scholarly journals Biological vs. Crystallographic Protein Interfaces: An Overview of Computational Approaches for Their Classification

Crystals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 114 ◽  
Author(s):  
Katarina Elez ◽  
Alexandre M. J. J. Bonvin ◽  
Anna Vangone
Keyword(s):  
Protein Complexes ◽  
Classification Problem ◽  
Empirical Knowledge ◽  
Comprehensive Overview ◽  
X Ray ◽  
Biologically Relevant ◽  
X Ray Crystallography ◽  
The Past ◽  
Protein Interfaces

Complexes between proteins are at the basis of almost every process in cells. Their study, from a structural perspective, has a pivotal role in understanding biological functions and, importantly, in drug development. X-ray crystallography represents the broadest source for the experimental structural characterization of protein-protein complexes. Correctly identifying the biologically relevant interface from the crystallographic ones is, however, not trivial and can be prone to errors. Over the past two decades, computational methodologies have been developed to study the differences of those interfaces and automatically classify them as biological or crystallographic. Overall, protein-protein interfaces show differences in terms of composition, energetics and evolutionary conservation between biological and crystallographic ones. Based on those observations, a number of computational methods have been developed for this classification problem, which can be grouped into three main categories: Energy-, empirical knowledge- and machine learning-based approaches. In this review, we give a comprehensive overview of the training datasets and methods so far implemented, providing useful links and a brief description of each method.

scholarly journals Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

2012 ◽  
Vol 13 (8) ◽  
pp. 10537-10552 ◽  
Author(s):  
Vincent J. B. Ruigrok ◽  
Mark Levisson ◽  
Johan Hekelaar ◽  
Hauke Smidt ◽  
Bauke W. Dijkstra ◽  
...  
Keyword(s):  
Protein Complexes ◽  
X Ray ◽  
X Ray Crystallography ◽  
Alternative Approaches

scholarly journals Synthesis, Solution, and Structural Characterization of Tetrahydrofuranyl-2,2-Bisphosphonic Acid Disodium Salt

2010 ◽  
Vol 2010 ◽  
pp. 1-7 ◽  
Author(s):  
Elena Maltezou ◽  
Marios Stylianou ◽  
Sudeshna Roy ◽  
Chryssoula Drouza ◽  
Anastasios D. Keramidas
Keyword(s):  
Disodium Salt ◽  
Phosphorus Acid ◽  
Phosphorus Trichloride ◽  
Total Charge ◽  
Two Dimensional ◽  
X Ray ◽  
Biologically Relevant ◽  
X Ray Crystallography ◽  
Synthesis Solution

Bisphosphonates are biologically relevant therapeutics for bone disorders and cancer. Reaction ofγ-chlorobutyric acid, phosphorus acid, and phosphorus trichloride without the use of solvent gave the tetrahydrofuranyl-2,2-bisphosphonate sodium salt (Na2H2L). TheNa2H2Lwas isolated, characterized in solution byH,C, andPNMR spectroscopy and in solid state by single X-Ray crystallography. The crystal structure showed that theNa2H2Lforms in the crystal infinite two-dimensional sheets stacked one parallel to the other. A comparison of the chelating properties ofH2L2−with similar hydroxyl bisphosphonate ligands shows that the strength of the Na–O(furanyl/hydroxyl) bond is directly related to the total charge of the ligand anion.

The Use of Advanced Analytical Techniques for Characterization of the Chemical, Physical, and Crystallographic Nature of a Surface

1973 ◽  
Vol 31 ◽  
pp. 132-133 ◽  
Author(s):  
R. E. Herfert
Keyword(s):  
Surface Characterization ◽  
Analytical Techniques ◽  
X Ray Diffraction ◽  
Depth Of Penetration ◽  
X Ray ◽  
The Past ◽  
Transmission Electron ◽  
Scanning Electron

Studies of the nature of a surface, either metallic or nonmetallic, in the past, have been limited to the instrumentation available for these measurements. In the past, optical microscopy, replica transmission electron microscopy, electron or X-ray diffraction and optical or X-ray spectroscopy have provided the means of surface characterization. Actually, some of these techniques are not purely surface; the depth of penetration may be a few thousands of an inch. Within the last five years, instrumentation has been made available which now makes it practical for use to study the outer few 100A of layers and characterize it completely from a chemical, physical, and crystallographic standpoint. The scanning electron microscope (SEM) provides a means of viewing the surface of a material in situ to magnifications as high as 250,000X.

scholarly journals Structural Characterization of Heterodinuclear ZnII-LnIII Complexes (Ln = Pr, Nd) with a Ring-Contracted H2valdien-Derived Schiff Base Ligand

2021 ◽  
Author(s):  
Shabana Noor ◽  
Richard Goddard ◽  
Fehmeeda Khatoon ◽  
Sarvendra Kumar ◽  
Rüdiger W. Seidel
Keyword(s):  
Molecular Structure ◽  
Schiff Base ◽  
Structural Characterization ◽  
Schiff Base Ligand ◽  
Crystal And Molecular Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Imidazoline Ring

AbstractSynthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes with the formula [ZnLn(HL)(µ-OAc)(NO3)2(H2O)x(MeOH)1-x]NO3 · n H2O · n MeOH [Ln = Pr (1), Nd (2)] and the crystal and molecular structure of [ZnNd(HL)(µ-OAc)(NO3)2(H2O)] [ZnNd(HL)(OAc)(NO3)2(H2O)](NO3)2 · n H2O · n MeOH (3) are reported. The asymmetrical compartmental ligand (E)-2-(1-(2-((2-hydroxy-3-methoxybenzylidene)amino)-ethyl)imidazolidin-2-yl)-6-methoxyphenol (H2L) is formed from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation, resulting in a peripheral imidazoline ring. The structures of 1–3 were revealed by X-ray crystallography. The smaller ZnII ion occupies the inner N2O2 compartment of the ligand, whereas the larger and more oxophilic LnIII ions are found in the outer O2O2’ site. Graphic Abstract Synthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes (Ln = Pr, Nd) bearing an asymmetrical compartmental ligand formed in situ from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation are reported.

Three-dimensional crystallization of membrane proteins

1988 ◽  
Vol 21 (4) ◽  
pp. 429-477 ◽  
Author(s):  
W. Kühlbrandt
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Membrane Protein Complexes ◽  
Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

Structural determination and characterization of copper and zinc bis-glycinates with X-ray crystallography and mass spectrometry

2010 ◽  
Vol 63 (19) ◽  
pp. 3335-3347 ◽  
Author(s):  
Sanjit Konar ◽  
Kevin Gagnon ◽  
Abraham Clearfield ◽  
Charles Thompson ◽  
Jennifer Hartle ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Structural Determination ◽  
X Ray ◽  
X Ray Crystallography ◽  
Copper And Zinc

Synthesis and structural characterization of a magnesium phthalocyanine(3–) anion

2012 ◽  
Vol 16 (01) ◽  
pp. 154-162 ◽  
Author(s):  
Edwin W.Y. Wong ◽  
Daniel B. Leznoff
Keyword(s):  
Absorption Spectrum ◽  
Solid State ◽  
Single Crystal ◽  
Structural Characterization ◽  
Heterometallic Complex ◽  
State Structure ◽  
Solid State Structure ◽  
X Ray ◽  
X Ray Crystallography

The reduction of magnesium phthalocyanine (MgPc) with 2.2 equivalents of potassium graphite in 1,2-dimethoxyethane (DME) gives [K2(DME)4]PcMg(OH)(1) in 67% yield. Compound 1 was structurally characterized using single crystal X-ray crystallography and was found to be a monomeric, heterometallic complex consisting of a μ3-OH ligand that bridges a [MgIIPc3-]- anion to two potassium cations solvated by four DME molecules. An absorption spectrum of 1 confirms the Pc ligand is singly reduced and has a 3–charge. The solid-state structure of 1 does not indicate breaking of the aromaticity of the Pc ligand. Compound 1 is only the second Pc3- complex and the first reduced MgPc to be isolated and structurally characterized.

Preparation and characterization of a new series of Cr(II) hydroborates

1995 ◽  
Vol 73 (7) ◽  
pp. 1126-1134 ◽  
Author(s):  
Michel Dionne ◽  
Shoukang Hao ◽  
Sandro Gambarotta
Keyword(s):  
Trinuclear Complex ◽  
Synthesis And Characterization ◽  
Crystal Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Quadruple Bond ◽  
Quadruple Bonds ◽  
Reaction Proceeds

The synthesis and characterization of a new series of mono-, di-, and trinuclear Cr(II) borohydride compounds is described. The reaction of CrCl2(TMEDA) with two equivalents of NaBH4 afforded the thermally unstable (TMEDA)Cr(BH4)2 (1), which was converted by treatment with pyridine into the octahedral monomeric (Py)4Cr(BH4)2 (2). The reaction proceeds via formation of an intermediate trinuclear complex {[(TMEDA)(Py)Cr(η2-BH4)]2[(Py)2Cr(η2-BH4)2]}(µ,η1-BH4)2 (3), which was isolated and characterized by X-ray crystallography. Reaction of 1 and 2 with both CO2 and RN=C=NR (R = Cy, iPr) afforded hydride insertion and formation of the corresponding diamagnetic lantern-type Cr(II) formate (HCO2)4Cr2Py2 (4) and formamidinate compounds [RNC(H)NR]2Cr2(µ-BH)4 (R = Cy (5a), iPr (5b)), respectively, with supershort Cr—Cr quadruple bonds. The structures of 1, 2, 3, and 5b were elucidated by X-ray analysis. Crystal data are as follows. 1: C6H24N2B2Cr, monoclinic, Cc, a = 8.517(2) Å, b = 15.921(5) Å, c = 9.624(2) Å, β = 115.59(1)°, Z = 4, R = 0.022, Rw = 0.029; 2: C28H44N4B2O2Cr, monoclinic, P21/n, a = 12.021(1) Å, b = 15.555(1) Å, c = 15.723(1) Å, β = 90.13(2)°, Z = 4, R = 0.074, Rw = 0.086; 3: C32H76N8B6Cr3, monoclinic, P21/n, a = 8.515(1) Å, b = 14.525(1) Å, c = 18.286(2) Å, β = 91.38(1)°, Z = 2, R = 0.051, Rw = 0.060; 5b: C21H49N6BCr2, monoclinic, C2/c, a = 17.000(1) Å, b = 9.033(1) Å, c = 19.160(1) Å, β = 105.579(9)°, Z = 4, R = 0.069, Rw = 0.078. Keywords: divalent chromium, borohydride, Cr—Cr quadruple bond.

Synthesis and characterization of the binuclear diamido titanium chalcogenides [(Ar)NCH2CH2CH2N(Ar)]2Ti(µ-E)2 (E = Se, Te)

2002 ◽  
Vol 80 (11) ◽  
pp. 1524-1529 ◽  
Author(s):  
Tianle Zhang ◽  
Warren E Piers ◽  
Masood Parvez
Keyword(s):  
Solid State ◽  
Key Words ◽  
Synthesis And Characterization ◽  
Catalyst Precursor ◽  
Tellurium Atom ◽  
Titanium Complex ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atom Source

Reaction of McConville's chelating amido titanium complex [(Ar)NCH2CH2CH2N(Ar)]Ti(CH3)2 (Ar = 2,6-i-Pr2C6H3) with either elemental Se or the tellurium atom source Te=PBu3 resulted in the formation of bis-µ-chalcogenido dimers [(Ar)NCH2CH2CH2N(Ar)]2Ti(µ-E)2 (E = Se, 2; Te, 3) with concommitant loss of EMe2. The dimers 2 and 3 were characterized spectroscopically and via X-ray crystallography. The two compounds are isostructural in the solid state. The tellurido dimer 3 may also be synthesized by reduction of the diamido dichloride [(Ar)NCH2CH2CH2N(Ar)]2TiCl2 with Na–Hg amalgam followed by treatment with Te=PBu3. This dimer is unreactive toward further Te=PBu3 or stannanes such as HSnBu3. Unlike decamethyltitanocene derivatives, the diamido complex is not an effective catalyst precursor for the heterohydrodecoupling of Te=PBu3 and HSnBu3.Key words: diamido titanium complexes, selenides, tellurides.

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