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Biomedical subjects

Lennart Nilsson

Publications and source records attributed to Lennart Nilsson.

At least 19 recordsLinked to original sources
PubMed2007

A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide.

Six different molecular dynamics simulations of Cyclophilin A, three with the protein free in water and three with the Ala-Pro dipeptide bound to the protein, have been performed, and analysed with respect to structure and hydration of the active site. The water structure in the binding pocket of the free Cyclophilin A was found to mimic the experimentally obtained binding cis conformation of the dipeptide. Cyclophilin A is a peptidyl-prolyl cis-trans isomerase (PPIase), but the mechanism of the cis/trans isomerization is not exactly clear. This study was performed to understand better the binding between dipeptide and Cyclophilin A, but also two previously proposed isomerization mechanisms are discussed.

Binding Sites↗
PubMed2006

Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics.

Unbinding pathways of retinoic acid (RA) bound to retinoic acid receptor (RAR) have been explored by the random expulsion molecular dynamics (REMD) method. Our results show that RA may exit the binding site of RAR through flexible regions close to the H1-H3 loop and beta-sheets, without displacing H12 from its agonist position. This result may explain kinetic differences between agonist and antagonist ligands observed for other nuclear receptors. The extended and flexible structure of RA initiated a methodological study in a simplified two-dimensional model system. The REMD force should in general be distributed to all atoms of the ligand to obtain the most unbiased results, but for a ligand which is tightly bound in the binding pocket through a strong electrostatic interaction, application of the REMD force on a single atom is preferred.

Binding Sites↗
PubMed2006

Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain.

Zinc ions are frequently found in DNA-binding proteins. p53 is a cancer-related transcriptional factor, and its DNA-binding domain (DBD) contains a Zn2+, which has been shown to be important for aggregation and sequence-specific DNA binding. We have carried out molecular dynamics simulations to investigate the influence of Zn2+ on the p53 DNA recognition and the stability of the DBD. In the simulation with Zn2+ present, the protein attracted to the DNA phosphate backbone, allowing for Arg248 on loop L3 to be inserted into the minor groove for specific contact with the DNA base. The insertion of Arg248 between the backbone phosphate groups in the minor groove caused a narrowing of the minor groove, which is not seen in the simulation without Zn2+. Structurally, the zinc ion coordinated the motions among the different protein structural elements, which could also be important for optimal binding and core packing. The influence of Zn2+ on protein stability was mainly localized to the L2 loop. Our results suggest that L2 may be a frustrated and highly flexible element and play an important role in aggregation of Zn-free p53. Zn2+ keeps the L2 structured and probably prevents aggregation.

Arginine↗
PubMed2006

Increased plasma concentration of matrix metalloproteinase-7 in patients with coronary artery disease.

BACKGROUND: Plaque rupture is often associated with breakdown of the extracellular matrix in the shoulder region of a plaque. We tested whether plasma concentrations of various matrix metalloproteinases (MMPs) and tissue inhibitor of metalloproteinase-1 (TIMP-1) could serve as markers for plaque instability as well as relationships between plasma MMPs and inflammatory markers. METHODS: The study group included 65 men with angiographically verified CAD (45 with stable and 20 with unstable CAD) and 28 healthy controls. Circulating MMP, TIMP-1, C-reactive protein, and cytokine concentrations were measured by ELISA. Leukocyte subtype counts in whole blood were determined, and T-cell subsets and natural killer cells were measured by flow cytometry. Differences in continuous variables between groups were tested by ANOVA with the Scheffé F-test used as a post hoc test, and correlations were analyzed by a linear regression method. RESULTS: The plasma concentration of MMP-7 was increased in patients with stable and unstable CAD, whereas MMP-2 and -3 concentrations were decreased. The plasma concentration of TIMP-1 was significantly increased in patients with unstable CAD. MMP-2, -3, and -7 showed no correlations with established markers of inflammation. However, MMP-2 correlated positively with the number of natural killer cells in patients with stable and unstable CAD. CONCLUSION: Plasma concentrations of MMPs and TIMPs may be markers of CAD but appear to be differentially regulated.

C-Reactive Protein↗
PubMed2006

The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA.

Previous kinetic investigations of the N-terminal RNA recognition motif (RRM) domain of spliceosomal protein U1A, interacting with its RNA target U1 hairpin II, provided experimental evidence for a 'lure and lock' model of binding in which electrostatic interactions first guide the RNA to the protein, and close range interactions then lock the two molecules together. To further investigate the 'lure' step, here we examined the electrostatic roles of two sets of positively charged amino acids in U1A that do not make hydrogen bonds to the RNA: Lys20, Lys22 and Lys23 close to the RNA-binding site, and Arg7, Lys60 and Arg70, located on 'top' of the RRM domain, away from the RNA. Surface plasmon resonance-based kinetic studies, supplemented with salt dependence experiments and molecular dynamics simulation, indicate that Lys20 predominantly plays a role in association, while nearby residues Lys22 and Lys23 appear to be at least as important for complex stability. In contrast, kinetic analyses of residues away from the RNA indicate that they have a minimal effect on association and stability. Thus, well-positioned positively charged residues can be important for both initial complex formation and complex maintenance, illustrating the multiple roles of electrostatic interactions in protein-RNA complexes.

Amino Acid Sequence↗
PubMed2006

Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations.

Anisotropic network model (ANM) is used to analyze the collective motions of restriction enzyme EcoRI in free form and in complex with DNA. For comparison, three independent molecular dynamics (MD) simulations, each of 1.5 ns duration, are also performed for the EcoRI-DNA complex in explicit water. Although high mobility (equilibrium fluctuations) of inner and outer loops that surround the DNA is consistent in both methods and experiments, MD runs sample different conformational subspaces from which reliable collective dynamics cannot be extracted. However, ANM employed on different conformations from MD simulations indicates very similar collective motions. The stems of the inner loops are quite immobile even in the free enzyme and form a large, almost fixed, pocket for DNA binding. As a result, the residues that make specific and non-specific interactions with the DNA exhibit very low fluctuations in the free enzyme. The vibrational entropy difference between the EcoRI complex and free protein + unkinked DNA is positive (favorable), which may partially counteract the unfavorable enthalpy difference of DNA kink formation. Dynamic domains in EcoRI complex and cross-correlations between residue fluctuations indicate possible means of communication between the distal active sites.

Computer Simulation↗
PubMed2005

Decreased plasma CXCL16/SR-PSOX concentration is associated with coronary artery disease.

OBJECTIVES: To investigate for the first time whether the plasma CXCL16 concentration is altered in coronary artery disease (CAD) patients. BACKGROUND: Accumulating evidence suggests that the novel chemokine/scavenger receptor CXCL16/SR-PSOX is involved in the development of atherosclerosis and CAD. METHODS: Using ELISA we assessed the plasma CXCL16 concentration in 40 stable angina pectoris (SAP) patients, 17 unstable angina pectoris/non-ST-elevation myocardial infarction (UAP/non-STEMI) patients, 387 survivors of a first myocardial infarction (MI) and healthy control subjects (44 controls for SAP and UAP/non-STEMI patient groups and 387 controls for post-MI patients). RESULTS: SAP patients exhibited significantly lower median CXCL16 levels (2111 pg/ml) than the corresponding control subjects (2678 pg/ml) (P=0.0012). UAP/non-STEMI patients also appeared to have lower CXCL16 levels (2192 pg/ml) compared with controls (NS). Patients investigated 3 months after MI tended (P=0.07) to have lower CXCL16 levels (2529 pg/ml) than the corresponding controls (2638 pg/ml). There were no significant correlations between CXCL16 levels and different measures of CAD severity determined by quantitative coronary angiography in post-MI patients. Neither patients nor controls exhibited significant correlations between CXCL16 levels and plasma lipoprotein fractions, inflammatory cytokines, C-reactive protein or numbers of inflammatory cells in peripheral blood. CONCLUSIONS: The finding that lower plasma CXCL16 concentration is associated with CAD might indicate a potential atheroprotective function of CXCL16.

Blood Chemical Analysis↗
PubMed2005

Molecular origin of time-dependent fluorescence shifts in proteins.

Time-resolved fluorescence spectroscopy is used increasingly to probe molecular motions at the aqueous interfaces of biological macromolecules and membranes. By recording the time variation of the fluorescence frequency, thermal atomic fluctuations in the vicinity of the chromophore can be probed. From such fluorescence Stokes shift (FSS) experiments, it has been inferred that water motions in the hydration layer are slowed down by 1-3 orders of magnitude. To provide a more secure foundation for the interpretation of FSS data, we use molecular dynamics simulations to examine the molecular origin of the FSS from a tryptophan residue in a protein. By using linear response theory to decompose the FSS into its water and protein components, we find that the water component dominates the static FSS but decays rapidly. Thus, after a few picoseconds, the FSS essentially reflects protein dynamics, including the self-motion of the chromophore. Because of its collective nature, the FSS response is insensitive to the motion of individual water molecules. Collective water displacement by slowly fluctuating protein groups introduces a long-time tail in the water autocorrelation function, but this dynamic coupling is hardly manifested in the observed FSS. Our analysis reconciles FSS data with the picture of a highly dynamic hydration layer, derived mainly from magnetic relaxation dispersion and simulation studies, and calls for a revision of previous interpretations of FSS decays in terms of slow hydration dynamics at biomolecular and other interfaces.

Protein Conformation↗
PubMed2005

Plasminogen activator inhibitor-1 4G/5G polymorphism and risk of stroke: replicated findings in two nested case-control studies based on independent cohorts.

BACKGROUND AND PURPOSE: Impaired fibrinolytic function secondary to elevated plasminogen activator inhibitor-1 (PAI-1) levels has been implicated in ischemic stroke. PAI-1 levels are determined by genetic factors and environmental factors, triglyceride levels in particular. The aim of this study was to investigate the common functional 4/5 guanosine (4G/5G) polymorphism in the promoter region of the PAI-1 gene and the risk of stroke. METHODS: A nested case-control study design was applied, using baseline data for 2 independent cohorts obtained at population-based surveys in northern Sweden. In study A, there were 113, and in study B, there were 275 individuals without major concomitant disease at baseline who later experienced a first-ever stroke. Blood samples obtained at baseline were analyzed for potential risk factors, including the 4G/5G polymorphism of the PAI-1 gene. RESULTS: The 4G allele of the PAI-1 polymorphism was associated with an increased risk of future ischemic stroke in both studies (odds ratio [OR] of 4G homozygosity, 1.87; 95% CI, 1.12 to 3.15 in study A; OR of 4G homozygosity, 1.56; 95% CI, 1.12 to 2.16 in study B). Individuals with the combination of hypertriglyceridemia and 4G homozygosity were at the greatest risk of developing stroke. Multiple logistic regression analysis identified 4G homozygosity, systolic blood pressure, and diabetes as independent predictors of ischemic stroke. CONCLUSIONS: Identical findings in 2 independent studies strongly suggest a true and clinically important association between PAI-1 4G/5G genotype and risk of future ischemic stroke. The observed modification of the genotype effect by triglycerides may be interpreted as a gene-environment interaction.

Adult↗
PubMed2005

Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization.

Molecular dynamics simulations of a ribonuclease A C-peptide analog and a sequence variant were performed in water at 277 and 300 K and in 8 M urea to clarify the molecular denaturation mechanism induced by urea and the early events in protein unfolding. Spectroscopic characterization of the peptides showed that the C-peptide analog had a high alpha-helical content, which was not the case for the variant. In the simulations, interdependent side-chain interactions were responsible for the high stability of the alpha-helical C-peptide analog in the different solvents. The other peptide displayed alpha-helical unwinding that propagated cooperatively toward the N-terminal. The conformations sampled by the peptides depended on their sequence and on the solvent. The ability of water molecules to form hydrogen bonds to the peptide as well as the hydrogen bond lifetimes increased in the presence of urea, whereas water mobility was reduced near the peptide. Urea accumulated in excess around the peptide, to which it formed long-lived hydrogen bonds. The unfolding mechanisms induced by thermal denaturation and by urea are of a different nature, with urea-aqueous solutions providing a better peptide solvation than pure water. Our results suggest that the effect of urea on the chemical denaturation process involves both the direct and indirect mechanisms.

Computer Simulation↗
PubMed2005

Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides.

The eight nucleoside constituents of nucleic acids were simulated for 50 ns in explicit water with molecular dynamics. This provides equilibrium populations of the torsional degrees of freedom, their kinetics of interconversion, their couplings, and how they are influenced by water. This is important, given that a full and quantitative characterization of the nucleosides in aqueous solution by experimental means has been elusive, despite immense efforts in that direction. It is with the anti/syn equilibrium that the simulations are most complementary to experiment, by accessing directly the influence of the sugar type, sugar pucker, and base on the anti/syn populations. The glycosidic torsion distributions in the anti conformation are strongly affected by water and depart from the corresponding X-ray modal values and the associated energy minima in vacuo. Water also preferentially stabilizes some sugar conformations, showing that potential energies in vacuo are not sufficient to understand the nucleosides. Deoxythymidine (but not other pyrimidines) significantly populates the syn orientation. Guanine favors the syn orientation more than adenine. The ribose favors the syn orientation significantly more than the deoxyribose. The NORTH pucker coexists with the syn conformers. A hydrogen bond is frequently formed between the 5'-OH group and the syn bases, despite competition by water. The rate of the anti/syn transitions with purines is on the nanosecond time scale, confirming a long held assumption underpinning the interpretation of ultrasonic relaxation studies. Therefore, our knowledge of the structure and dynamics of nucleosides in solvent is only limited by the accuracy of the potential used to simulate them, and it is shown that such simulations provide a distinct and unique test of nucleic acid force fields. This confirmed that the widely distributed CHARMM27 force field is, overall, well-balanced with a particularly good representation of the ribose. Specific improvements, however, are suggested for the deoxyribose and torsion gamma.

Crystallography, X-Ray↗
PubMed2005

Thermal unfolding simulations of a multimeric protein--transition state and unfolding pathways.

The folding of an oligomeric protein poses an extra challenge to the folding problem because the protein not only has to fold correctly; it has to avoid nonproductive aggregation. We have carried out over 100 molecular dynamics simulations using an implicit solvation model at different temperatures to study the unfolding of one of the smallest known tetramers, p53 tetramerization domain (p53tet). We found that unfolding started with disruption of the native tetrameric hydrophobic core. The transition state for the tetramer to dimer transition was characterized as a diverse ensemble of different structures using Phi value analysis in quantitative agreement with experimental data. Despite the diversity, the ensemble was still native-like with common features such as partially exposed tetramer hydrophobic core and shifts in the dimer-dimer arrangements. After passing the transition state, the secondary and tertiary structures continued to unfold until the primary dimers broke free. The free dimer had little secondary structure left and the final free monomers were random-coil like. Both the transition states and the unfolding pathways from these trajectories were very diverse, in agreement with the new view of protein folding. The multiple simulations showed that the folding of p53tet is a mixture of the framework and nucleation-condensation mechanisms and the folding is coupled to the complex formation. We have also calculated the entropy and effective energy for the different states along the unfolding pathway and found that the tetramerization is stabilized by hydrophobic interactions.

Cluster Analysis↗
PubMed2005

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

The family of adenosine deaminases acting on RNA (ADARs) targets adenosines in RNA that is mainly double stranded. Some substrates are promiscuously deaminated whereas others, such as the mammalian glutamate receptor B (gluR-B) pre-mRNA, are more selectively deaminated. Many DNA/RNA-base modification enzymes use a base flipping mechanism to be able to reach their target base and it is believed that ADARs function in a similar way. In this study we used molecular dynamics (MD) simulations to describe two sites on the gluR-B pre-mRNA, the selectively targeted R/G site and the nontargeted 46 site, in an attempt to explain the substrate specificity. We used regular MD and also a forced base flipping method with umbrella sampling to calculate the free energy of base opening. Spontaneous opening of the mismatched adenosine was observed for the R/G site but not for the 46 site.

Adenosine↗
PubMed2005

Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization.

Two-point mutations in the human glucocorticoid receptor have been studied by computer simulations to rationalize experimental data, where mutants comprising the V571M substitution improve both transcriptional activity and affinity for aldosterone despite large distances between the mutated residue and the coactivator-binding surface and ligand-binding pocket, respectively. Our molecular dynamics simulations show that the V571M mutation modifies the coactivator-binding site defined by helices 3, 4, and 12, and that specific structural rearrangement of the coactivator-binding site correlates well with transactivation data. A similar reorganization of the coactivator-binding cleft is observed in crystallographic structures of the estrogen receptor in the presence of coactivator peptide, compared with structures without peptide, indicating that induced fit for coactivator binding is a general phenomenon for nuclear receptors. These results suggest that the V571M substitution facilitates recruitment of coactivator protein by promotion of a conformational substate reducing the energetic penalty for the induced fit of the receptor-coactivator complex. Furthermore, our simulations of V571M mutants showed reduced fluctuations of residues lining the ligand-binding pocket. This indicates that a reduction of the entropic cost for ligand binding may explain the increased affinity of V571M mutants for certain ligands.

Allosteric Site↗
PubMed2005

Subway particles are more genotoxic than street particles and induce oxidative stress in cultured human lung cells.

Epidemiological studies have shown an association between airborne particles and a wide range of adverse health effects. The mechanisms behind these effects include oxidative stress and inflammation. Even though traffic gives rise to high levels of particles in the urban air, people are exposed to even higher levels in the subway. However, there is a lack of knowledge regarding how particles from different urban subenvironments differ in toxicity. The main aim of the present study was to compare the ability of particles from a subway station and a nearby very busy urban street, respectively, to damage DNA and to induce oxidative stress. Cultured human lung cells (A549) were exposed to particles, DNA damage was analyzed using single cell gel electrophoresis (the comet assay), and the ability to induce oxidative stress was measured as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) formation in lung cell DNA. We found that the subway particles were approximately eight times more genotoxic and four times more likely to cause oxidative stress in the lung cells. When the particles, water extracts from the particles, or particles treated with the metal chelator deferoxamine mesylate were incubated with 2'-deoxyguanosine (dG) and 8-oxodG was analyzed, we found that the oxidative capacity of the subway particles was due to redox active solid metals. Furthermore, analysis of the atomic composition showed that the subway particles to a dominating degree (atomic %) consisted of iron, mainly in the form of magnetite (Fe3O4). By using electron microscopy, the interaction between the particles and the lung cells was shown. The in vitro reactivity of the subway particles in combination with the high particle levels in subway systems give cause of concern due to the high number of people that are exposed to subway particles on a daily basis. To what extent the subway particles cause health effects in humans needs to be further evaluated.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2005

Immunogenicity and tolerability of a heptavalent pneumococcal conjugate vaccine administered at 3, 5 and 12 months of age.

BACKGROUND: The recommended vaccination schedule for the pneumococcal conjugate vaccine (PCV) includes 4 immunizations, according to the national programs in the United States and some European countries. Other countries use a national schedule for routine vaccinations in early childhood that includes only 3 doses. AIMS: The goals were to assess the immunogenicity and tolerability of PCV with a vaccination schedule that included 3 doses during the first 1 year of life (a 2+1 dose schedule) and to determine the immune responses to concomitantly administered Haemophilus influenzae type b (Hib) vaccine. METHODS: A total of 101 healthy Swedish infants were enrolled in an open, nonrandomized, multicenter study. PCV was administered concomitantly with (at separate sites) a diphtheria-tetanus toxoids-acellular pertussis vaccine, inactivated polio vaccine and Hib conjugate vaccine combination at 3, 5 and 12 months of age. IgG antibody concentrations for the 7 serotypes included in the PCV and the Hib capsular polysaccharide in serum samples taken at 3, 6, 12 and 13 months were determined with enzyme immunoassays. Local and systemic reactions were monitored for 3 days after each immunization, and serious adverse reactions were monitored for the whole study period. RESULTS: Two doses of PCV induced satisfactory antibody responses, with the exception of serotypes 6B and 23F. The third dose evoked strong responses for all serotypes, which suggests good immunologic priming with the primary series of 2 doses. The mean anti-Hib antibody concentrations were similar to those noted in earlier studies among Swedish children. The PCV was well tolerated. CONCLUSION: The pneumococcal antibody concentrations at 13 months were comparable with those noted previously with the 4-dose schedule. The results suggest that the implementation of a 2+1 dose schedule for PCV should be considered.

Antibodies, Bacterial↗
PubMed2005

Early rapid weight gain and current overweight in relation to asthma in adolescents born with very low birth weight.

Early catch-up growth and subsequent overweight are suggested to be associated with later cardiovascular diseases and later type II diabetes. However, the impact of early catch-up growth and childhood overweight on the development of asthma has been less studied, particularly in children born with very low birth weight (VLBW). A birth cohort of 74 VLBW children (birth weight < or = 1500 g) was followed from birth and investigated on asthma at 12 yr of age. Early rapid weight gain was in one way defined as an increase of weight > or =1 standard deviation score (SDS) at 6 months of corrected postnatal age. Current overweight was defined by body mass index (BMI) exceeding 21.2 and 21.7 kg/m(2), respectively, for boys and girls at 12 yr of age. Current asthma was diagnosed by a pediatrician, according to asthma ever in combination with a positive response to hypertonic saline bronchial provocation test and/or wheeze at physical examination at 12 yr old. Being overweight at 12 yr of age was associated with an increased risk for current asthma in the VLBW children [crude odds ratio (OR): 5.5, 95% confidence interval (CI): 1.3-22.2]. After adjustment for early weight gain and neonatal risk, the OR of overweight increased nearly three times (adjusted OR: 15.3, 95% CI: 2.5-90.6). Early rapid weight gain seemed to be inversely associated with current asthma (adjusted OR: 0.49 for an increase of weight equal to 1 SDS, 95% CI: 0.23-1.02, p = 0.06). In addition, early rapid weight gain was inversely associated with the magnitude of bronchial responsiveness at 12 yr (coefficient -1.15, p < 0.01). There was a strong and positive association between overweight and asthma at 12 yr of age in the VLBW children. This strong association had been reduced by early rapid weight gain, possibly via the reduction of bronchial responsiveness.

Adolescent↗