Bernd Van Buuren | Radbouduniversity Nijmegen Netherlands (original) (raw)

Papers by Bernd Van Buuren

Molecules

Dengue is an important arboviral infectious disease for which there is currently no specific cure... more Dengue is an important arboviral infectious disease for which there is currently no specific cure. We report gemini-like (geminoid) alkylated amphiphilic peptides containing lysines in combination with glycines or alanines (C15H31C(O)-Lys-(Gly or Ala)nLys-NHC16H33, shorthand notation C16-KXnK-C16 with X = A or G, and n = 0–2). The representatives with 1 or 2 Ala inhibit dengue protease and human furin, two serine proteases involved in dengue virus infection that have peptides with cationic amino acids as their preferred substrates, with IC50 values in the lower µM range. The geminoid C16-KAK-C16 combined inhibition of DENV2 protease (IC50 2.3 µM) with efficacy against replication of wildtype DENV2 in LLC-MK2 cells (EC50 4.1 µM) and an absence of toxicity. We conclude that the lysine-based geminoids have activity against dengue virus infection, which is based on their inhibition of the proteases involved in viral replication and are therefore promising leads to further developing ant...

Angewandte Chemie International Edition, 2004

(SW), the DFG (GR1211/2-4, En111/11-3) (C.G., H.S.), the Karl Winnacker foundation (H.S.), and th... more (SW), the DFG (GR1211/2-4, En111/11-3) (C.G., H.S.), the Karl Winnacker foundation (H.S.), and the European LSF for Biomolecular NMR (ER-BCT950034). We thank Janny Hof for critical reading of the manuscript. Supporting information for this article is available on the WWW under http://www.angewandte.org or from the author. Included are the fit results, the original J CH values as a function of magnetic field, and the derived mRDCs.

Current Nutrition &# 38; …, 2008

... The released ferrous iron enters the iron pool and follows the same storage and export route ... more ... The released ferrous iron enters the iron pool and follows the same storage and export route described for the non-heme iron. ... 1 Miret et al. ... Inhibitors of iron absorption form precipitates or stable complexes, with binding constants much higher than that corresponding to DMT1. ...

Journal of Chemical Information and Modeling, Nov 1, 2006

We have applied the k-nearest neighbor (kNN) modeling technique to the prediction of melting poin... more We have applied the k-nearest neighbor (kNN) modeling technique to the prediction of melting points. A data set of 4119 diverse organic molecules (data set 1) and an additional set of 277 drugs (data set 2) were used to compare performance in different regions of chemical space, and we investigated the influence of the number of nearest neighbors using different types of molecular descriptors. To compute the prediction on the basis of the melting temperatures of the nearest neighbors, we used four different methods (arithmetic and geometric average, inverse distance weighting, and exponential weighting), of which the exponential weighting scheme yielded the best results. We assessed our model via a 25-fold Monte Carlo cross-validation (with approximately 30% of the total data as a test set) and optimized it using a genetic algorithm. Predictions for drugs based on drugs (separate training and test sets each taken from data set 2) were found to be considerably better [root-mean-squared error (RMSE) ) 46.3°C, r 2 ) 0.30] than those based on nondrugs (prediction of data set 2 based on the training set from data set 1, RMSE ) 50.3°C, r 2 ) 0.20). The optimized model yields an average RMSE as low as 46.2°C (r 2 ) 0.49) for data set 1, and an average RMSE of 42.2°C (r 2 ) 0.42) for data set 2. It is shown that the kNN method inherently introduces a systematic error in melting point prediction. Much of the remaining error can be attributed to the lack of information about interactions in the liquid state, which are not well-captured by molecular descriptors.

Angewandte Chemie International Edition, 2004

Branched nucleic acids play important biological roles, and well-known examples such as the Hamme... more Branched nucleic acids play important biological roles, and well-known examples such as the Hammerhead ribozyme, the all-RNA enzyme, a three-way junction (3H according to IUPAC nomenclature [1a] ), and the Holliday junctions [1b] or DNA four-way junctions (J6, a; 4H according to IUPAC nomenclature [1a] ) have recently been reviewed. [2a-c] The Holliday junctions form the central intermediates in both homologous and site-specific recombination. In solution, in the presence of multivalent ions and thus under physiological salt conditions, their structure consists of two quasi-continuously stacked helices in an essentially canonical conformation . [2b,c] Four recent crystal structures of 4H [2d-g] confirm these structural features, but no coherence is observed in the value of the interhelix angle y (defined in ; three structures show right-handed interhelix

Nucleic Acids Research, 2004

Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. The... more Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. They consist of three double helical arms (A to C), connected at the junction point, with or without a number of unpaired bases in one or more of the three different strands. Three-way junctions with two unpaired bases in one strand (3HS 2 ) have a high tendency to adopt either of two alternative stacked conformations in which two of the three arms A, B and C are coaxially stacked, i.e. A/B-stacked or A/C-stacked. Empirical stacking rules, which successfully predict for DNA 3HS 2 A/B-stacking preference from sequence, have been extended to A/C-stacked conformations. Three novel DNA 3HS 2 sequences were designed to test the validity of these extended stacking rules and their conformational behavior was studied by solution NMR. All three show the predicted A/C-stacking preference even in the absence of multivalent cations. The stacking preference for both classes of DNA 3HS 2 can thus be predicted from sequence. The high-resolution NMR solution structure for one of the stacked 3HS 2 is also reported. It shows a welldefined local and global structure defined by an extensive set of classical NMR restraints and residual dipolar couplings. Analysis of its global conformation and that of other representatives of the 3H family, shows that the relative orientations of the stacked and non-stacked arms, are restricted to narrow regions of conformational space, which can be understood from geometric considerations. Together, these findings open up the possibility of full prediction of 3HS 2 conformation (stacking and global fold) directly from sequence.

Nucleic Acids Research, 2002

Under the influence of multivalent cations these molecules undergo a conformational change, from ... more Under the influence of multivalent cations these molecules undergo a conformational change, from an extended planar form to a quasi-continuous stacked X-structure. Recently, a number of X-ray structures and a nuclear magnetic resonance (NMR) structure of 4Hs have been reported and in three of these the position of multivalent cations is revealed. These structures belong to two main families, characterized by the angle between the two co-axial stacked helices, which is either around +40 to +55° or around -70 to -80°. To investigate the role of metal-ion binding on the conformation of folded 4Hs we performed Brownian-dynamics simulations on the set of available structures. The simulations confirm the proposed metal-ion binding sites in the NMR structure and in one of the X-ray structures. Furthermore, the calculations suggest positions for metal-ion binding in the other X-ray structures. The results show a striking dependence of the ion density on the helical environment (B-helix or A-helix) and the structural family.

Methods in Enzymology, 2002

ASSIGNMENT AND STRUCTURE DERIVATION FOR RNA 371 (during which the initial WPM alternates), so tha... more ASSIGNMENT AND STRUCTURE DERIVATION FOR RNA 371 (during which the initial WPM alternates), so that any NOE from the isochronous protons cancels out. Another advantage of sequence (f) is that the zero initial magnetization of the other protons helps in avoiding artifacts, arising for instance from imperfect signal, cancellation over the phase cycle. This is particularly useful for measurements with short mixing times, e.g., 5 ms in the case of proton exchange (J. L. Leroy, in preparation). In fact, a useful test of any sequence involving a mixing time is the examination of artifacts in the case of zero mixing time, for which the ideal result is strictly null.

Progress in Nuclear Magnetic Resonance Spectroscopy, 1998

Nucleic Acids Research, 2004

Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. The... more Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. They consist of three double helical arms (A to C), connected at the junction point, with or without a number of unpaired bases in one or more of the three different strands. Three-way junctions with two unpaired bases in one strand (3HS 2 ) have a high tendency to adopt either of two alternative stacked conformations in which two of the three arms A, B and C are coaxially stacked, i.e. A/B-stacked or A/C-stacked. Empirical stacking rules, which successfully predict for DNA 3HS 2 A/B-stacking preference from sequence, have been extended to A/C-stacked conformations. Three novel DNA 3HS 2 sequences were designed to test the validity of these extended stacking rules and their conformational behavior was studied by solution NMR. All three show the predicted A/C-stacking preference even in the absence of multivalent cations. The stacking preference for both classes of DNA 3HS 2 can thus be predicted from sequence. The high-resolution NMR solution structure for one of the stacked 3HS 2 is also reported. It shows a welldefined local and global structure defined by an extensive set of classical NMR restraints and residual dipolar couplings. Analysis of its global conformation and that of other representatives of the 3H family, shows that the relative orientations of the stacked and non-stacked arms, are restricted to narrow regions of conformational space, which can be understood from geometric considerations. Together, these findings open up the possibility of full prediction of 3HS 2 conformation (stacking and global fold) directly from sequence.

Journal of Structural and Functional Genomics, 2000

Structural genomics, the determination of protein structures on a genome-wide scale, is still in ... more Structural genomics, the determination of protein structures on a genome-wide scale, is still in its infancy for eukaryotes due to the number and size of their genes. Low protein expression and solubility of eukaryotic geneproducts are the major bottlenecks in high-throughput (HTP) recombinant protein production with the E. coli expression systems. To circumvent this problem we decided to focus on separate protein domains. We describe here a fast microtiterplate based, expression and solubility screening procedure, using a combination of in vitro and in vivo expression, and purification with nickel-NTA magnetic beads. All steps are optimized for automatic HTP processing using a liquid handling station. Furthermore, large-scale expression and protein purification conditions are optimized, permitting the purification of 24 protein samples per week. We further show that results obtained from the expression screening can be extrapolated to the production of protein samples for NMR. Starting with 81 cloned human protein domains, in vivo expression was detected in 54 cases, and from 28 of those milligrams of protein were purified. An informative HSQC spectrum was recorded for 18 proteins (22%), half of which were indicative of a folded protein. The success rate and quality of the HSQC spectra suggest that the domain approach holds promise for human proteins.

Journal of Molecular Biology, 2000

The solution structure of a DNA three-way junction (3H) containing two unpaired thymidine bases a... more The solution structure of a DNA three-way junction (3H) containing two unpaired thymidine bases at the branch site (3HT2), was determined by NMR. Arms A and B of the 3HT2 form a quasi-continuous stacked helix, which is underwound at the junction and has an increased helical rise. The unstacked arm C forms an acute angle of approximately 55 degrees with the unique arm A. The stacking of the unpaired thymidine bases on arm C resembles the folding of hairpin loops. From this data, combined with the reported stacking behavior of 23 other 3HS2 s, two rules are derived that together correctly reproduce their stacking preference. These rules predict, from the sequence of any 3HS2, its stacking preference. The structure also suggests a plausible mechanism for structure-specific recognition of branched nucleic acids by proteins.

Journal of Chemical Information and Modeling, 2006

We have applied the k-nearest neighbor (kNN) modeling technique to the prediction of melting poin... more We have applied the k-nearest neighbor (kNN) modeling technique to the prediction of melting points. A data set of 4119 diverse organic molecules (data set 1) and an additional set of 277 drugs (data set 2) were used to compare performance in different regions of chemical space, and we investigated the influence of the number of nearest neighbors using different types of molecular descriptors. To compute the prediction on the basis of the melting temperatures of the nearest neighbors, we used four different methods (arithmetic and geometric average, inverse distance weighting, and exponential weighting), of which the exponential weighting scheme yielded the best results. We assessed our model via a 25-fold Monte Carlo cross-validation (with approximately 30% of the total data as a test set) and optimized it using a genetic algorithm. Predictions for drugs based on drugs (separate training and test sets each taken from data set 2) were found to be considerably better [root-mean-squared error (RMSE) ) 46.3°C, r 2 ) 0.30] than those based on nondrugs (prediction of data set 2 based on the training set from data set 1, RMSE ) 50.3°C, r 2 ) 0.20). The optimized model yields an average RMSE as low as 46.2°C (r 2 ) 0.49) for data set 1, and an average RMSE of 42.2°C (r 2 ) 0.42) for data set 2. It is shown that the kNN method inherently introduces a systematic error in melting point prediction. Much of the remaining error can be attributed to the lack of information about interactions in the liquid state, which are not well-captured by molecular descriptors.

Journal of Biomolecular Structure and Dynamics, 2000

Abstract The stacking preference of a DNA Four-Way junction (4H), with a novel junction sequence,... more Abstract The stacking preference of a DNA Four-Way junction (4H), with a novel junction sequence, has been determined in the presence of magnesium ions as well as in the presence of cobalt(III)hexammine ions by means of NMR spectroscopy. In both cases this 4H has a strong preference (>80%) to fold in an A/D-stacked conformer. NOESY spectra showed intermolecular NOE contacts between 4H protons and the ammine protons of the cobalt(III)hexammine complex. These contacts define the metal-ion binding site, located in the vicinity of the junction. The position is similar to the observed site in a recent X-ray structure of a RNA/DNA hybrid 4H and consistent with the position deduced from an uranyl ion photoprobing study on 4Hs with different sequences.

Amino Acids, 2005

Isoprostanes, non-enzymatic peroxidation products of arachidonic acid, are attractive biomarkers ... more Isoprostanes, non-enzymatic peroxidation products of arachidonic acid, are attractive biomarkers of oxidative stress in research in biology, medicine and nutrition. For the appropriate use of biomarkers it is required that these are both biologically and technically valid. Whereas the biological validity of isoprostanes is well-established, it is technically quite complicated to measure isoprostanes and its metabolites in body fluids, and its rapid disappearance from plasma may hamper practical application. This paper shortly introduces isoprostanes as a biomarker for studies with humans, describes a novel fast and sensitive method for measuring isoprostanes in plasma by high-performance liquid chromatography and tandem mass spectrometry, and provides several examples of the use of the method in studies in humans. By taking care of the biological and technical validity of this biomarker it is possible to establish the antioxidant effects of some food ingredients in studies with human volunteers.

Angewandte Chemie International Edition, 2004

Branched nucleic acids play important biological roles, and well-known examples such as the Hamme... more Branched nucleic acids play important biological roles, and well-known examples such as the Hammerhead ribozyme, the all-RNA enzyme, a three-way junction (3H according to IUPAC nomenclature [1a] ), and the Holliday junctions [1b] or DNA four-way junctions (J6, a; 4H according to IUPAC nomenclature [1a] ) have recently been reviewed. [2a-c] The Holliday junctions form the central intermediates in both homologous and site-specific recombination. In solution, in the presence of multivalent ions and thus under physiological salt conditions, their structure consists of two quasi-continuously stacked helices in an essentially canonical conformation . [2b,c] Four recent crystal structures of 4H [2d-g] confirm these structural features, but no coherence is observed in the value of the interhelix angle y (defined in ; three structures show right-handed interhelix

Molecules

Dengue is an important arboviral infectious disease for which there is currently no specific cure... more Dengue is an important arboviral infectious disease for which there is currently no specific cure. We report gemini-like (geminoid) alkylated amphiphilic peptides containing lysines in combination with glycines or alanines (C15H31C(O)-Lys-(Gly or Ala)nLys-NHC16H33, shorthand notation C16-KXnK-C16 with X = A or G, and n = 0–2). The representatives with 1 or 2 Ala inhibit dengue protease and human furin, two serine proteases involved in dengue virus infection that have peptides with cationic amino acids as their preferred substrates, with IC50 values in the lower µM range. The geminoid C16-KAK-C16 combined inhibition of DENV2 protease (IC50 2.3 µM) with efficacy against replication of wildtype DENV2 in LLC-MK2 cells (EC50 4.1 µM) and an absence of toxicity. We conclude that the lysine-based geminoids have activity against dengue virus infection, which is based on their inhibition of the proteases involved in viral replication and are therefore promising leads to further developing ant...

Angewandte Chemie International Edition, 2004

(SW), the DFG (GR1211/2-4, En111/11-3) (C.G., H.S.), the Karl Winnacker foundation (H.S.), and th... more (SW), the DFG (GR1211/2-4, En111/11-3) (C.G., H.S.), the Karl Winnacker foundation (H.S.), and the European LSF for Biomolecular NMR (ER-BCT950034). We thank Janny Hof for critical reading of the manuscript. Supporting information for this article is available on the WWW under http://www.angewandte.org or from the author. Included are the fit results, the original J CH values as a function of magnetic field, and the derived mRDCs.

Current Nutrition &# 38; …, 2008

... The released ferrous iron enters the iron pool and follows the same storage and export route ... more ... The released ferrous iron enters the iron pool and follows the same storage and export route described for the non-heme iron. ... 1 Miret et al. ... Inhibitors of iron absorption form precipitates or stable complexes, with binding constants much higher than that corresponding to DMT1. ...

Journal of Chemical Information and Modeling, Nov 1, 2006

We have applied the k-nearest neighbor (kNN) modeling technique to the prediction of melting poin... more We have applied the k-nearest neighbor (kNN) modeling technique to the prediction of melting points. A data set of 4119 diverse organic molecules (data set 1) and an additional set of 277 drugs (data set 2) were used to compare performance in different regions of chemical space, and we investigated the influence of the number of nearest neighbors using different types of molecular descriptors. To compute the prediction on the basis of the melting temperatures of the nearest neighbors, we used four different methods (arithmetic and geometric average, inverse distance weighting, and exponential weighting), of which the exponential weighting scheme yielded the best results. We assessed our model via a 25-fold Monte Carlo cross-validation (with approximately 30% of the total data as a test set) and optimized it using a genetic algorithm. Predictions for drugs based on drugs (separate training and test sets each taken from data set 2) were found to be considerably better [root-mean-squared error (RMSE) ) 46.3°C, r 2 ) 0.30] than those based on nondrugs (prediction of data set 2 based on the training set from data set 1, RMSE ) 50.3°C, r 2 ) 0.20). The optimized model yields an average RMSE as low as 46.2°C (r 2 ) 0.49) for data set 1, and an average RMSE of 42.2°C (r 2 ) 0.42) for data set 2. It is shown that the kNN method inherently introduces a systematic error in melting point prediction. Much of the remaining error can be attributed to the lack of information about interactions in the liquid state, which are not well-captured by molecular descriptors.

Angewandte Chemie International Edition, 2004

Branched nucleic acids play important biological roles, and well-known examples such as the Hamme... more Branched nucleic acids play important biological roles, and well-known examples such as the Hammerhead ribozyme, the all-RNA enzyme, a three-way junction (3H according to IUPAC nomenclature [1a] ), and the Holliday junctions [1b] or DNA four-way junctions (J6, a; 4H according to IUPAC nomenclature [1a] ) have recently been reviewed. [2a-c] The Holliday junctions form the central intermediates in both homologous and site-specific recombination. In solution, in the presence of multivalent ions and thus under physiological salt conditions, their structure consists of two quasi-continuously stacked helices in an essentially canonical conformation . [2b,c] Four recent crystal structures of 4H [2d-g] confirm these structural features, but no coherence is observed in the value of the interhelix angle y (defined in ; three structures show right-handed interhelix

Nucleic Acids Research, 2004

Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. The... more Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. They consist of three double helical arms (A to C), connected at the junction point, with or without a number of unpaired bases in one or more of the three different strands. Three-way junctions with two unpaired bases in one strand (3HS 2 ) have a high tendency to adopt either of two alternative stacked conformations in which two of the three arms A, B and C are coaxially stacked, i.e. A/B-stacked or A/C-stacked. Empirical stacking rules, which successfully predict for DNA 3HS 2 A/B-stacking preference from sequence, have been extended to A/C-stacked conformations. Three novel DNA 3HS 2 sequences were designed to test the validity of these extended stacking rules and their conformational behavior was studied by solution NMR. All three show the predicted A/C-stacking preference even in the absence of multivalent cations. The stacking preference for both classes of DNA 3HS 2 can thus be predicted from sequence. The high-resolution NMR solution structure for one of the stacked 3HS 2 is also reported. It shows a welldefined local and global structure defined by an extensive set of classical NMR restraints and residual dipolar couplings. Analysis of its global conformation and that of other representatives of the 3H family, shows that the relative orientations of the stacked and non-stacked arms, are restricted to narrow regions of conformational space, which can be understood from geometric considerations. Together, these findings open up the possibility of full prediction of 3HS 2 conformation (stacking and global fold) directly from sequence.

Nucleic Acids Research, 2002

Under the influence of multivalent cations these molecules undergo a conformational change, from ... more Under the influence of multivalent cations these molecules undergo a conformational change, from an extended planar form to a quasi-continuous stacked X-structure. Recently, a number of X-ray structures and a nuclear magnetic resonance (NMR) structure of 4Hs have been reported and in three of these the position of multivalent cations is revealed. These structures belong to two main families, characterized by the angle between the two co-axial stacked helices, which is either around +40 to +55° or around -70 to -80°. To investigate the role of metal-ion binding on the conformation of folded 4Hs we performed Brownian-dynamics simulations on the set of available structures. The simulations confirm the proposed metal-ion binding sites in the NMR structure and in one of the X-ray structures. Furthermore, the calculations suggest positions for metal-ion binding in the other X-ray structures. The results show a striking dependence of the ion density on the helical environment (B-helix or A-helix) and the structural family.

Methods in Enzymology, 2002

ASSIGNMENT AND STRUCTURE DERIVATION FOR RNA 371 (during which the initial WPM alternates), so tha... more ASSIGNMENT AND STRUCTURE DERIVATION FOR RNA 371 (during which the initial WPM alternates), so that any NOE from the isochronous protons cancels out. Another advantage of sequence (f) is that the zero initial magnetization of the other protons helps in avoiding artifacts, arising for instance from imperfect signal, cancellation over the phase cycle. This is particularly useful for measurements with short mixing times, e.g., 5 ms in the case of proton exchange (J. L. Leroy, in preparation). In fact, a useful test of any sequence involving a mixing time is the examination of artifacts in the case of zero mixing time, for which the ideal result is strictly null.

Progress in Nuclear Magnetic Resonance Spectroscopy, 1998

Nucleic Acids Research, 2004

Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. The... more Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. They consist of three double helical arms (A to C), connected at the junction point, with or without a number of unpaired bases in one or more of the three different strands. Three-way junctions with two unpaired bases in one strand (3HS 2 ) have a high tendency to adopt either of two alternative stacked conformations in which two of the three arms A, B and C are coaxially stacked, i.e. A/B-stacked or A/C-stacked. Empirical stacking rules, which successfully predict for DNA 3HS 2 A/B-stacking preference from sequence, have been extended to A/C-stacked conformations. Three novel DNA 3HS 2 sequences were designed to test the validity of these extended stacking rules and their conformational behavior was studied by solution NMR. All three show the predicted A/C-stacking preference even in the absence of multivalent cations. The stacking preference for both classes of DNA 3HS 2 can thus be predicted from sequence. The high-resolution NMR solution structure for one of the stacked 3HS 2 is also reported. It shows a welldefined local and global structure defined by an extensive set of classical NMR restraints and residual dipolar couplings. Analysis of its global conformation and that of other representatives of the 3H family, shows that the relative orientations of the stacked and non-stacked arms, are restricted to narrow regions of conformational space, which can be understood from geometric considerations. Together, these findings open up the possibility of full prediction of 3HS 2 conformation (stacking and global fold) directly from sequence.

Journal of Structural and Functional Genomics, 2000

Structural genomics, the determination of protein structures on a genome-wide scale, is still in ... more Structural genomics, the determination of protein structures on a genome-wide scale, is still in its infancy for eukaryotes due to the number and size of their genes. Low protein expression and solubility of eukaryotic geneproducts are the major bottlenecks in high-throughput (HTP) recombinant protein production with the E. coli expression systems. To circumvent this problem we decided to focus on separate protein domains. We describe here a fast microtiterplate based, expression and solubility screening procedure, using a combination of in vitro and in vivo expression, and purification with nickel-NTA magnetic beads. All steps are optimized for automatic HTP processing using a liquid handling station. Furthermore, large-scale expression and protein purification conditions are optimized, permitting the purification of 24 protein samples per week. We further show that results obtained from the expression screening can be extrapolated to the production of protein samples for NMR. Starting with 81 cloned human protein domains, in vivo expression was detected in 54 cases, and from 28 of those milligrams of protein were purified. An informative HSQC spectrum was recorded for 18 proteins (22%), half of which were indicative of a folded protein. The success rate and quality of the HSQC spectra suggest that the domain approach holds promise for human proteins.

Journal of Molecular Biology, 2000

The solution structure of a DNA three-way junction (3H) containing two unpaired thymidine bases a... more The solution structure of a DNA three-way junction (3H) containing two unpaired thymidine bases at the branch site (3HT2), was determined by NMR. Arms A and B of the 3HT2 form a quasi-continuous stacked helix, which is underwound at the junction and has an increased helical rise. The unstacked arm C forms an acute angle of approximately 55 degrees with the unique arm A. The stacking of the unpaired thymidine bases on arm C resembles the folding of hairpin loops. From this data, combined with the reported stacking behavior of 23 other 3HS2 s, two rules are derived that together correctly reproduce their stacking preference. These rules predict, from the sequence of any 3HS2, its stacking preference. The structure also suggests a plausible mechanism for structure-specific recognition of branched nucleic acids by proteins.

Journal of Chemical Information and Modeling, 2006

We have applied the k-nearest neighbor (kNN) modeling technique to the prediction of melting poin... more We have applied the k-nearest neighbor (kNN) modeling technique to the prediction of melting points. A data set of 4119 diverse organic molecules (data set 1) and an additional set of 277 drugs (data set 2) were used to compare performance in different regions of chemical space, and we investigated the influence of the number of nearest neighbors using different types of molecular descriptors. To compute the prediction on the basis of the melting temperatures of the nearest neighbors, we used four different methods (arithmetic and geometric average, inverse distance weighting, and exponential weighting), of which the exponential weighting scheme yielded the best results. We assessed our model via a 25-fold Monte Carlo cross-validation (with approximately 30% of the total data as a test set) and optimized it using a genetic algorithm. Predictions for drugs based on drugs (separate training and test sets each taken from data set 2) were found to be considerably better [root-mean-squared error (RMSE) ) 46.3°C, r 2 ) 0.30] than those based on nondrugs (prediction of data set 2 based on the training set from data set 1, RMSE ) 50.3°C, r 2 ) 0.20). The optimized model yields an average RMSE as low as 46.2°C (r 2 ) 0.49) for data set 1, and an average RMSE of 42.2°C (r 2 ) 0.42) for data set 2. It is shown that the kNN method inherently introduces a systematic error in melting point prediction. Much of the remaining error can be attributed to the lack of information about interactions in the liquid state, which are not well-captured by molecular descriptors.

Journal of Biomolecular Structure and Dynamics, 2000

Abstract The stacking preference of a DNA Four-Way junction (4H), with a novel junction sequence,... more Abstract The stacking preference of a DNA Four-Way junction (4H), with a novel junction sequence, has been determined in the presence of magnesium ions as well as in the presence of cobalt(III)hexammine ions by means of NMR spectroscopy. In both cases this 4H has a strong preference (>80%) to fold in an A/D-stacked conformer. NOESY spectra showed intermolecular NOE contacts between 4H protons and the ammine protons of the cobalt(III)hexammine complex. These contacts define the metal-ion binding site, located in the vicinity of the junction. The position is similar to the observed site in a recent X-ray structure of a RNA/DNA hybrid 4H and consistent with the position deduced from an uranyl ion photoprobing study on 4Hs with different sequences.

Amino Acids, 2005

Isoprostanes, non-enzymatic peroxidation products of arachidonic acid, are attractive biomarkers ... more Isoprostanes, non-enzymatic peroxidation products of arachidonic acid, are attractive biomarkers of oxidative stress in research in biology, medicine and nutrition. For the appropriate use of biomarkers it is required that these are both biologically and technically valid. Whereas the biological validity of isoprostanes is well-established, it is technically quite complicated to measure isoprostanes and its metabolites in body fluids, and its rapid disappearance from plasma may hamper practical application. This paper shortly introduces isoprostanes as a biomarker for studies with humans, describes a novel fast and sensitive method for measuring isoprostanes in plasma by high-performance liquid chromatography and tandem mass spectrometry, and provides several examples of the use of the method in studies in humans. By taking care of the biological and technical validity of this biomarker it is possible to establish the antioxidant effects of some food ingredients in studies with human volunteers.

Angewandte Chemie International Edition, 2004

Branched nucleic acids play important biological roles, and well-known examples such as the Hamme... more Branched nucleic acids play important biological roles, and well-known examples such as the Hammerhead ribozyme, the all-RNA enzyme, a three-way junction (3H according to IUPAC nomenclature [1a] ), and the Holliday junctions [1b] or DNA four-way junctions (J6, a; 4H according to IUPAC nomenclature [1a] ) have recently been reviewed. [2a-c] The Holliday junctions form the central intermediates in both homologous and site-specific recombination. In solution, in the presence of multivalent ions and thus under physiological salt conditions, their structure consists of two quasi-continuously stacked helices in an essentially canonical conformation . [2b,c] Four recent crystal structures of 4H [2d-g] confirm these structural features, but no coherence is observed in the value of the interhelix angle y (defined in ; three structures show right-handed interhelix