Application of the periodic bond chain (PBC) theory to the analysis of the molecular packing in protein crystals

Frey, Michel; Génovésio-Taverne, Jean-Claude

doi:10.1016/0022-0248(88)90321-1

Cited by 19 publications

(7 citation statements)

References 21 publications

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“…3 with the sides of the block numbered from 1 to 6. the tetragonal space group P432~2 of the crystal and the 79.1 × 79.1 × 37.9 ~ dimensions of the unit cell (Imoto et al, 1972). Other crystal forms may dictate different representations, such as hexagonal blocks for the packing found in the monoclinic rubredoxin crystals (Frey et at., 1988(Frey et at., , 1992. The structures of the reference molecule M and the nine other molecules surrounding it were systematically searched to identify all interatomic bonds between them.…”

Section: Methods Of Analysismentioning

confidence: 99%

“…This has resulted in some simplifications in the application of PBC theory to protein crystals. In one study crystals of a bacterial rubredoxin and of two scorpion neurotoxins were analyzed (Frey, Genovesio-Taverne & Fontecilla-Camps, 1988. The number of bonds and the size of the contact area between molecules were substituted for the interaction energy between them and simple spheres were used to represent molecules.…”

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confidence: 99%

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Growth Mechanism and Morphology of Tetragonal Lysozyme Crystals

Nadarajah¹,

Pusey²

1996

Acta Cryst D

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The tetragonal form of hen egg-white lysozyme is the most investigated protein crystal for growth studies, but the relationship between its surface morphology and internal structure is still not well understood. One method of determining this relationship for inorganic crystals is by employing the periodic bond chain (PBC) theory of Hartman & Perdok [Hartman & Perdok (1955).Acta Co'st. 8,[49][50][51][52][521][522][523][524][525][526][527][528][529]. However, complexities resulting from the packing arrangements and the number of intermolecular bonds in protein crystals have resulted in the use of only simplified versions of this theory so far. In this study a more complete PBC analysis of tetragonal lysozyme crystals was carried out, coupled with an approach incorporating the molecular orientations of the crystal structure. The analysis revealed the existence of a helical tetramer building block of the entire crystal structure, centered around the 43 crystallographic axes, resulting in doublelayered slices and PBC's throughout. The analysis also indicated that the crystallizing units for the faces are at least as large as this tetramer, with the experimental evidence suggesting that it is a tetramer unit for the { 101 } faces and an octamer unit for the {110} faces. The { 110} faces were shown to be molecularly smooth F faces, while the { 101 } to be essentially rough S faces. The predicted morphology and growth mechanisms were found to explain numerous experimental observations from electron and atomic force microscopy, etching studies, lysozyme aggregation studies and measurements of growth kinetics.

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Section: Methods Of Analysismentioning

confidence: 99%

mentioning

confidence: 99%

Growth Mechanism and Morphology of Tetragonal Lysozyme Crystals

Nadarajah¹,

Pusey²

1996

Acta Cryst D

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“…A periodic bond chain is a repeating array of growth units in a single direction held together by strong inter-growth-unit interactions within the crystal. For organic molecular crystals, these strong interactions usually represent the short bonds within the first coordination sphere around a particular growth unit in the lattice [43][44][45][46]. As a result of these favorable interactions, on each face crystalline surface structures are typically bounded by the in-plane PBCs (a PBC vector denotes the full translation distance of the chain's repeat unit in the PBC direction).…”

Section: Hartman-perdok Theorymentioning

confidence: 99%

“…As a result of these favorable interactions, on each face crystalline surface structures are typically bounded by the in-plane PBCs (a PBC vector denotes the full translation distance of the chain's repeat unit in the PBC direction). These strong interactions represent bonds formed between growth units during crystallization [43][44][45][46] and therefore exclude any intra-growth unit interactions.…”

Section: Hartman-perdok Theorymentioning

confidence: 99%

A design aid for crystal growth engineering

Tilbury

Kim

et al. 2016

Progress in Materials Science

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With the highly competitive development of chemical and pharmaceutical industries, mastering crystal growth is becoming increasingly necessary. Modern industrial manufacturers place high importance on the ability to grow crystals with a specific habit using tailored operating conditions. A detailed understanding of crystal growth is, therefore, vital for researchers in crystallography and crystallization to respond and realize this objective. Various models to predict crystal shape in the literature are reviewed here. The most commonly adopted are usually non-mechanistic and limited in their predictive power and utility, especially for products of industrial interest. Mechanistic models offer far more potential for rational crystal design, but

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“…Note also that several studies report that direct protein-protein contacts are reinforced by well-ordered solvent molecules. Extended patterns of hydrogen bonds can therefore be formed to supplement and strengthen the few direct interactions between residues (Frey et al, 1988;Salemme et al, 1988). This contribution to the interaction energy potential is not included in the Skolnick interaction parameters.…”

Section: Streptavidin 2d Crystallizationmentioning

confidence: 99%

Streptavidin Tetramerization and 2D Crystallization: A Mean-Field Approach

Coussaert

Völkel

Noolandi

et al. 2001

Biophysical Journal

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A mean-field theoretical approach is applied to streptavidin tetramerization and two-dimensional (2D) crystallization. This theory includes, in particular, solvent-residue interactions following the inhomogeneous Flory-Huggins model for polymers. It also takes into account residue-residue interactions by using tabulated pair interaction parameters. This theory allows one to explicitly calculate the entropy of the inhomogeneous system. We show that hydrophobic interactions are responsible for the stability of tetramerization. Within the present theory, the equilibrium distance between the two dimers is the same as that determined experimentally. The free energy of tetramerization (i.e., dissociation of the two dimers) is 50 k(B)T. Unlike tetramerization, hydrophobic interactions alone are not sufficient to stabilize the 2D crystal C(222), but solvent-mediated residue-residue interactions give the most important contribution.

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Application of the periodic bond chain (PBC) theory to the analysis of the molecular packing in protein crystals

Cited by 19 publications

References 21 publications

Growth Mechanism and Morphology of Tetragonal Lysozyme Crystals

Growth Mechanism and Morphology of Tetragonal Lysozyme Crystals

A design aid for crystal growth engineering

Streptavidin Tetramerization and 2D Crystallization: A Mean-Field Approach

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