scholarly journals Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds

2021 ◽  
Vol 17 (3) ◽  
pp. e1008061
Author(s):  
Brian Coventry ◽  
David Baker
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Protein Design ◽  
Protein Sequence ◽  
Quadratic Function ◽  
Energetic Cost ◽  
Energy Term ◽  
Sequence Optimization ◽  
Polar Groups ◽  
Sidechain Rotamers

In aqueous solution, polar groups make hydrogen bonds with water, and hence burial of such groups in the interior of a protein is unfavorable unless the loss of hydrogen bonds with water is compensated by formation of new ones with other protein groups. For this reason, buried “unsatisfied” polar groups making no hydrogen bonds are very rare in proteins. Efficiently representing the energetic cost of unsatisfied hydrogen bonds with a pairwise-decomposable energy term during protein design is challenging since whether or not a group is satisfied depends on all of its neighbors. Here we describe a method for assigning a pairwise-decomposable energy to sidechain rotamers such that following combinatorial sidechain packing, buried unsaturated polar atoms are penalized. The penalty can be any quadratic function of the number of unsatisfied polar groups, and can be computed very rapidly. We show that inclusion of this term in Rosetta sidechain packing calculations substantially reduces the number of buried unsatisfied polar groups.

scholarly journals Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds

2020 ◽  
Author(s):  
Brian Coventry ◽  
David Baker
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Protein Design ◽  
Protein Sequence ◽  
Quadratic Function ◽  
Energetic Cost ◽  
Energy Term ◽  
Sequence Optimization ◽  
Polar Groups ◽  
Sidechain Rotamers

AbstractIn aqueous solution, polar groups make hydrogen bonds with water, and hence burial of such groups in the interior of a protein is unfavorable unless the loss of hydrogen bonds with water is compensated by formation of new ones with other protein groups. Hence, buried “unsatisfied” polar groups making no hydrogen bonds are very rare in proteins. Efficiently representing the energetic cost of unsatisfied hydrogen bonds with a pairwise-decomposable energy term during protein design is challenging since whether or not a group is satisfied depends on all of its neighbors. Here we describe a method for assigning a pairwise-decomposable energy to sidechain rotamers such that following combinatorial sidechain packing, buried unsaturated polar atoms are penalized. The penalty can be any quadratic function of the number of unsatisfied polar groups, and can be computed very rapidly. We show that inclusion of this term in Rosetta sidechain packing calculations substantially reduces the number of buried unsatisfied polar groups.

Ab initio QM/MM dynamics of anion–water hydrogen bonds in aqueous solution

2005 ◽  
Vol 403 (4-6) ◽  
pp. 314-319 ◽  
Author(s):  
Anan Tongraar ◽  
Bernd Michael Rode
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Water Hydrogen

scholarly journals Crystal structure of the new hybrid material bis(1,4-diazoniabicyclo[2.2.2]octane) di-μ-chlorido-bis[tetrachloridobismuthate(III)] dihydrate

2015 ◽  
Vol 71 (11) ◽  
pp. 1384-1387
Author(s):  
Marwen Chouri ◽  
Habib Boughzala
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Room Temperature ◽  
Molar Ratio ◽  
Water Molecules ◽  
Site Symmetry ◽  
Two Dimensional ◽  
Slow Evaporation ◽  
Solution Ph

The title compound bis(1,4-diazoniabicyclo[2.2.2]octane) di-μ-chlorido-bis[tetrachloridobismuthate(III)] dihydrate, (C6H14N2)2[Bi2Cl10]·2H2O, was obtained by slow evaporation at room temperature of a hydrochloric aqueous solution (pH = 1) containing bismuth(III) nitrate and 1,4-diazabicyclo[2.2.2]octane (DABCO) in a 1:2 molar ratio. The structure displays a two-dimensional arrangement parallel to (100) of isolated [Bi2Cl10]4−bioctahedra (site symmetry -1) separated by layers of organic 1,4-diazoniabicyclo[2.2.2]octane dications [(DABCOH2)2+] and water molecules. O—H...Cl, N—H...O and N—H...Cl hydrogen bonds lead to additional cohesion of the structure.

scholarly journals Do all backbone polar groups in proteins form hydrogen bonds?

2005 ◽  
Vol 14 (7) ◽  
pp. 1911-1917 ◽  
Author(s):  
Patrick J. Fleming ◽  
George D. Rose
Keyword(s):  
Hydrogen Bonds ◽  
Polar Groups

scholarly journals Crystal structure of β-D,L-fructose

2015 ◽  
Vol 71 (10) ◽  
pp. o719-o720 ◽  
Author(s):  
Tomohiko Ishii ◽  
Tatsuya Senoo ◽  
Akihide Yoshihara ◽  
Kazuhiro Fukada ◽  
Genta Sakane
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Equimolar Mixture ◽  
Compound C ◽  
Dimensional Network ◽  
Hydroxy Groups

The title compound, C6H12O6, was crystallized from an aqueous solution of equimolar mixture of D- and L-fructose (1,3,4,5,6-pentahydroxyhexan-2-one,arabino-hexulose or levulose), and it was confirmed that D-fructose (or L-fructose) formed β-pyranose with a2C5(or5C2) conformation. In the crystal, two O—H...O hydrogen bonds between the hydroxy groups at the C-1 and C-3 positions, and at the C-4 and C-5 positions connect homochiral molecules into a column along theaaxis. The columns are linked by other O—H...O hydrogen bonds between D- and L-fructose molecules, forming a three-dimensional network.

(R)-1-Phenylethanaminium–(S,S)-2,3-dibromosuccinate–(R,R)-2,3-dibromosuccinic acid–water (2/1/1/2)

2006 ◽  
Vol 62 (4) ◽  
pp. o1281-o1283
Author(s):  
Andreas Fischer
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Quantitative Yield ◽  
Acid Water ◽  
Two Dimensional ◽  
Rotation Axes ◽  
Compound C ◽  
Dimensional Network ◽  
Network Of Hydrogen Bonds

From an aqueous solution of racemic 2,3-dibromosuccinic acid and (R)-1-phenylethanamine, crystals of the title compound, C8H12N+·0.5C4H2Br2O4 2−·0.5C4H4Br2O4·H2O, were obtained in almost quantitative yield. The structure contains both enantiomers of the starting material, dibromosuccinic acid. The S,S enantiomer is present as a dianion and the R,R enantiomer as the neutral acid; both of these components lie on twofold rotation axes. The structure features a complex two-dimensional network of hydrogen bonds.

Na6[TeMo6O24]·22 H2O – A Layered Heteropoly Compound with the Chain-Like Polycation {Na3(Η2O)1111}n3n+

1993 ◽  
Vol 48 (4) ◽  
pp. 404-408 ◽  
Author(s):  
Christian Robl ◽  
Mona Frost
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Single Crystals ◽  
Solution Space ◽  
Heteropoly Compound ◽  
Water Molecules ◽  
Space Group ◽  
The Third ◽  
Bonding Mode

Colourless triclinic single crystals of Na6[TeMo6O24] · 22 H2O were grown from aqueous solution (space group P 1, a = 1030.89(9), b = 1056.7(1), c = 1106.32(9) pm, α = 90.120(7), β = 115.220(6), γ = 105.195(7), Ζ = 1, 295 Κ, 336 parameters, 3181 reflections, Rg = 0.0186). There are three crystallographically independent Na+ cations. Two of them are coordinated octahedrally by water molecules only. The third Na+ cation is bound to five H2O and one oxygen atom (O(4)) belonging to the Anderson-Evans type anion [TeMo6O24]6-. The sodium-centered coordination octahedra are linked by common edges exclusively formed by water molecules to yield chain-like polycations {Na3(H2O)11}n,3n+ which are bound by the Na(1)-O(4) contact to the anions situated on crystallographic centers of inversion forming a layer-like arrangement. Further connections between the polycations and the [TeMo6O24]6- anions are established by hydrogen bonds involving all the oxygen atoms of the anion except O(4) as almost equivalent proton acceptors regardless of their bonding mode to Te or Mo.

Two new CdII MOFs of 1,4-bis(1H-benzimidazol-1-yl)butane and flexible dicarboxylate ligands: luminescence sensing towards Fe3+

2020 ◽  
Vol 76 (11) ◽  
pp. 1024-1033
Author(s):  
Fang-Hua Zhao ◽  
Shi-Yao Li ◽  
Wen-Yu Guo ◽  
Zi-Hao Zhao ◽  
Xiao-Wen Guo ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Layer Structure ◽  
Three Dimensional ◽  
Supramolecular Network ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Vis Spectroscopy

Two new CdII MOFs, namely, two-dimensional (2D) poly[[[μ2-1,4-bis(1H-benzimidazol-1-yl)butane](μ2-heptanedioato)cadmium(II)] tetrahydrate], {[Cd(C7H10O4)(C18H18N4)]·4H2O} n or {[Cd(Pim)(bbimb)]·4H2O} n (1), and 2D poly[diaqua[μ2-1,4-bis(1H-benzimidazol-1-yl)butane](μ4-decanedioato)(μ2-decanedioato)dicadmium(II)], [Cd2(C10H16O4)2(C18H18N4)(H2O)2] n or [Cd(Seb)(bbimb)0.5(H2O)] n (2), have been synthesized hydrothermally based on the 1,4-bis(1H-benzimidazol-1-yl)butane (bbimb) and pimelate (Pim2−, heptanedioate) or sebacate (Seb2−, decanedioate) ligands. Both MOFs were structurally characterized by single-crystal X-ray diffraction. In 1, the CdII centres are connected by bbimb and Pim2− ligands to generate a 2D sql layer structure with an octameric (H2O)8 water cluster. The 2D layers are further connected by O—H...O hydrogen bonds, resulting in a three-dimensional (3D) supramolecular structure. In 2, the CdII centres are coordinated by Seb2− ligands to form binuclear Cd2 units which are linked by bbimb and Seb2− ligands into a 2D hxl layer. The 2D layers are further connected by O—H...O hydrogen bonds, leading to an 8-connected 3D hex supramolecular network. IR and UV–Vis spectroscopy, thermogravimetric analysis and solid-state photoluminescence analysis were carried out on both MOFs. Luminescence sensing experiments reveal that both MOFs have good selective sensing towards Fe3+ in aqueous solution.

Sign in / Sign up

Export Citation Format

Share Document