Packing topology in crystals of proteins and small molecules: a comparison

Carugo, Oliviero; Blatova, Olga A.; Medrish, Elena O.; Блатов, В. А.; Proserpio, Davide M.

doi:10.1038/s41598-017-12699-4

Cited by 35 publications

(28 citation statements)

References 51 publications

(58 reference statements)

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“…In conclusion, the mechanisms of protein crystal packing are complex and unclear, and the effects of additives are generally not well understood (Luo et al, 2018;Carugo et al, 2017). In this study, we discuss the unique crystallization behaviour of C-phycocyanin, which includes effortless highquality crystal formation with the majority of available crystallization precipitants.…”

Section: Crystallization Solution Phmentioning

confidence: 94%

C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening

Sarrou¹,

Feiler²,

Peard³

et al. 2021

Acta Cryst Sect D Struct Biol

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The unique crystallization properties of the antenna protein C-phycocyanin (C-PC) from the thermophilic cyanobacterium Thermosynechococcus elongatus are reported and discussed. C-PC crystallizes in hundreds of significantly different conditions within a broad pH range and in the presence of a wide variety of precipitants and additives. Remarkably, the crystal dimensions vary from a few micrometres, as used in serial crystallography, to several hundred micrometres, with a very diverse crystal morphology. More than 100 unique single-crystal X-ray diffraction data sets were collected from randomly selected crystals and analysed. The addition of small-molecule additives revealed three new crystal packings of C-PC, which are discussed in detail. The high propensity of this protein to crystallize, combined with its natural blue colour and its fluorescence characteristics, make it an excellent candidate as a superior and highly adaptable model system in crystallography. C-PC can be used in technical and methods development approaches for X-ray and neutron diffraction techniques, and as a system for comprehending the fundamental principles of protein crystallography.

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Section: Crystallization Solution Phmentioning

confidence: 94%

C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening

Sarrou¹,

Feiler²,

Peard³

et al. 2021

Acta Cryst Sect D Struct Biol

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“…Therefore, this trimmer can be considered as a secondary building unit of the crystal. Representation of the crystal structure as packing of the H‐bonded trimmer leads to the uninodal 14‐c packing net with bcu‐x topology, which is typical for packing organic molecules [22c] . We did not take water molecules into account due to their small size when simplifying the net of the trimers.…”

Section: Resultsmentioning

confidence: 99%

A Proton‐Transfer Complex Containing 5‐Hydroxy‐isophthalic Acid with 3,3′‐(Piperazine‐1,4‐diylbis (methylene)) Dibenzonitrile: Structural Topology, Hirshfeld Analysis, NLO, and DFT Studies

et al. 2021

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This work focuses on the study of a proton‐transfer complex (1) of 5‐hydroxy‐isophthalic acid (HIPA) and 3,3′‐(piperazine‐1,4‐diylbis(methylene)) dibenzonitrile (PBN). The single‐crystal XRD reveals that the HIPA and PBN molecules in complex (1) are mutually connected through intricate N+−H−O− H‐bonding interactions. Herein, close and open aperture measurement for the third‐order nonlinear optical response of the complex (1) has been investigated using the Z‐scan technique which shows its potential application in optoelectronic and photonic devices. Further, DFT calculations have been done for the HOMO‐LUMO energy gap and Mulliken atomic charge analysis which helps us to understand the proton‐transfer mechanism in the complex (1). The topological and Hirshfeld surface analysis were also achieved to understand the importance of non‐covalent interactions in the stability of the supramolecular structure and NLO properties.

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“…The freezing point of the dissolved compound can be changed by its concentration in the solution. The arrangement of molecules in crystals often resembles the close packing of rigid spheres, with the coordination number of 12 or somewhat larger (Kitaigorodskii, 1973;Carugo et al, 2017). In this respect it resembles the closely packed rigid spheres, which fill 74% of the space, leaving the remaining quarter of space as empty voids.…”

Section: Towards Universal Laws and Rules Of High-pressure Transformamentioning

confidence: 99%

Lab in a DAC – high-pressure crystal chemistry in a diamond-anvil cell

Katrusiak

2019

Acta Crystallogr B Struct Sci Cryst Eng Mater

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The diamond‐anvil cell (DAC) was invented 60 years ago, ushering in a new era for material sciences, extending research into the dimension of pressure. Most structural determinations and chemical research have been conducted at ambient pressure, i.e. the atmospheric pressure on Earth. However, modern experimental techniques are capable of generating pressure and temperature higher than those at the centre of Earth. Such extreme conditions can be used for obtaining unprecedented chemical compounds, but, most importantly, all fundamental phenomena can be viewed and understood from a broader perspective. This knowledge, in turn, is necessary for designing new generations of materials and applications, for example in the pharmaceutical industry or for obtaining super‐hard materials. The high‐pressure chambers in the DAC are already used for a considerable variety of experiments, such as chemical reactions, crystallizations, measurements of electric, dielectric and magnetic properties, transformations of biological materials as well as experiments on living tissue. Undoubtedly, more applications involving elevated pressure will follow. High‐pressure methods become increasingly attractive, because they can reduce the sample volume and compress the intermolecular contacts to values unattainable by other methods, many times stronger than at low temperature. The compressed materials reveal new information about intermolecular interactions and new phases of single‐ and multi‐component compounds can be obtained. At the same time, high‐pressure techniques, and particularly those of X‐ray diffraction using the DAC, have been considerably improved and many innovative developments implemented. Increasingly more equipment of in‐house laboratories, as well as the instrumentation of beamlines at synchrotrons and thermal neutron sources are dedicated to high‐pressure research.

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Packing topology in crystals of proteins and small molecules: a comparison

Cited by 35 publications

References 51 publications

C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening

C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening

A Proton‐Transfer Complex Containing 5‐Hydroxy‐isophthalic Acid with 3,3′‐(Piperazine‐1,4‐diylbis (methylene)) Dibenzonitrile: Structural Topology, Hirshfeld Analysis, NLO, and DFT Studies

Lab in a DAC – high-pressure crystal chemistry in a diamond-anvil cell

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