Metastable Hydrogen-bonds Featuring Negative Dissociation Energies in Protein-bound DNA in Hole Migration

doi:10.7503/cjcu20150651

Abstract

Abstract:

We theoretically investigated the properties of hydrogen bonds in the protein-bound DNA trimer(protona-ted arginine…guanine…cytosine, ArgH⁺-GC) units as hole migration carriers using density functional theory calculations. Results suggest these hydrogen bonds are metastable and feature considerable negative dissociation energies upon hole migration through the ArgH⁺-GC units of the carriers. Normally, the ArgH⁺ group can H-bond with the guanine-cytosine(GC) base pair in the major/minor-groove face with positive dissociation energy. However, hole trapping weakens the H-bonds to being metastable with a mild dissociation barrier and considerable negative dissociation energy. This barrier-inhibited negative dissociation energy phenomenon implies that the trimer motif can store energy(ca.108.48 kJ/mol) in its ArgH⁺…N7/O6 bond zone due to hole-trapping. This H-bond dissociation channel is governed by a balance between electrostatic repulsion and H-bonding attraction in the two associated moieties and different attenuations of two opposite interactions with respect to the H-bond distance. The topological properties of electron densities and the Laplacian values at the bond critical points clarify that this energetic phenomenon mainly originates from additional electrostatic repulsions between two moieties linked via high-energy H-bonds(ArgH⁺…N7/O6). Proton transfer from G induced by hole-trapping can expand the negative dissociation energy zone to both the ArgH⁺…N7/O6 and Watson-Crick(WC) H-bond zones. In addition, the placement of ArgH⁺ at the major/minor grooves of DNA where ArgH⁺ could interact with the GC unit increases its ionization potential, and thus weakens its hole-relaying ability in different degrees, depending on the separation between ArgH⁺ and GC. Similar phenomena can be observed in the protonated lysine-GC and protonated histidine-GC cases. Clearly, such property-tunable metastable H-bonds can regulate the hole migration mechanism. This work provides some important energetic information for understanding the protein-regulated hole migration mechanism in DNA.

Key words: Metastable hydrogen bond, Negative dissociation energy, Protein-regulated DNA hole migration, Protonated arginine residue, Hole trapping

CLC Number:

O641

TrendMD:

WANG Mei, WANG Jun, BU Yuxiang. Metastable Hydrogen-bonds Featuring Negative Dissociation Energies in Protein-bound DNA in Hole Migration[J]. Chem. J. Chinese Universities, 2015, 36(11): 2271.

Figures/Tables 11

Fig.1 Schematic diagram of positive charged arginine residues bound to guanine-cytosine base pair in the major/minor groove face

Fig.2 Optimized geometrical structures of eight complexes ArgH+-G+C-n(n=1—8) in which positive charged arginine residue resides in the major-groove face of DNA base pair

Table 1 Lengths(nm) of two hydrogen bonds(N—H…N7 H-bond and N—H…O6 H-bond) and dissociation energies(ΔE) of eight complexes ArgH+-G+C-n(n=1—8)*

Complex	R(N—H…N)	R(N—H…O)	RE	ΔE	ΔE_BSSE	DE	AIP
ArgH⁺-G⁺C-1	0.2354	0.2123	11.25	-118.95	-120.79	5.56	911.19
ArgH⁺-G⁺C-2	0.2203	0.2290	9.75	-117.45	-119.04	4.81	908.51
ArgH⁺-G⁺C-3	0.2150	0.2003	3.01	-110.67	-113.22	5.98	919.22
ArgH⁺-G⁺C-4	0.2101	0.2017	0.38	-108.07	-110.46	6.07	918.05
ArgH⁺-G⁺C-5	0.2153	0.2429	9.87	-117.53	-119.12	4.56	920.73
ArgH⁺-G⁺C-6	0.2101	0.2050	0	-111.21	-113.72	6.40	937.09
ArgH⁺-G⁺C-7	0.2104	0.2011	3.51	-107.70	-110.08	5.94	934.50
ArgH⁺-G⁺C-8	0.2117	0.2687	11.21	-118.87	-120.67	4.48	922.99

Fig.3 Schematic profiles of PES along WC and Hoogsteen H-bond dissociation coordinates of trimer complex units in their initial(ArgH+-GC) and oxidized(ArgH+-G+C) The corresponding dissociation are also shown. All the energies are expressed in kJ/mol.

Fig.4 Spin densities maps of the optimized structures of ArgH+-G+C-maj(A) and ArgH+-G(-H+)Cp (B)(isovalue=0.004)

Fig.5 Variation of electrostatic potential(ESP) surfaces of the ArgH+-GC-maj unit upon hole trapping(molecular total electron density=4×10-4 a.u.)

Fig.6 Schematic profile for the three types of interaction mode in the trimer complex ArgH+-G+C

Fig.7 Effects of R(ArgH+…O6)(the distance between ArgH+ and O6 atom) on attraction interaction between ArgH+ and GC in ArgH+-GC, and added electrostatic repulsion upon one-electron oxidation The data for this figure are given in Table S4(see the Electronic Supporting Information of this paper).

Fig.8 Potential energy surfaces of complexes XGC, X+GC(A) and their one-electron oxidized derivatives(XGC)+ and (X+GC)+(B) when the monomer X(or X+) is separated from GC and G+C, respectively En is the corresponding energy; the corresponding IPs are also shown.

Fig.9 Schematic diagram of the proton transfer process of ArgH+-G+C, and the corresponding potential-energy curves and energies

Fig.10 Schematic representation of potential energy landscapes through duplex DNA oligomers The DNA sequence is shown in Fig.S1. The “G”, “GG” and “GGG” denote an “isolated” guanine and two or three adjacent guanines, respectively. The “T” or “A” or “C” separates G or GG steps. The X-axis(“G-index”) indicates the position of guanines, GG steps, and GGG triplet along the oligomer and the energy barriers may be one base pair or some base pairs. The numbers in black and red indicate the band intensity relative to that of G24 in the protein-bound DNA duplex in the absence and presence of BamHI.

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