Refinement of proteins at subatomic resolution with<i>MOPRO</i>

Guillot, Benoı̂t; Viry, L.; Guillot, Régis; Lecomte, Claude; Jelsch, Christian

doi:10.1107/s0021889801001753

Cited by 171 publications

(229 citation statements)

References 24 publications

Supporting

Mentioning

228

Contrasting

Order By: Relevance

“…Experimental Charge Density Refinement-Charge density refinement for acutohaemolysin was carried out using the program MOPRO (33), an extension of the program MOLLY (16) for biological macromolecules. This program is able to refine large structures with the use of conjugate gradient iterations, and the sparse matrix principle was applied to the least squares method.…”

Section: Methodsmentioning

confidence: 99%

The Crystal Structure of a Novel, Inactive, Lysine 49 PLA2 from Agkistrodon acutus Venom

Liu

Huang

Teng

et al. 2003

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

The crystal structure of acutohaemolysin, a lysine 49 phospholipase A2 protein with 1010 non-hydrogen protein atoms and 232 water molecules, has been determined ab initio using the program SnB at an ultrahigh resolution of 0.8 Å. The lack of catalytic activity appears to be related to the presence of Phe 102 , which prevents the access of substrate to the active site. The substitution of tryptophan for leucine at residue 10 interferes with dimer formation and may be responsible for the additional loss of hemolytic activity. The ultrahigh resolution of the experimental diffraction data permits alternative conformations to be modeled for disordered residues, many hydrogen atoms to be located, the protonation of the N⑀2 atom in the catalytic residue His 48 to be observed experimentally, and the density of the bonding electrons to be analyzed in detail.

show abstract

Section: Methodsmentioning

confidence: 99%

The Crystal Structure of a Novel, Inactive, Lysine 49 PLA2 from Agkistrodon acutus Venom

Liu

Huang

Teng

et al. 2003

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…The distance from each atom of the bond to the critical point yields the atomic covalent radii (Bouhmaida et al, 2002;Novaković et al, 2007). Finally, the electrostatic interaction energy between molecules was estimated by the method developed in MOPRO and VMOPRO computer programs (Guillot et al, 2001;Jelsch et al, 2005).…”

Section: Electrostatic Potential Field and Interaction Energymentioning

confidence: 99%

Charge density and electrostatic potential analyses in paracetamol

Bouhmaida

Bonhomme

Guillot

et al. 2009

Acta Crystallogr Sect B

Self Cite

View full text Add to dashboard Cite

The electron density of monoclinic paracetamol was derived from high-resolution X-ray diffraction at 100 K. The HansenCoppens multipole model was used to refine the experimental electron density. The topologies of the electron density and the electrostatic potential were carefully analyzed. Numerical and analytical procedures were used to derive the charges integrated over the atomic basins. The highest charge magnitude (À1.2 e) was found for the N atom of the paracetamol molecule, which is in agreement with the observed nucleophilic attack occurring in the biological media. The electric field generated by the paracetamol molecule was used to calculate the atomic charges using the divergence theorem. This was simultaneously applied to estimate the total electrostatic force exerted on each atom of the molecule by using the Maxwell stress tensor. The interaction electrostatic energy of dimers of paracetamol in the crystal lattice was also estimated.

show abstract

“…[45] The multipolar 1(r) model was expanded up to the dipolar order (l = 1) for the H atoms and up to the octupolar order (l = 3) for the C and N atoms, applying the corresponding geometrical constrains using the pro-gram MOPRO. [35,36,46] Optimization of the used restrains based on free R factors [47] was performed. CCDC 1062475 and 1062476 contain the supplementary crystallographic data for this paper.…”

Section: Methodsmentioning

confidence: 99%

“…[35,36,46] Optimization of the used restrains based on free R factors [47] was performed. CCDC 1062475 and 1062476 contain the supplementary crystallographic data for this paper.…”

Section: Methodsmentioning

confidence: 99%

“…For one of them, we obtained high-quality experimental data that allowed reliable results on the experimental electron density to be derived. Atomic multipolar expansions [35,36] were used to reconstruct the experimental electron density 1(r) of 1A in the solid state. Dipole, quadrupole, and octupole moments were the most relevant terms to recover the experimental anisotropic 1(r) features of the crystal structure of 1 A.…”

Section: Figure2mentioning

confidence: 99%

See 1 more Smart Citation

Nature of Noncovalent Carbon‐Bonding Interactions Derived from Experimental Charge‐Density Analysis

2015

View full text Add to dashboard Cite

In an effort to better understand the nature of noncovalent carbon-bonding interactions, we undertook accurate high-res-olution X-ray diffraction analysis of single crystals of 1,1,2,2-tetracyanocyclopropane. We selected this compound to study the fundamental characteristics of carbon-bonding interactions, because it provides accessible s holes. The study required extremely accurate experimental diffraction data, because the in-teraction of interest is weak. The electron-density distribution around the carbon nuclei, as shown by the experimental maps of the electrophilic bowl defined by a (CN)2C-C(CN)2 unit, was assigned as the origin of the interaction. This fact was also evidenced by plotting the D21(r) distribution. Taken together, the obtained results clearly indicate that noncovalent carbon bonding can be explained as an interaction between confront-ed oppositely polarized regions. The interaction is, thus elec-trophilic-nucleophilic (electrostatic) in nature and unambigu-ously considered as attractive.Attractive intermolecular electrostatic interactions encompass electron-rich and electron-poor regions of two molecules that complement each other.[1] Electron-rich entities are typically anions or lone-pair electrons and the most well-known elec-tron-poor entity is the hydrogen atom. Consequently, hydro-gen bonding is undoubtedly the most exploited supramolec-ular interaction.[2] Nowadays, another common electron-poor entity is attracting increasing attention in the literature. It is the 's hole', which can be defined as an electron-deficient anti-bonding orbital of a covalent bond. [3-13] Such regions of posi-tive electrostatic potential have been largely studied for atoms of groups V, VI, and VII (pnicogen, [14,15] chalcogen, [16][17][18] and hal-ogen [19-22] bonding, respectively [23] ) . Many reviews have described halogen bonding in detail, which is the best-known s-hole interaction. [6,[19][20][21][22] More recently, s-hole complexes with atoms of group IV, the tetrel (Tr) atoms, have been described, [24][25][26][27][28][29] and mostly focus on the heavier Tr atoms as tetrel-bond donors, leaving noncovalent carbon bonding much less studied. [30][31][32] In an sp 3 -hybridized electron-deficient C atom, there is only limited space available for an electron-rich guest molecule to nest itself. [31,32] To exem-plify this, we have represented in Figure 1 (right) the MEP sur- Figure 1.face of 1,1,2,2-tetracyanoethane (staggered conformation). The s hole is small and it is surrounded by negative belts, which hinder interactions with any concentration of negative charge (lone pair or anion). However, if the MEP surface is computed in the eclipsed conformation (C2v), the resulting s hole is more exposed and the electrostatic potential is considerable more positive. As a matter of fact, it has been recently demonstrated that the (CN) 2 C-C(CN) 2 motif of 1,1,2,2-tetracyanocyclopropane is an excellent carbon-bond donor, because the s hole is very exposed.[33] Moreover, it is synthetically accessible and the N_ C...

show abstract

Refinement of proteins at subatomic resolution withMOPRO

Cited by 171 publications

References 24 publications

The Crystal Structure of a Novel, Inactive, Lysine 49 PLA2 from Agkistrodon acutus Venom

The Crystal Structure of a Novel, Inactive, Lysine 49 PLA2 from Agkistrodon acutus Venom

Charge density and electrostatic potential analyses in paracetamol

Nature of Noncovalent Carbon‐Bonding Interactions Derived from Experimental Charge‐Density Analysis

Contact Info

Product

Resources

About