in B. stearotherrnophilus TIM, the structure comparisons do not directly correlate this higher ratio to the better stability of the B. stearothermophilus enzyme. A higher number of prolines contributes to the higher stability of B. stearothermophilus TIM. Analysis of the known TIM sequences points out that the replacement of a structurally crucial asparagine by a histidine at the interface of monomers, thus avoiding the risk of deamidation and thereby introducing a negative charge at the interface, may be one of the factors for adaptability at higher temperatures in the TIM family. Analysis of buried cavities and the areas lining these cavities also contributes to the greater thermal stability of the B. stearotherrnophilus enzyme. However, the most outstanding result of the structure comparisons appears to point to the hydrophobic stabilization of dimer formation by burying the largest amount of hydrophobic surface area in B. stearothermophilus TIM compared to all five other known TIM structures.

show abstract

Section: Methodsmentioning

confidence: 99%

Crystal structure of recombinant triosephosphate isomerase from bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three‐dimensional structures points to the importance of hydrophobic interactions

et al. 1995

View full text Add to dashboard Cite

show abstract

“…A generalized molecular replacement technique implemented in XPLOR was used in this study (Brunger, 1990).…”

Section: Structure Solutionmentioning

confidence: 99%

“…In order to select and refine the correct orientations from the rotation search, a Patterson correlation (PC) coefficient refinement technique (Brunger, 1990) was used. After PC refinement of the rotation search orientations, peak 6 in the ternary hexagonal crystal form and peak 22 in the apo-cubic crystal form became the highest peaks.…”

Section: Structure Solutionmentioning

confidence: 99%

Crystal structures of the myristylated catalytic subunit of cAMP‐dependent protein kinase reveal open and closed conformations

et al. 1993

View full text Add to dashboard Cite

Three crystal structures, representing two distinct conformational states, of the mammalian catalytic subunit of CAMP-dependent protein kinase were solved using molecular replacement methods starting from the refined structure of the recombinant catalytic subunit ternary complex (Zheng, J., et al., 1993a, Biochemistry 32,2154-2161). These structures correspond to the free apoenzyme, a binary complex with an iodinated inhibitor peptide, and a ternary complex with both ATP and the unmodified inhibitor peptide. The apoenzyme and the binary complex crystallized in an open conformation, whereas the ternary complex crystallized in a closed conformation similar to the ternary complex of the recombinant enzyme. The model of the binary complex, refined at 2.9 A resolution, shows the conformational changes associated with the open conformation. These can be described by a rotation of the small lobe and a displacement of the C-terminal30 residues. This rotation of the small lobe alters the cleft interface in the active-site region surrounding the glycine-rich loop and Thr 197, a critical phosphorylation site. In addition to the conformational changes, the myristylation site, absent in the recombinant enzyme, was clearly defined in the binary complex. The myristic acid binds in a deep hydrophobic pocket formed by four segments of the protein that are widely dispersed in the linear sequence. The N-terminal40 residues that lie outside the conserved catalytic core are anchored by the N-terminal myristylate plus an amphipathic helix that spans both lobes and is capped by Trp 30. Both posttranslational modifications, phosphorylation and myristylation, contribute directly to the stable structure of this enzyme.

show abstract

“…In practice, the method is implemented as a three-dimensional rotational search followed by a three-dimensional translational search [Lat85,Ros72]. We also performed a Patterson correlation refinement preceding the translational search to filter the peaks of the rotational search [Brün90]. The preliminary results have been encouraging as demonstrated by the model's ability to probe the position of molecules in the crystal.…”

Section: Future Workmentioning

confidence: 91%

Knowledge based structure prediction of the light-harvesting complex II of rhodospirillum molischianum

Hamer

et al. 1995

Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein F

View full text Add to dashboard Cite

Abstract. We illustrate in this article how one proceeds to predict the structure of integral membrane proteins using a combined approach in which molecular dynamics simulations and energy minimization are performed based on structural information from conventional structure prediction methods and experimental constraints derived from biochemical and spectroscopical data. We focus here on the prediction of the structure of the light-harvesting complex II (LH-II) of Rhodospirillum molischianum, an integral membrane protein of 16 polypeptides aggregating and binding to 24 bacteriochlorophyll a's and 12 lycopenes. Hydropathy analysis was performed to identify the putative transmembrane segments. Multiple sequence alignment propensity analyses further pinpointed the exact sites of the 20 residue long transmembrane segment and the four residue long terminal sequence at both ends, which were independently verified and improved by homology modeling. A consensus assignment for secondary structure was derived from a combination of all the prediction methods used. The three-dimensional structures for the α-and the β-apoprotein were built by comparative modeling. The resulting tertiary structures were combined into an αβ dimer pair with bacteriochlorophyll a's attached under constraints provided by site directed mutagenesis and FT Resonance Raman spectra, as well as by conservation of residues. The αβ dimer pairs were then aggregated into a quaternary structure through molecular dynamics simulations and energy minimization. The structure of LH-II, so determined, was an octamer of αβ heterodimers forming a ring with a diameter of 70Å. We discuss how the resulting structure may be used to solve the phase problem in X-ray crystallography in a procedure called molecular replacement.

show abstract

Extension of molecular replacement: a new search strategy based on Patterson correlation refinement

Cited by 313 publications

References 18 publications

Crystal structure of recombinant triosephosphate isomerase from bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three‐dimensional structures points to the importance of hydrophobic interactions

Crystal structure of recombinant triosephosphate isomerase from bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three‐dimensional structures points to the importance of hydrophobic interactions

Crystal structures of the myristylated catalytic subunit of cAMP‐dependent protein kinase reveal open and closed conformations

Knowledge based structure prediction of the light-harvesting complex II of rhodospirillum molischianum

Contact Info

Product

Resources

About