Rudolf H. Winger

Unexpected BII Conformer Substate Population in Unoriented Hydrated Films of the d(CGCGAATTCGCG)2 Dodecamer and of Native B-DNA from Salmon Testes

Conformational substates of B-DNA had been observed so far in synthetic oligonucleotides but not in naturally occurring highly polymeric B-DNA. Our low-temperature experiments show that native B-DNA from salmon testes and the d(CGCGAATTCGCG)2 dodecamer have the same BI and BII substates. Nonequilibrium distribution of conformer population was generated by quenching hydrated unoriented films to 200 K, and isothermal structural relaxation toward equilibrium by interconversion of substates was followed by Fourier transform infrared spectroscopy. BI interconverts into BII on isothermal relaxation at 200 K, whereas on slow cooling from ambient temperature, BII interconverts into BI. Our estimation of the dodecamers BI-to-BII conformer substate population by curve resolution of the symmetrical stretching vibration of the ionic phosphate is 2.4 +/- 0.5 to 1 at 200 K, and it is 1.3 +/- 0.5 to 1 between 270 and 290 K. Pronounced spectral changes upon BI-to-BII interconversion are consistent with base destacking coupled with migration of water from ionic phosphate toward the phosphodiester and sugar moieties. Nonspecific interaction of proteins with the DNA backbone could become specific by induced-fit-type interactions with either BI or BII backbone conformations. This suggests that the BI-to-BII substate interconversion could be a major contributor to the protein recognition process.

Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4

SummaryA large comparative study is presented in which the binding of approximately 30 different ligands to two IgE antibodies (La2 and Lb4) is analyzed by means of an automated-docking procedure based on simulated annealing. The method is able to reproduce experimentally verified binding orientations, as shown by application to the Ig-AN02-hapten complex. The main address of the study is to investigate the concept of antibody multispecificity. Problems and usefulness of docking in this context are discussed. The results indicate reasons for multispecific binding properties and how they can be understood from the topology of the binding site. Though similar in general behaviour, the two antibodies show interesting differences in their binding characteristics. The binding sites of both antibodies are described and the main interacting residues revealed.

The role of water in B-DNAs BI to BII conformer substates interconversion: a combined study by calorimetry, FT-IR spectroscopy and computer simulation

Abstract Conformational substates of B-DNA had been observed so far in synthetic oligonucleotides but not in naturally occurring highly polymeric B-DNA. Our low-temperature experiments show that native B-DNA from salmon testes and the d(CGCGAATTCGCG) 2 dodecamer have the same B I and B II substates. Nonequilibrium distribution of conformer population was generated by quenching hydrated nonoriented films or fibers into the glassy state, and isothermal structural relaxation towards equilibrium by interconversion of substates was followed either by differential scanning calorimetry or by Fourier transform infrared spectroscopy. B I converts to B II on isothermal relaxation between 180 and 220 K, whereas on slow cooling from ambient temperature, B II converts to B I . State-of-the-art molecular dynamics simulation of the d(CGCGAATTCGCG) 2 dodecamer revealed that the B I →B II transition involves not only destacking of adjacent base pairs, but is coupled with migration of water from ionic phosphate to the sugar oxygen. These results are consistent with pronounced infrared spectral changes observed upon B I →B II interconversion. The B II substate is stabilized in comparison to B I by enhanced hydrogen-bond interaction with the migrating water. Curve resolution of infrared spectra showed that in hydrated nonoriented films of the d(CGCGAATTCGCG) 2 dodecamer, the B II population is enhanced in comparison to that in single crystals. Thus, the B II substate could be of biological relevance, and the B I to B II substate interconversion could be a major contributor to the protein recognition process.

Significance of Ligand Tails for Interaction with the Minor Groove of B-DNA

Minor groove binding ligands are of great interest due to their extraordinary importance as transcription controlling drugs. We performed three molecular dynamics simulations of the unbound d(CGCGAATTCGCG)(2) dodecamer and its complexes with Hoechst33258 and Netropsin. The structural behavior of the piperazine tail of Hoechst33258, which has already been shown to be a contributor in sequence-specific recognition, was analyzed. The simulations also reveal that the tails of the ligands are able to influence the width of the minor groove. The groove width is even sensitive for conformational transitions of these tails, indicating a high adaptability of the minor groove. Furthermore, the ligands also exert an influence on the B(I)/B(II) backbone conformational substate behavior. All together these results are important for the understanding of the binding process of sequence-specific ligands.

Comparative molecular field analysis of artemisinin derivatives: Ab initio versus semiempirical optimized structures

Based on the belief that structural optimization methods, producing structures more closely to the experimental ones, should give better, i.e. more relevant, steric fields and hence more predictive CoMFA models, comparative molecular field analyses of artemisinin derivatives were performed based on semiempirical AM1 and HF/3-21G optimized geometries. Using these optimized geometries, the CoMFA results derived from the HF/3-21G method are found to be usually but not drastically better than those from AM1. Additional calculations were performed to investigate the electrostatic field difference using the Gasteiger and Marsili charges, the electrostatic potential fit charges at the AM1 level, and the natural population analysis charges at the HF/3-21G level of theory. For the HF/3-21G optimized structures no difference in predictability was observed, whereas for AM1 optimized structures such differences were found. Interestingly, if ionic compounds are omitted, differences between the various HF/3-21G optimized structure models using these electrostatic fields were found.

Heteroligation of a mouse monoclonal IgE antibody (La2) with small molecules, analysed by computer-aided automated docking

A mouse monoclonal anti-TNP IgE antibody (IgE-La2) was screened by a competitive-binding ELISA with a random pool of over 2000 small molecules, mostly drugs, drug derivatives and metabolites. Thirteen of these (naproxene, beta-carboxy-chi-naphthol, oxolinic acid, hymecromone, 8-aminoquinoline, beta-naphthylamine, chi-nitrilo-cinnamic acid, 1,5-diaminonaphthaline, prolonium iodide, diaspirin, 3,4,5-trimethoxy-cinnamic acid, cycrimine, hemimellitic acid) were found to bind as strongly, or stronger, to the antibody as the immunizing hapten. We have used a Monte Carlo search technique for simulated docking of the DNP and non-DNP ligands to a model of the Fv region of IgE(La2). The validity of structural predictions made by the AutoDock program were tested on IgG(ANO2), the three-dimensional structure of which had been obtained previously by X-ray crystallography and 2D-NMR. The rms differences between the experimentally determined and auto-docked complexes in the energetically most favored binding modes were 0.31-0.44 A. Evaluation of structures of IgE(La2)-ligand complexes [including 2,4-dinitrophenol (DNP), 16 DNP amino acids, and the 13 non-DNP ligands listed above] obtained by computer-aided automated docking, suggested the existence of two subsites within an approximately 12 x 18 A2 groove extending between the H and L CDRs. Some of the ligands (DNP-Glu, 8-aminoquinoline, prolonium-I, beta-naphthylamine) were found to bind exclusively to subsite 1, others (DNP-Ala, chi-nitrilo-cinnamic acid, hemimellitic acid, beta-carboxy-chi-naphthol) to subsite 2. The majority of DNP amino acids and other ligands (oxolinic acid, 3,4,5-trimethoxy-cinnamic acid, diaspirin, [R]-cycrimine) were found to occupy an overlapping area including subsites 1 and 2, while some of the compounds (DNP-Asn, DNP-Pro, hymecromone, 1,5-naphthylenediamine) were predicted to interact with either of these subsites with comparable probabilities. When all of the docked La2-ligand complexes were taken into account, five tyrosine residues (H33, L32, L91, L92, L96) were found to provide the majority (53.4%) of all observed contact points. Thus, a multitude of interactions with aromatic residues, and a combinatorial type of interaction within the binding region, seem to be the major factors to explain the mechanism of heteroligation by IgE(La2).

PvuII-endonuclease induces structural alterations at the scissile phosphate group of its cognate DNA.

We investigated the PvuII endonuclease with its cognate DNA by means of molecular dynamics simulations. Comparing the complexed DNA with a reference simulation of free DNA, we saw structural changes at the scissile phosphodiester bond. At this GpC step, the enzyme induces the highest twist and axial rise, inclination is increased and the minor groove widened. The distance between the scissile phosphate group and the phosphate group of the following thymine base is shortened significantly, indicating a substrate-assisted catalysis. A feasible reason for this vicinity is the catalytically important amino acid residue lysine 70, which bridges the free oxygen atoms of the successive phosphate groups. Due to this geometry, a compact reaction pocket is formed where a water molecule can be held, thus bringing the reaction partners for hydrolysis into contact. The O1-P-O2 angle of the scissile nucleotide is decreased, probably due to a complexation of the negative oxygen atoms through protein and solvent contacts.

B-DNA's dynamics and conformational substates revealed by calorimetric enthalpy relaxation and fourier transform infrared spectroscopy

Abstract The combination of calorimetric enthalpy relaxation and its recovery with isothermal FT-IR spectroscopic studies of the relaxing molecular motions is a powerful tool for investigating structure and dynamics of B-DNA. Hydrated fibers and films, with hydration level between 0.20 and 1.1 (g of water)/(g of DNA) were investigated. Isothermal relaxation of hydrated samples of the sodium salt of DNA from salmon testes in the glass→liquid transition region was compared with that of the hydrated nonoriented d(CGCGAATTCGCG) 2 dodecamer. Between 180 and 220 K, relaxation toward equilibrium occurs via interconversion of the B I to the B II , conformer substate of B-DNA. The kinetics of the effects on isothermal relaxation is described by a stretched exponential for both techniques. Relaxation times of polymeric B-DNA from salmon, testes and of the dodecamer are, for a given hydration and temperature, nearly identical and therefore, the molecular motions involved must be localized.

Estimation of the BII Conformer Substate Population in Nonoriented Hydrated B-DNA via Curve Resolution of Infrared Spectra

Hydrated films of the self-complementary B-type d(CGCGAATTCGCG)2 dodecamer, with 13 or 14 water molecules per nucleotide, were studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated samples between 290 and 260 K or, after quenching into the glassy state, as nonequilibrated films isothermally at 200 K. IR spectral changes on isothermal relaxation at 200 K revealed that difference spectra are caused by interconversion of B-DNAs conformer substates, BI converting into BII. Curve resolution of IR spectra in the spectral region containing the symmetric stretching vibration of the ionic phosphate group, with a composite band centered at 1087 cm−1 for BI and at 1109 cm−1 for BII, gives the BI/BII conformer substate population ratio and its dependence on temperature between 290 and 260 K, and on time for isothermal relaxation at 200 K. Curve resolution of the overlapping composite band profile was optimized by comparison of second-derivative and of difference curves, aiming thereby for optimal correspondence between experimental and curve-fitted bands as a criterion for goodness-of-fit. The spectroscopic aspects relevant for reliable curve resolution of the overlapping composite band profile are reported and discussed in detail.

Prediction of IgE(Lb4)–ligand complex structures by automated docking

A mouse monoclonal anti‐2,4,6‐trinitrophenyl IgE (clone Lb4) was screened with a random set of over 2000 compounds, and several ligands were found to bind with affinities comparable to that of the immunizing hapten (KD in the μM range). An automated docking algorithm was used for the prediction of complex structures formed by 2,4‐dinitrophenyl (DNP) and non‐DNP ligands in the fragment variable region of IgE(Lb4). All ligands were found to dock in an L‐shaped cavity of 15 × 16 × 10 Å, surrounded by complementary‐determining regions L1, L3, H2 and H3. The ligands were found to occupy the same binding site in different orientations. For rigid ligands the most stable orientation could be predicted with high probability, based on the calculated energy of binding and the occurrence frequencies of identical complexes obtained by repeated simulations. The localization of a flexible ligand (cycrimine‐R) was more ambiguous, but it still docked in the same site. The results support a model for heteroligating antibody (Ab) binding sites, where different ligands utilize the total set of available contacts in different combinations. It is suggested that although pseudoenergies calculated by the docking algorithm do not correlate with experimentally measured binding energies, the screening‐and‐docking procedure can be useful for the mapping of Ab and other receptor binding sites ligating small molecules.