A group refinement procedure in protein crystallography using Fourier transforms

Huber, R.; Schneider, Matthias N.

doi:10.1107/s0021889885010044

Cited by 56 publications

(28 citation statements)

References 11 publications

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“…Rigid-body refinement of the rotation and translation parameters (19) led to small shifts in these values. The parameters relating the crystallographic coordinate systems of the two species and the initial orientation of the model are given in Table 1.…”

Section: Resultsmentioning

confidence: 99%

Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction.

Allen¹,

Fehér²,

Yeates³

et al. 1986

Proc. Natl. Acad. Sci. U.S.A.

347

165

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Crystals of the reaction center (RC) from RCs from purple photosynthetic bacteria contain three subunits, L, M, and H (present in a 1:1:1 stoichiometry) and a number of cofactors: four bacteriochlorophylls (BChls), two bacteriopheophytins, two quinones, QA (primary electron acceptor), and QB (secondary electron acceptor), and one nonheme iron (for reviews, see refs. 1 and 2). Although RCs from different species exhibit many similarities in structure, there are some significant structural differences.The RCs from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis that are the subject of this investigation show the following differences. In R. sphaeroides the secondary, water-soluble cytochrome is not present in purified RCs. In contrast, RCs from R. viridis contain a fourth subunit, a cytochrome, that has four heme groups associated with it. The two species contain different types of BChl: R. sphaeroides has BChl-a whereas R. viridis contains BChl-b. The primary quinone in R. sphaeroides is a ubiquinone, whereas in R. viridis it is a menaquinone. Furthermore, the two quinones that serve as acceptors are retained in purified RCs from R. sphaeroides, but one is apparently lost from R. viridis during the purification.Although extensive work has been done during the past two decades to characterize RCs, until recently there was very little information available on their three-dimensional structure. The reason was the lack of crystals suitable for x-ray diffraction studies. This situation changed with the successful crystallization of RCs from R. viridis (3) and R. sphaeroides (4, §). These crystals are of sufficient size and quality to obtain good x-ray diffraction data. The structure of the RCs from R. viridis has been reported recently at a resolution of 3 A (5, 6).In this work we describe the use of the Patterson search (molecular replacement) method (for reviews, see refs. 7 and 8) to obtain a low-resolution electron density map of the RC from R. sphaeroides and to show the homology between the structures of the RCs from the two bacterial species. A preliminary account of this work has been presented (9).EXPERIMENTAL PROCEDURES Crystallization. The RC from R. sphaeroides was crystallized by using the vapor diffusion technique. Different crystallization conditions produced a variety of forms as reported (4,10,11). The crystal form used for these structural studies was grown under the following conditions. The initial protein solution consisted of 5 mg of RC per ml, 0.36 M NaCl, 3.9%

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Section: Resultsmentioning

confidence: 99%

Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction.

Allen¹,

Fehér²,

Yeates³

et al. 1986

Proc. Natl. Acad. Sci. U.S.A.

347

165

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“…The translation function had highest peaks in all three Harker sections at consistent locations. The rotational and translational parameters were further refined with the Fourier-transform fitting program TRAREF [29].…”

Section: Methodsmentioning

confidence: 99%

Geometry of binding of the benzamidine‐ and arginine‐based inhibitors N^α‐(2‐naphthyl‐sulphonyl‐glycyl)‐dl‐p‐amidinophenylalanyl‐piperidine (NAPAP) and (2R,4R)‐4‐methyl‐1‐[N^α‐(3‐methyl‐1,2,3,4‐tetrahydro‐8‐quinolinesulphonyl)‐l‐arginyl]‐2‐piperidine carboxylic acid (MQPA) to human α‐thrombin

Bode

Turk

Stürzebecher

1990

European Journal of Biochemistry

125

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The X-ray crystal structure of the trypsin complex formed with N"-(2-naphthyl-sulphonyl-glycyl)-~~-pamidinophenylalanyl-piperidine (NAPAP) was determined with X-ray data to 0.18-nm resolution and crystallographically refined. NAPAP binds into the active site of trypsin in a quite compact form: the pamidinophenylalanine moiety of the D-stereoisomer binds into the specificity pocket; the glycyl group is hydrogen bonded with Gly216; the naphthyl group stands perpendicular to the indole moiety of Trp215; the piperidine ring is tightly packed between this naphthyl moiety and His.57; in consequence the carboxy-terminal amido bond of NAPAP is located in such a way that it is not susceptible to the active-site perfectly into the much more restricted active site of thrombin. The accommodation of the 5'-aryl moieties in the 'aryl-binding site' and of the piperidine rings in the S2 subsite of thrombin are particularly favourable. The preference of thrombin for distinctly substituted piperidine derivatives and its generally higher (compared with trypsin) affinity for benzamidine and arginine-based inhibitors can be accounted for by these thrombin inhibitor models.Thrombin, a trypsin-like serine proteinase, plays a central role in thrombosis and hemostasis. a-Thrombin converts fibrinogen into fibrin which forms part of the blood clot. It has also been implicated in platelet activation, activates other blood coagulation factors and interacts with various cells. The formation of clots in various thrombotic diseases has been attributed to the action of thrombin (see [l]). In cases of thrombotic disorder the quick supplementation with selective thrombin inhibitors (besides antithrombin 111) might offer an attractive means of therapy. Besides hirudin, an extremely potent and specific protein inhibitor from the medical leech [2 -61, various synthetic thrombin inhibitors have been foundCarrespondence to

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“…A consistent solution for a single trypsin position in the asymmetric unit of the enanthiomorphic space group P3,21 was found; these results are inconsistent with an asymmetric unit comprising a complete ternary complex (see below). The rotational and translational parameters were further refined with the Fourier-transform fitting program TRAREF (Huber and Schneider, 1985).…”

Section: Crystallographymentioning

confidence: 99%

The 0.25‐nm X‐ray structure of the Bowman‐Birk‐type inhibitor from mung bean in ternary complex with porcine trypsin

Lin

Bode

Huber

et al. 1993

European Journal of Biochemistry

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The structure of the Bowman-Birk-type inhibitor from mung bean Phuseolus uureus has been determined in ternary complex with porcine trypsin. The complex formed crystals of the trigonal space group P3,21 which diffracted to a resolution of 250 pm. Each of the two mung bean protease reactive sites is bound to trypsin according to the standard mechanism for serine proteinase inhibition. The binding loops thereby adopt the canonical conformation for the standard mechanism; however, the sub-van der Waals contact between the active-site serine O Y (195) and the P1 carbonyl carbon of both loops is significantly smaller (210 pm) than hitherto observed, with continuous electron density connecting the two atoms. The inhibitor is formed by two double-stranded antiparallel P-sheets, which are connected into a moderately twisted P-sheet by a network of hydrogen bonds involving main-chain atoms and two water molecules. All contacts with neighbors in the crystal lattice occur between trypsin molecules. This apparently gives rise to an unusual form of disorder where the complexes pack in two orientations Ta : MaMb : Tb and Tb : MbMa : Ta (Ta, Tb = trypsin, Ma = mung bean loop I, Mb = mung bean loop II), such that the asymmetric unit consists of the ternary complex in two orientations, each with half occupancy. This is nearly equivalent to an asymmetric unit which has one trypsin molecule with full occupancy and one mung bean inhibitor with half occupancy and a crystallographic twofold symmetry axis through its center. Because of the approximate twofold symmetry of the inhibitor itself, however, the electron density was interpretable for most of the inhibitor (17 residues at the termini were not resolved) and shows evidence of its double orientation.The Bowman-Birk-type inhibitors, isolated from leguminous seeds (Bowman, 1946), are quite small (60-90 residues) and are characterized (Birk et. al., 1963) by a high sulfur content and the ability to independently and simultaneously inhibit two serine proteinases, typically trypsin or chymotrypsin. The covalent structure, first determined for the soybean inhibitor (Odani and Jkenaka, 1973), showed the residue sequence to contain seven disulfide bridges and two tandem repeats, each with an active binding loop. Their physiological function is not known, although many potential roles have been suggested; anticarcinogenic effects have been observed. For reviews of Bowman-Birk inhibitors, see Ikenaka and Norioka (1986) or Birk (1985).The specificity of the Bowman-Birk inhibitors indicated that they inhibit via the standard mechanism (Laskowski and Kato, 1980), by which inhibitors with lysine or arginine at the P1 residue typically bind trypsin, and those with an aro- Read and James, 1986), show that these inhibitors mimic substrates, whereby the binding loop adopts the 'canonical conformation' at the reactive site and the adjoining residues. This conformation is common to all the standard inhibitors despite quite different folding motifs and differing stabilizing interactions between th...

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A group refinement procedure in protein crystallography using Fourier transforms

Cited by 56 publications

References 11 publications

Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction.

Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction.

The 0.25‐nm X‐ray structure of the Bowman‐Birk‐type inhibitor from mung bean in ternary complex with porcine trypsin

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