Crystallization of dienelactone hydrolase in two space groups: structural changes caused by crystal packing

Dienelactone hydrolase (DLH) is a monomeric protein with a simple α/β-hydrolase fold structure. It readily crystallizes in space groupP212121from either a phosphate or ammonium sulfate precipitation buffer. Here, the structure of DLH at 1.85 Å resolution crystallized in space groupC2 with two molecules in the asymmetric unit is reported. When crystallized in space groupP212121DLH has either phosphates or sulfates bound to the protein in crucial locations, one of which is located in the active site, preventing substrate/inhibitor binding. Another is located on the surface of the enzyme coordinated by side chains from two different molecules. Crystallization in space groupC2 from a sodium citrate buffer results in new crystallographic protein–protein interfaces. The protein backbone is highly similar, but new crystal contacts cause changes in side-chain orientations and in loop positioning. In regions not involved in crystal contacts, there is little change in backbone or side-chain configuration. The flexibility of surface loops and the adaptability of side chains are important factors enabling DLH to adapt and form different crystal lattices.

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Structure-Activity Relationships of Sandalwood Odorants: Synthesis of a New Campholene Derivative

Natural Product Communications ◽

10.1177/1934578x1000500902 ◽

2010 ◽

Vol 5 (9) ◽

pp. 1934578X1000500

Author(s):

Iris Stappen ◽

Joris Höfinghoff ◽

Gerhard Buchbauer ◽

Peter Wolschann

Keyword(s):

Structural Changes ◽

Great Influence ◽

Complete Loss ◽

Side Chain ◽

Side Chains ◽

Quaternary Carbon ◽

Structural Modifications ◽

Structure Activity ◽

Highly Sensitive ◽

Sandalwood Odorants

Structural modifications of natural (-)-( Z)-β-santalol have shown that the sandalwood odor impression is highly sensitive, even to small structural changes. Particularly, the substitution of the quaternary carbon is of great influence on the scent. Epi-compounds with side chains in the endo-position possess sandalwood odor in only a few derivatives, whereas modifications at this side chain, as well as modification at the bicyclic ring systems mostly lead to a complete loss of sandalwood fragrance.

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Effects of heme modification on oxygen affinity and cooperativity of human adult hemoglobin

Journal of Porphyrins and Phthalocyanines ◽

10.1142/s1088424615500200 ◽

2015 ◽

Vol 19 (01-03) ◽

pp. 301-307 ◽

Cited By ~ 3

Author(s):

Tomokazu Shibata ◽

Eisuke Furuichi ◽

Kiyohiro Imai ◽

Akihiro Suzuki ◽

Yasuhiko Yamamoto

Keyword(s):

Structural Changes ◽

Oxygen Affinity ◽

Side Chain ◽

Side Chains ◽

Human Adult ◽

Alkaline Transition ◽

Functional Control ◽

Adult Hemoglobin ◽

The Relationship ◽

Heme Cofactor

We substituted strongly electron-withdrawing trifluoromethyl ( CF 3) group(s) as heme side chain(s) of human adult hemoglobin (Hb) to achieve large alterations of the heme electronic structure, in order to elucidate the relationship between the oxygen ( O 2) binding properties of Hb and the electronic properties of heme peripheral side chains. The obtained results were compared with those of similar studies performed on myoglobin (Mb), e.g. (Nishimura R, Matsumoto D, Shibata T, Yanagisawa S, Ogura T, Tai H, Matsuo T, Hirota S, Neya S, Suzuki A, and Yamamoto Y. Inorg. Chem. 2014; 53: 9156–9165). These two proteins shared the common feature of a decrease in O 2 affinity upon the CF 3 substitution(s). Using the P50 value, which is the partial pressure of O 2 required for 50% oxygenation of a protein, and the equilibrium constant ( p K a ) of the "acid-alkaline transition" in the met form of a protein as measures of the O 2 affinity and the electron density of heme Fe atom of the protein, respectively, a linear p K a - log (1/P50) relationship was demonstrated for the Hb and Mb systems. The native Hb, however, deviated from the p K a - log (1/P50) relationship, while the native Mb followed it. These results highlighted the significance of the vinyl side chains of the heme cofactor in the functional control of Hb through tertiary and quaternary structural changes upon the oxygenation of the protein.

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Temperature dependant structural changes in thin films of random semifluorinated PMMA copolymers

Powder Diffraction ◽

10.1017/s0885715613001073 ◽

2013 ◽

Vol 28 (S2) ◽

pp. S144-S160 ◽

Cited By ~ 5

Author(s):

Dieter Jehnichen ◽

Peter Friedel ◽

Romy Selinger ◽

Andreas Korwitz ◽

Martin Wengenmayr ◽

...

Keyword(s):

Thin Films ◽

Phase Separation ◽

Structural Changes ◽

Bulk Material ◽

Fluorine Content ◽

Film Surface ◽

Phase Behaviour ◽

Side Chain ◽

Side Chains ◽

Polymer Backbone

Semifluorinated (SF) side chain polymers show phase separation between polymer backbone and SF side chains. Due to strong interaction between SF segments the side chains determine the structure behaviour strongly, often resulting in layered structures in which backbones and layers of SF side chains alternate. The interest in this work was directed to find out the dependence of these structures on concentration of SF side chains. Thin films of random copolymers consisting of methylmethacrylate (MMA) and semifluorinated side chain methacrylate (SFMA) segments and with different fluorine content in the perfluoroalkyl side chains (abbreviated as H10F10 and H2F8) were prepared by spin-coating. Phase separation and structure changes were initiated by external subsequent annealing. Corresponding bulk material served as basic information. Generation of ordered structures and variation of film parameters were observed using different X-ray scattering methods (XRR, GIWAXS, and GISAXS). The phase behaviour in bulk is governed by the SF side chain amount and their specific fluorine content which control the self-organization tendency of SF side chains. Additionally, the confinement in thin films generates an orientation of side chains normally to film surface.

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Temperature-induced phase transitions for amino acids with linear side chains

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314098295 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C170-C170

Author(s):

Carl Henrik Görbitz ◽

Pavel Karen ◽

Michal Dusek ◽

Václav Petříček

Keyword(s):

Amino Acids ◽

Low Temperature ◽

Side Chain ◽

Side Chains ◽

Ambient Conditions ◽

Short Side ◽

Space Groups ◽

Cell Parameters ◽

Commensurate Phase ◽

Chain Conformations

Two polymorphs are known to exist under ambient conditions for a number of amino acids (three for glycine). While investigations at high pressure have revealed a number of additional polymorphs, temperature-induced changes are rare. Low-temperature structures with modified side-chain conformations were identified for L- and DL-cysteine. Furthermore, racemates with linear side chains, such as DL-methionine and the non-standard DL-aminobutyric acid (DL-Abu), DL-aminopentanoic acid (DL-norvaline, DL-Nva) and DL-aminohexanoic acid (DL-norleucine, DL-Nle), undergo major crystalline rearrangements on transitions between P21/c and C2/c space groups [1], some of them entropy driven (disordering). As for the corresponding enantio-pure amino acids, we recently described related P21 and I2 structures at 105 K for L-Abu, both with Z' = 4 [2]. A short side-chain C–C bond (1.426 Å) in the only available CSD entry for L-Nle (at 298 K) [3] lead us to suspect that disorder could have been overlooked in the original refinement. L-Nva has not been described previously. We now present single-crystal X-ray determinations between 105 and 405 K for L-Abu, L-Nva and L-Nle, showing phase behavior of unprecedented complexity. For L-Abu and L-Nva we find three different forms in this temperature interval, while four different phases were found for L-Nle. Its known C2 structure with Z' = 1 prevails between 200 and 390 K, and the side chain is indeed disordered 2:1 over two positions. Above 390 K disorder is extensive; the space group remains C2 but cell parameters change. Upon cooling new low-temperature forms are observed at 200 and 170 K. Both are modulated, but to a different extent: data collected at 100 K reveal an almost commensurate phase, while the 180 K phase is fully incommensurate. This is, to our knowledge, the first observation of modulated structures for an amino acid, and also the first observations of major crystalline rearrangements akin to those seen for the corresponding racemates.

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Impact of morphology, side-chains, and crystallinity on charge-transport properties of π-extended double helicenes

Physical Chemistry Chemical Physics ◽

10.1039/c8cp06982d ◽

2019 ◽

Vol 21 (2) ◽

pp. 901-914 ◽

Cited By ~ 2

Author(s):

Ilhan Yavuz ◽

Janice B. Lin ◽

K. N. Houk

Keyword(s):

Charge Transport ◽

Transport Properties ◽

Crystal Packing ◽

Computational Study ◽

Side Chain ◽

Side Chains

We report a computational study on the effect of side-chain substitution, heteroaromatic substitution and unique crystal packing on the charge transport and mobility of three double helicene molecules.

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Structures of L-valyl-L-glutamine and L-glutamyl-L-valine

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768196006817 ◽

1996 ◽

Vol 52 (6) ◽

pp. 999-1006 ◽

Cited By ~ 10

Author(s):

C. H. Görbitz ◽

P. H. Backe

Keyword(s):

Hydrogen Bond ◽

Crystal Packing ◽

Molecular Geometry ◽

Side Chain ◽

Monoclinic Space Group ◽

Orthorhombic Space Group ◽

Acta Cryst ◽

Space Group ◽

Cell Parameters ◽

Additional Hydrogen Bond

L-Val-L-Gln crystallizes in the orthorhombic space group P21212 with a = 16.419 (3), b = 15.309 (3) and c = 4.708 (1) Å. The final wR(F o 2) is 0.100 for 2044 independent reflections, R(Fo ) = 0.050 for 1475 reflections with I > 2.0σ(I). L-Glu-L-Val crystallizes in the monoclinic space group P21 with a = 6.487 (2), b = 5.505 (2), c = 16.741 (4) Å and β = 97.22 (2)°. The final wR(F F o 2) is 0.111 for 1920 independent reflections, R(Fo ) = 0.047 for 1576 reflections with I > 2.0σ(I). Molecular geometries are normal, except for a unique eclipsed orientation of the charged amino group of L-Glu-L-Val. Dipeptides with a N-terminal hydrophobic residue and C-terminal hydrophilic residue are shown to have crystal packing patterns fundamentally different from those of dipeptides with the same types of residues in reversed order. Accordingly, the structure of L-Val-L-Glu [Eggleston (1984). Acta Cryst. C40, 1250 –1252] is rather similar to L-Val-L-Gln, but different from its retroanalogue L-Glu-L-Val. Nevertheless, the pairing of hydrogen-bond donors and acceptors is the same for L-Val-L-Glu and L-Glu-L-Val, indicating very distinct hydrogen-bonding preferences. This is the first demonstration of such a coincidence among dipeptide structures. The differences between L-Val-L-Glu and L-Val-L-Gln structures stem from modifications of the molecular geometry and cell parameters due to the formation of an additional hydrogen bond from the extra donor in the L-Gln side chain.

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Influence of packing interactions on the average conformation of B-DNA in crystalline structures

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444999000591 ◽

1999 ◽

Vol 55 (4) ◽

pp. 810-819 ◽

Cited By ~ 12

Author(s):

V. Tereshko ◽

J. A. Subirana

Keyword(s):

Crystal Packing ◽

Double Helix ◽

Strong Relationship ◽

Dna Conformation ◽

Base Pairs ◽

Space Group ◽

Space Groups ◽

Related Space ◽

End To End ◽

Packing Interactions

The molecular interactions in crystals of oligonucleotides in the B form have been analysed and in particular the end-to-end interactions. Phosphate–phosphate interactions in dodecamers are also reviewed. A strong influence of packing constraints on the average conformation of the double helix is found. There is a strong relationship between the space group, the end-to-end interactions and the average conformation of DNA. Dodecamers must have a B-form average conformation with 10 ± 0.1 base pairs per turn in order to crystallize in the P212121 and related space groups usually found. Decamers show a wider range of conformational variation, with 9.7–10.6 base pairs per turn, depending on the terminal sequence and the space group. The influence of the space group in decamers is quite striking and remains unexplained. Only small variations are allowed in each case. Thus, crystal packing is strongly related to the average DNA conformation in the crystals and deviations from the average are rather limited. The constraints imposed by the crystal lattice explain why the average twist of the DNA in solution (10.6 base pairs per turn) is seldom found in oligonucleotides crystallized in the B form.

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Influence of Flexible Side-Chains on the Breathing Phase Transition of Pillared Layer MOFs: A Force Field Investigation

10.26434/chemrxiv.11720679.v1 ◽

2020 ◽

Author(s):

Julian Keupp ◽

Johannes P. Dürholt ◽

Rochus Schmid

Keyword(s):

First Principles ◽

Good Accuracy ◽

Field Investigation ◽

Square Lattice ◽

Side Chain ◽

Second Step ◽

Side Chains ◽

Dynamics Simulations ◽

Complex Phenomena ◽

Closed Pore

The prototypical pillared layer MOFs, formed by a square lattice of paddle- wheel units and connected by dinitrogen pillars, can undergo a breathing phase transition by a “wine-rack” type motion of the square lattice. We studied this not yet fully understood behavior using an accurate first principles parameterized force field (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc: benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi- cations for an interface between a closed and an open pore phase traveling through the system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. In conventional simulations in small supercells this mechanism is prevented by periodic boundary conditions (PBC), enforcing a synchronous transformation of the entire crystal. Here, we extend this investigation to pillared layer MOFs with flexible side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen- tally known to have different properties with the side-chains acting as fixed guest molecules. First, in order to extend the parameterization for such flexible groups, 1a new parametrization strategy for MOF-FF had to be developed, using a multi- structure force based fit method. The resulting parametrization for a library of fu-MOFs is then validated with respect to a set of reference systems and shows very good accuracy. In the second step, a series of fu-MOFs with increasing side-chain length is studied with respect to the influence of the side-chains on the breathing behavior. For small supercells in PBC a systematic trend of the closed pore volume with the chain length is observed. However, for a nanocrystallite model a distinct interface between a closed and an open pore phase is visible only for the short chain length, whereas for longer chains the interface broadens and a nearly concerted trans- formation is observed. Only by molecular dynamics simulations using accurate force fields such complex phenomena can be studied on a molecular level.

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Packing Effect on the Transfer Integrals and Mobility in α,α′-bis(dithieno[3,2-b:2′,3′-d]thiophene) (BDT) and its Heteroatom-Substituted Analogues

Australian Journal of Chemistry ◽

10.1071/ch11162 ◽

2011 ◽

Vol 64 (12) ◽

pp. 1587 ◽

Cited By ~ 25

Author(s):

Ahmad Irfan ◽

Abdullah G. Al-Sehemi ◽

Shabbir Muhammad ◽

Jingping Zhang

Keyword(s):

Electron Transfer ◽

Electron Mobility ◽

Hole Mobility ◽

Experimental Investigations ◽

Hole Transfer ◽

Space Group ◽

Space Groups ◽

Transfer Integrals ◽

Packing Effect ◽

Good Agreement

Theoretically calculated mobility has revealed that BDT is a hole transfer material, which is in good agreement with experimental investigations. The BDT, NHBDT, and OBDT are predicted to be hole transfer materials in the C2/c space group. Comparatively, hole mobility of BHBDT is 7 times while electron mobility is 20 times higher than the BDT. The packing effect for BDT and designed crystals was investigated by various space groups. Generally, mobility increases in BDT and its analogues by changing the packing from space group C2/c to space groups P1 or . In the designed ambipolar material, BHBDT hole mobility has been predicted 0.774 and 3.460 cm2 Vs–1 in space groups P1 and , which is 10 times and 48 times higher than BDT (0.075 and 0.072 cm2 Vs–1 in space groups P1 and ), respectively. Moreover, the BDT behaves as an electron transfer material by changing the packing from the C2/c space group to P1 and .

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Effects of Amino Acid Side-Chain Length and Chemical Structure on Anionic Polyglutamic and Polyaspartic Acid Cellulose-Based Polyelectrolyte Brushes

Polymers ◽

10.3390/polym13111789 ◽

2021 ◽

Vol 13 (11) ◽

pp. 1789

Author(s):

Dmitry Tolmachev ◽

George Mamistvalov ◽

Natalia Lukasheva ◽

Sergey Larin ◽

Mikko Karttunen

Keyword(s):

Glutamic Acid ◽

Chain Length ◽

Chemical Structure ◽

Side Chain ◽

Side Chains ◽

Side Chain Length ◽

Polyelectrolyte Brushes ◽

Grafting Density ◽

The Difference ◽

Cellulose Surface

We used atomistic molecular dynamics (MD) simulations to study polyelectrolyte brushes based on anionic α,L-glutamic acid and α,L-aspartic acid grafted on cellulose in the presence of divalent CaCl2 salt at different concentrations. The motivation is to search for ways to control properties such as sorption capacity and the structural response of the brush to multivalent salts. For this detailed understanding of the role of side-chain length, the chemical structure and their interplay are required. It was found that in the case of glutamic acid oligomers, the longer side chains facilitate attractive interactions with the cellulose surface, which forces the grafted chains to lie down on the surface. The additional methylene group in the side chain enables side-chain rotation, enhancing this effect. On the other hand, the shorter and more restricted side chains of aspartic acid oligomers prevent attractive interactions to a large degree and push the grafted chains away from the surface. The difference in side-chain length also leads to differences in other properties of the brush in divalent salt solutions. At a low grafting density, the longer side chains of glutamic acid allow the adsorbed cations to be spatially distributed inside the brush resulting in a charge inversion. With an increase in grafting density, the difference in the total charge of the aspartic and glutamine brushes disappears, but new structural features appear. The longer sides allow for ion bridging between the grafted chains and the cellulose surface without a significant change in main-chain conformation. This leads to the brush structure being less sensitive to changes in salt concentration.

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