Origin of the homochirality of biomolecules

1995 ◽  
Vol 28 (4) ◽  
pp. 473-507 ◽  
Author(s):  
L. Keszthelyi
Keyword(s):  
Amino Acids ◽  
Three Dimensional ◽  
Polarized Light ◽  
Mirror Image ◽  
Reference Points ◽  
Dimensional Structure ◽  
Theoretical Treatment ◽  
Chiral Molecules ◽  
Amino Groups ◽  
The Right

Molecules built up from a given set of atoms may differ in their three-dimensional structure. They may have one or more asymmetric centres that serve as reference points for the steric distribution of the atoms. Carbon atoms, common to all biomolecules, are often such centres. For example, the Cα atom between the carboxyl and amino groups in amino acids is an asymmetric centre: looking ON ward (i.e. from the carbOxyl to the amiNo group, with the Cα oriented so that it is above the carboxyl and amino groups) the radical characterizing the amino acid may be to the right (D-molecules) or to the left (L-molecules). Nineteen of the 20 amino acids occurring in proteins have such a structure (the exception is glycine, where the radical is a hydrogen atom). These pairs of molecules cannot be brought into coincidence with their own mirror image, as is the situation with our hands. The phenomenon has therefore been named handedness, or chirality, from the Greek word cheir, meaning hand. The two forms of the chiral molecules are called enantiomers or antipodes. They differ in rotating the plane of the polarized light either to the right or to the left. The sense of rotation depends on the wavelength of the measuring light, but at a given wavelength it is always opposite for a pair of enantiomers. Chirality may also occur when achiral molecules form chiral substances during crystallization (for example, quartz forms D-quartz or Lquartz). A detailed theoretical treatment of molecular chirality is given by Barron (1991).

Anomalous scattering and absolute configuration

2010 ◽  
Author(s):  
Jenny Pickworth Glusker ◽  
Kenneth N. Trueblood
Keyword(s):  
Carbon Atom ◽  
Absolute Configuration ◽  
Three Dimensional ◽  
Polarized Light ◽  
Mirror Image ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
The Absolute ◽  
Asymmetric Carbon

The concept of the carbon atom with four bonds extending in a tetrahedral fashion was put forward by van’t Hoff and Le Bel in 1874. It coincided with the realization that such an arrangement could be asymmetric if the four substituents were different, as shown in Figure 10.1a (van’t Hoff, 1874; Le Bel, 1874). Thus, for any compound containing one such asymmetric carbon atom, there are two isomers of opposite chirality (individually called enantiomers), for which threedimensional representations of their structural formulas are related by a mirror plane. Aqueous solutions of these enantiomers rotate the plane of polarized light in opposite directions. As discussed in Chapter 7, Pasteur showed that crystals of sodium ammonium tartrate had small asymmetrically located faces and that crystals with these so-called “hemihedral faces” rotated the plane of polarization of light clockwise, while crystals with similar faces in mirror-image positions rotated this plane of polarization counterclockwise. Thus the external form (that is, the morphology) of the crystals illustrated in Figure 10.1b was used to separate enantiomers (see Patterson and Buchanan, 1945). Pure enantiomers can only crystallize in noncentrosymmetric space groups unless both isomers are present. But even if the chemical formula and the three-dimensional structure of a molecule such as tartaric acid have been determined by standard X-ray diffraction methods, there is an ambiguity about the absolute configuration. Information about the absolute configuration is not contained in the diffraction pattern of the crystal as it is normally measured. Thus, although the substituents on the asymmetric carbon atoms have been identified, and even the detailed three-dimensional geometry of the molecule has been determined, it is not known which of the two enantiomers (mirror-image forms, analogous to those shown in Figure 10.1a) represents the three-dimensional structure of a particular individual molecule that has some distinguishing chiral property, such as the ability to rotate the plane of polarized light to the right. In other words, what is the absolute structure of the dextrorotatory form of the compound under study? A means of determining the absolute configurations of molecules was, however, provided by X-ray crystallographic studies.

Brief Organic Review

2016 ◽  
Author(s):  
Gary W. Morrow
Keyword(s):  
Functional Groups ◽  
Lewis Acids ◽  
Three Dimensional ◽  
Polarized Light ◽  
Mirror Image ◽  
Bond Line ◽  
Organic Chemical ◽  
Chemical Structures ◽  
Or Groups ◽  
Standard Formalism

In addition to simple hydrocarbon structures (alkanes, alkenes, alkynes, and aromatic systems) and alkyl groups (methyl, ethyl, propyl, isopropyl, etc.), this text assumes a familiarity with the most common functional groups associated with organic chemical structures and their basic reactivity patterns. Table 1.1 summarizes the names and structures of some of the more important functional groups we will be dealing with throughout the remainder of the book. It is important to remember that functional groups containing O or N with nonbonding electrons have an affinity for both protic and Lewis acids and are important participators in H-bonding. Groups containing a carbonyl (C=O) function are especially important, as these bonds are strongly polarized (δ+C=Oδ–), the C atom being electron deficient and the O atom electron excessive; this strong polarization is mainly responsible for the familiar reactivity patterns associated with carbonyl compounds. Figure 1.1 depicts the standard classification of isomers in organic chemical structures. Recall that constitutional isomers are compounds with the same molecular formula but different atom connectivity, such as 1-butanol versus 2-butanol. Stereoisomers, on the other hand, are compounds with the same formula and the same atom connectivity, differing from one another only in the three-dimensional orientation of their atoms in space. These are divided into two groups: enantiomers and diastereomers. Enantiomers are nonsuperimposable mirror image molecules whose asymmetry is usually the result of a tetrahedral carbon atom with four different atoms or groups attached to it, as in the 2-butanol enantiomers. Such chiral molecules rotate the plane of polarized light either (+) or (−) and so are said to be optically active. Achiral molecules, such as 1-butanol, do not rotate the plane of polarized light and so are optically inactive. A standard formalism for representation of a chiral center is to use bond line drawings with two of the four atoms or groups lying in the plane of the paper, a third projecting outward (wedge bond), and the fourth projecting inward (dashed bond).

PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ENZYMATIC PART OF T-PA

1987 ◽  
Author(s):  
A Heckel ◽  
K M Hasselbach
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Active Site ◽  
Serine Proteases ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Salt Bridges ◽  
Three Dimensional Structure ◽  
Insertions And Deletions

Up to now the three-dimensional structure of t-PA or parts of this enzyme is unknown. Using computer graphical methods the spatial structure of the enzymatic part of t-PA is predicted on the hypothesis, the three-dimensional backbone structure of t-PA being similar to that of other serine proteases. The t-PA model was built up in three steps:1) Alignment of the t-PA sequence with other serine proteases. Comparison of enzyme structures available from Brookhaven Protein Data Bank proved elastase as a basis for modeling.2) Exchange of amino acids of elastase differing from the t-PA sequence. The replacement of amino acids was performed such that backbone atoms overlapp completely and side chains superpose as far as possible.3) Modeling of insertions and deletions. To determine the spatial arrangement of insertions and deletions parts of related enzymes such as chymotrypsin or trypsin were used whenever possible. Otherwise additional amino acid sequences were folded to a B-turn at the surface of the proteine, where all insertions or deletions are located. Finally the side chain torsion angles of amino acids were optimised to prevent close contacts of neigh bouring atoms and to improve hydrogen bonds and salt bridges.The resulting model was used to explain binding of arginine 560 of plasminogen to the active site of t-PA. Arginine 560 interacts with Asp 189, Gly 19 3, Ser 19 5 and Ser 214 of t-PA (chymotrypsin numbering). Furthermore interaction of chromo-genic substrate S 2288 with the active site of t-PA was studied. The need for D-configuration of the hydrophobic amino acid at the N-terminus of this tripeptide derivative could be easily explained.

scholarly journals Isolation and Characterization of Mutations in theEscherichia coli Regulatory Protein XapR

1999 ◽  
Vol 181 (14) ◽  
pp. 4397-4403 ◽  
Author(s):  
Casper Jørgensen ◽  
Gert Dandanell
Keyword(s):  
Amino Acids ◽  
Purine Nucleoside Phosphorylase ◽  
Mutational Analysis ◽  
Regulatory Protein ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Wild Type ◽  
Isolation And Characterization ◽  
In The Wild

ABSTRACT In this work, the LysR-type protein XapR has been subjected to a mutational analysis. XapR regulates the expression of xanthosine phosphorylase (XapA), a purine nucleoside phosphorylase inEscherichia coli. In the wild type, full expression of XapA requires both a functional XapR protein and the inducer xanthosine. Here we show that deoxyinosine can also function as an inducer in the wild type, although not to the same extent as xanthosine. We have isolated and characterized in detail the mutants that can be induced by other nucleosides as well as xanthosine. Sequencing of the mutants has revealed that two regions in XapR are important for correct interactions between the inducer and XapR. One region is defined by amino acids 104 and 132, and the other region, containing most of the isolated mutations, is found between amino acids 203 and 210. These regions, when modelled into the three-dimensional structure of CysB from Klebsiella aerogenes, are placed close together and are most probably directly involved in binding the inducer xanthosine.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

scholarly journals Crystal structures and hydrogen bonding in the co-crystalline adducts of 3,5-dinitrobenzoic acid with 4-aminosalicylic acid and 2-hydroxy-3-(1H-indol-3-yl)propenoic acid

2014 ◽  
Vol 70 (10) ◽  
pp. 183-187 ◽  
Author(s):  
Graham Smith ◽  
Daniel E. Lynch
Keyword(s):  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Acid Group ◽  
Dimensional Structure ◽  
Aminosalicylic Acid ◽  
Amino Groups ◽  
Propenoic Acid ◽  
Unit Graph ◽  
Ring Centroid ◽  
Hydrogen Bonded

The structures of the co-crystalline adducts of 3,5-dinitrobenzoic acid (3,5-DNBA) with 4-aminosalicylic acid (PASA), the 1:1 partial hydrate, C7H4N2O6·C7H7NO3·0.2H2O, (I), and with 2-hydroxy-3-(1H-indol-3-yl)propenoic acid (HIPA), the 1:1:1d6-dimethyl sulfoxide solvate, C7H4N2O6·C11H9NO3·C2D6OS, (II), are reported. The crystal substructure of (I) comprises two centrosymmetric hydrogen-bondedR22(8) homodimers, one with 3,5-DNBA, the other with PASA, and anR22(8) 3,5-DNBA–PASA heterodimer. In the crystal, inter-unit amine N—H...O and water O—H...O hydrogen bonds generate a three-dimensional supramolecular structure. In (II), the asymmetric unit consists of the three constituent molecules, which form an essentially planar cyclic hydrogen-bonded heterotrimer unit [graph setR32(17)] through carboxyl, hydroxy and amino groups. These units associate across a crystallographic inversion centre through the HIPA carboxylic acid group in anR22(8) hydrogen-bonding association, giving a zero-dimensional structure lying parallel to (100). In both structures, π–π interactions are present [minimum ring-centroid separations = 3.6471 (18) Å in (I) and 3.5819 (10) Å in (II)].

scholarly journals Purification, Characterization, and Gene Sequence of Michiganin A, an Actagardine-Like Lantibiotic Produced by the Tomato Pathogen Clavibacter michiganensis subsp. michiganensis

2006 ◽  
Vol 72 (9) ◽  
pp. 5814-5821 ◽  
Author(s):  
I. Holtsmark ◽  
D. Mantzilas ◽  
V. G. H. Eijsink ◽  
M. B. Brurberg
Keyword(s):  
Amino Acids ◽  
Three Dimensional ◽  
Reversed Phase ◽  
Dimensional Structure ◽  
Sequence Information ◽  
Type B ◽  
Clavibacter Michiganensis ◽  
Ring Rot ◽  
A Genome ◽  
Tomato Pathogen

ABSTRACT Members of the actinomycete genus Clavibacter are known to produce antimicrobial compounds, but so far none of these compounds has been purified and characterized. We have isolated an antimicrobial peptide, michiganin A, from the tomato pathogen Clavibacter michiganensis subsp. michiganensis, using ammonium sulfate precipitation followed by cation-exchange and reversed-phase chromatography steps. Upon chemical derivatization of putative dehydrated amino acids and lanthionine bridges by alkaline ethanethiol, Edman degradation yielded sequence information that proved to be sufficient for cloning of the gene by a genome-walking strategy. The mature unmodified peptide consists of 21 amino acids, SSSGWLCTLTIECGTIICACR. All of the threonine residues undergo dehydration, and three of them interact with cysteines via thioether bonds to form methyllanthionine bridges. Michiganin A resembles actagardine, a type B lantibiotic with a known three-dimensional structure, produced by Actinoplanes liguriae, which is a filamentous actinomycete. The DNA sequence of the gene showed that the michiganin A precursor contains an unusual putative signal peptide with no similarity to well-known secretion signals and only very limited similarity to the (only two) available leader peptides of other type B lantibiotics. Michiganin A inhibits the growth of Clavibacter michiganensis subsp. sepedonicus, the causal agent of ring rot of potatoes, with MICs in the low nanomolar range. Thus, michiganin A may have some potential in biological control of potato ring rot.

scholarly journals Altered affinity of insulin-like growth factor II (IGF-II) for receptors and IGF-binding proteins, resulting from limited modifications of the IGF-II molecule

1991 ◽  
Vol 278 (1) ◽  
pp. 249-254 ◽  
Author(s):  
Y Oh ◽  
M W Beukers ◽  
H M Pham ◽  
P A Smanik ◽  
M C Smith ◽  
...  
Keyword(s):  
Amino Acids ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Type I ◽  
Type Ii ◽  
Factor Ii ◽  
N Terminus ◽  
Severe Impairment ◽  
Igf Binding ◽  
Terminal Amino

The binding affinities of seven analogues of recombinant human insulin-like growth factor II (hIGF-II) were characterized for the IGF type-I and type-II receptors and insulin receptors, as well as for IGF-binding protein (IGFBP)-1, IGFBP-2, IGFPB-3 and human serum IGFBPs. A switch of two of the three cysteine bridges in hIGF-II, 9-47 and 46-51 to 9-46 and 47-51, severely impaired the binding of this analogue to all receptors and to the IGFBPs. The affinities for the IGF type-I receptor and the IGFBPs were decreased over 100-fold, while the binding to the insulin receptor and the IGF type-II receptor was less affected, with a 6-10-fold decrease in affinity. Slight modifications of the N-terminus had only minor effects upon the binding of hIGF-II to the IGFBPs or to the receptors. Deletion of both the N-terminal amino acid and the two C-terminal amino acids resulted in moderate decreases in affinity, with a 60% decrease in affinity for IGFBP-1 and the IGF type-I receptor. Acetylation of the N-terminus of Ala1 and the epsilon-nitrogen of Lys65 decreased the affinity, by 60-90%, of hIGF-II for all of the IGFBPs and receptors. The experiments involving acetylation of IGF-II or switching of its cysteine bridges indicated that these modifications (no substitution, deletion or addition of any of the 67 amino acids of hIGF-II) may lead to a severe impairment of the binding affinity of IGF-II for both the IGFBPs and the receptors. Acetylation of the epsilon-nitrogen of Lys65, which causes a charge change, or alteration of the three-dimensional structure, as shown by the cysteine bridge switch, lead to a severe impairment of the binding affinity for the binding proteins and for the receptors. In general, care should be taken with the synthesis of analogues and the interpretation of resulting binding data, since affinity alterations ascribed to amino acid changes may instead be caused by alterations of the charge or the three-dimensional structure of the protein.

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