Molecular replacement: the approach of the program<i>REMO</i>

Caliandro, Rocco; Carrozzini, Benedetta; Cascarano, G.; De, Liberato; Giacovazzo, Carmelo; Mazzone, A.; Siliqi, Dritan

doi:10.1107/s0021889806000331

Cited by 38 publications

(50 citation statements)

References 30 publications

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“…The solution of the structure has been obtained using molecular replacement and the program "il Milione" [24]. The structure of RIP from Phytolacca americana (PDB code 1qci) has been used as a starting model [25].…”

Section: Structure Determinationmentioning

confidence: 99%

Crystallization and Preliminary X-Ray Diffraction Analysis of PD-L4, a Ribosome Inactivating Protein from Phytolacca dioica L. leaves

Ruggiero¹,

Maro²,

Pisante³

et al. 2007

PPL

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PD-L4, a type 1 ribosome inactivating protein from Phytolacca dioica leaves, has been successfully crystallized using vapour diffusion methods and PEG 4000 as a precipitant agent. In addition, crystals of a PD-L4 mutant, which has been recently observed to have a lower polynucleotide-adenosine glycosidase activity on DNA, rRNA and poly (A) substrates, have been obtained. To gather information on PD-L4 reaction mechanism both forms have been co-crystallized with adenine, the major product of their catalytic reaction. Diffraction patterns extend to atomic resolution and crystals belong to the orthorhombic P2(1)2(1)2(1) space group, with one molecule in the asymmetric unit. Structure determination has been achieved using molecular replacement; preliminary electron density maps have clearly given evidence of adenine binding.

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Section: Structure Determinationmentioning

confidence: 99%

Crystallization and Preliminary X-Ray Diffraction Analysis of PD-L4, a Ribosome Inactivating Protein from Phytolacca dioica L. leaves

Ruggiero¹,

Maro²,

Pisante³

et al. 2007

PPL

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“…Data were collected and processed by using CrystalClear software (Rigaku). 23 The structure was solved by direct methods (SIR2008 24 ) and expanded by Fourier techniques. Refinements were performed by the full-matrix least-squares methods.…”

Section: Methodsmentioning

confidence: 99%

Trimethylsumanene: Enantioselective Synthesis, Substituent Effect on Bowl Structure, Inversion Energy, and Electron Conductivity

Higashibayashi

Tsuruoka

Soujanya

et al. 2012

Bulletin of the Chemical Society of Japan

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C 3 symmetric chiral trimethylsumanene was enantioselectively synthesized through Pd-catalyzed syn-selective cyclotrimerization of an enantiomerically pure iodonorbornenone, ring-opening/closing olefin metathesis, and oxidative aromatization where the sp 3 stereogenic center was transmitted to the bowl chirality. Chiral HPLC analysis/resolution of the derivatives were also achieved. Based on theoretical calculations, the columnar crystal packing structure of sumanene and trimethylsumanene was interpreted as due to attractive electrostatic or CH³ interaction. According to the experimental and theoretical studies, the bowl depth and inversion energy were found to increase on methylation for sumanene in contrast to corannulene. Dissimilarities of the effect of methylation on the bowl structure and inversion energy of sumanene and corannulene were ascribed to differences in steric repulsion. A double-well potential model was fitted to the bowl structureinversion energy correlation of substituted sumanenes, with a small deviation. The effects of various substituents on the sumanene structure and bowl-inversion energy were analyzed by density functional theory calculations, and it was shown that the bowl rigidity is controlled by a combination of electronic and steric effects of the substituents. The electron conductivity of trimethylsumanene was investigated by time-resolved microwave conductivity method, compared with that of sumanene.In the wake of the discovery of fullerene, the chemical and physical properties of buckybowls have attracted a great deal of interest because of their unique bowl-shaped ³-conjugated structure. 13 The science of buckybowls has grown as a result of the development of practical routes for the synthesis of compounds such as sumanene (1) 4 and corannulene (2) have also been studied. With this background knowledge, we studied five aspects of C 3 symmetric trimethylsumanene (3), as listed below. Direct Selective Synthesis of C 3 Symmetric Substituted Sumanenes. One of the major difficulties in studying the properties of sumanene (1) is that of selective synthesis of its derivatives. Because sumanene is C 3v symmetric, the selective synthesis of C 3 symmetric trisubstituted derivatives through functionalization at either methylene or benzene is difficult to achieve. Functionalization of the parent compound 1 results in mixtures of regioisomers, with the desired C 3 symmetric derivatives as minor products that are difficult to separate. 6c,6i Because of the importance of C 3 symmetric trisubstituted derivatives for studies on the physical properties of sumanene (1) and its derivatives or for further transformation into ³-conjugated derivatives, functionalized sumanenes have to be

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“…The fi rst was applied on a number of crystals (9 for HEWL, 16 for CONA) for monitoring their diffraction properties, the second on selected crystals (one from hydrogel membrane and one from reference for each protein) for assessing the results of the phasing process. Diffraction data were indexed by MOSFLM; [ 32 ] long scan data were reduced by POINTLESS and SCALA, [ 33 ] and phased by the molecular replacement (MR) program REMO [ 34 ] of the package IL MILIONE, [ 35 ] with structural models 1LYS and 3CNA for HEWL and CONA, respectively. MR solutions were refi ned without manual intervention by using ARP-WARP [ 36 ] and REFMAC [ 37 ] packages, and fi nal models were validated by using the program MOLPROBITY.…”

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confidence: 99%

Tailored Hydrogel Membranes for Efficient Protein Crystallization

Profio

Polino

Nicoletta

et al. 2013

Adv Funct Materials

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Crystallization still represents the bottleneck in the process of protein structure determination at high resolution, despite high-throughput structural genomics programs requiring optimized crystallization strategies regarding crystal quality, time, success rate, reproducibility, and used protein amount. On the other hand, the development of suitable materials for controlled heterogeneous nucleation might facilitate biomacromolecular crystallization in a variety of experimental conditions which are not conventionally fruitful. Here, the possibility to fabricate hydrogel membranes displaying controlled chemical composition and nanostructure and to use them as heterogeneous supports for biomacromolecular crystallization is demonstrated. Diverse gel morphologies are obtained by controlling phase separation kinetics during gel layer formation on membrane support. These composite materials are found to increase the effi ciency of the crystallization process so that crystals with enhanced diffraction properties are produced at lower protein concentration than conventional technique, thus affording the possibility to improve current approaches to protein crystallization and to be adapted to specifi c targets.

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Molecular replacement: the approach of the programREMO

Cited by 38 publications

References 30 publications

Crystallization and Preliminary X-Ray Diffraction Analysis of PD-L4, a Ribosome Inactivating Protein from Phytolacca dioica L. leaves

Crystallization and Preliminary X-Ray Diffraction Analysis of PD-L4, a Ribosome Inactivating Protein from Phytolacca dioica L. leaves

Trimethylsumanene: Enantioselective Synthesis, Substituent Effect on Bowl Structure, Inversion Energy, and Electron Conductivity

Tailored Hydrogel Membranes for Efficient Protein Crystallization

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