Three-center (bifurcated) hydrogen bonding in the crystal structures of amino acids

Jeffrey, G. A.; Mitra, J.

doi:10.1021/ja00331a025

Cited by 90 publications

(44 citation statements)

References 1 publication

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“…Only linear (two-center) hydrogen bonds were found for the NH> group in the crystal structure of DGSe(IV), similar to MGSe(IV) (4). In contrast to some related compounds of glycine (6)(7)(8), no bifurcated (three-center) hydrogen bond was found.…”

Section: The Crystal Structure Of Dgse(iv)contrasting

confidence: 79%

Study of the Family of Glycine–Selenious Acid Addition Compounds: Crystal Structure of Diglycine Hydrogen Selenite and Vibrational Spectra and DSC Measurement of Diglycine Hydrogen Selenite and Monoglycine–Selenious Acid Crystals

Němec

Cı́sařová

Mička

1998

Journal of Solid State Chemistry

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Section: The Crystal Structure Of Dgse(iv)contrasting

confidence: 79%

Study of the Family of Glycine–Selenious Acid Addition Compounds: Crystal Structure of Diglycine Hydrogen Selenite and Vibrational Spectra and DSC Measurement of Diglycine Hydrogen Selenite and Monoglycine–Selenious Acid Crystals

Němec

Cı́sařová

Mička

1998

Journal of Solid State Chemistry

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“…ab initio calculations (Kistenmacher et al, 1973), by searches of the structures of amino acids (Jeffrey and Mitra, 1984), and by experimental studies of the rotation of the ammonium ion in aqueous solution (Perrin and Gipe, 1986). The existence of two more interactions of the solvent molecule with the other Guan § group is noteworthy (see, e.g., O1~ of Structure I, in Fig.…”

Section: Calculationsmentioning

confidence: 99%

Contribution of unusual Arginine-Arginine short-range interactions to stabilization and recognition in proteins

et al. 1994

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Although the majority of the ion pairs found in proteins consists of two charges of opposite sign, the observation of some unusual arrangements of two arginines led us to a search of such occurrences in the Brookhaven Protein Data Bank. We have found 41 Arginine-Arginine interactions with a C zeta ... C zeta distance less than 5 A. Computer graphics analysis of these structures shows that most of the Arg-Arg pairs are found in the vicinity of the surface of the proteins, in an easily hydrated region. In order to determine which factors could stabilize such arrangements of species of similar charge, we have carried out AM1 semi-empirical calculations on a model of two guanidinium ions surrounded by several water molecules. The results show the existence of stable clusters with six or more water molecules, with distances between C zeta atoms around 3 A. The bridging role of the water molecules is an important structural and energetic feature and we find bridges of two and three molecules between the guanidinium ions. These results are in good agreement with the structures found in our search of the experimental data. Enhancement of the electrostatic potential around these clusters, when compared to one of the guanidinium ions alone, is also demonstrated.

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“…2a. The drug molecule displaces the spine, and each of its three amide NH groups forms a bifurcated or three-center hydrogen bond (20,21) between adjacent adenine N-3 or thymine 0-2 atoms, bridging the same groups as in the first shell water molecules of the spine (Fig. 3).…”

mentioning

confidence: 99%

The molecular origin of DNA-drug specificity in netropsin and distamycin.

Kopka¹,

Yoon²,

Goodsell³

et al. 1985

Proc. Natl. Acad. Sci. U.S.A.

800

577

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X-ray analysis of the complex of netropsin with the B-DNA dodecamer of sequence C-G-C-G-A-A-T-TBrC-G-C-G reveals that the antitumor antibiotic binds within the minor groove by displacing the water molecules of the spine of hydration. Netropsin amide NH furnish hydrogen bonds to bridge DNA adenine N-3 and thymine 0-2 atoms occurring on adjacent base pairs and opposite helix strands, exactly as with the spine of hydration. The narrowness of the groove forces the netropsin molecule to sit symmetrically in the center, with its two pyrrole rings slightly non-coplanar so that each ring is parallel to the walls of its respective region of the groove. Drug binding neither unwinds nor elongates the double helix, but it does force open the minor groove by 0.5-2.0 A, and it bends back the helix axis by 8°across the region of attachment. The netropsin molecule has an intrinsic twist that favors insertion into the minor groove of B-DNA, and it is given a small additional twist upon binding. The base specificity that makes netropsin bind preferentially to runs of four or more ACT base pairs is provided not by hydrogen bonding but by close van der Waals contacts between adenine C-2 hydrogens and CH groups on the pyrrole rings of the drug molecule. Substitution of one or more pyrroles by imidazole could permit recognition of G'C base pairs as well, and it could lead to a class of synthetic "lexitropsins," capable of reading any desired short sequence of DNA base pairs.Netropsin and its close relative distamycin ( Fig. 1) are antiviral antitumor antibiotics that, although too toxic for clinical use, have received extensive study as the paradigms of base-specific yet non-intercalative DNA-binding drug molecules. First isolated from Streptomyces netropsis in 1951 (1, 2), netropsin exerts its biological activity by binding tightly to double-helical B-DNA, interfering with both replication and transcription (3, 4). It shows little or no affinity for single-stranded DNA or RNA or for double-stranded RNA or DNA-RNA hybrids (3-5), suggesting that it does not bind to the A helix. It also fails to bind to left-handed Z-DNA; in fact, binding of netropsin to DNA favors A-to-B and Z-to-B helix transitions (6, 7).Chemical protection studies (3,4,8) and Overhauser NMR experiments (9) indicate that netropsin does not intercalate between base pairs, but it binds within the minor groove of the intact double helix, using hydrogen bonds between netropsin amide NH and exposed adenine N-3 and thymine 0-2 on the floor of the minor groove. The drug molecule attaches to clusters of four or more A'T or ITC, but not to G-C, base pairs (3, 10, 11). Alternating A-T-A-T regions bind netropsin less well than continuous runs of A or T (12, 13). Binding involves both an electrostatic component from the two cationic ends and hydrogen bonds from the central three amide NH groups, although neither aspect is absolute- FIG. 1. The netropsin molecule can be regarded as being assembled from (left to right): guanidinium, amide, methylpyrrole, amide, methylpyrr...

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Three-center (bifurcated) hydrogen bonding in the crystal structures of amino acids

Cited by 90 publications

References 1 publication

Study of the Family of Glycine–Selenious Acid Addition Compounds: Crystal Structure of Diglycine Hydrogen Selenite and Vibrational Spectra and DSC Measurement of Diglycine Hydrogen Selenite and Monoglycine–Selenious Acid Crystals

Study of the Family of Glycine–Selenious Acid Addition Compounds: Crystal Structure of Diglycine Hydrogen Selenite and Vibrational Spectra and DSC Measurement of Diglycine Hydrogen Selenite and Monoglycine–Selenious Acid Crystals

Contribution of unusual Arginine-Arginine short-range interactions to stabilization and recognition in proteins

The molecular origin of DNA-drug specificity in netropsin and distamycin.

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