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Results for “trajectory analysis”

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PubMed2026

Identifying JAK2 and ANXA5 as Key Genes Linking Obstructive Sleep Apnea and Oxidative Stress via Machine Learning and Multilayer Transcriptomic Integration With Functional Validation.

Obstructive sleep apnea (OSA) is a common and severe sleep disorder closely associated with oxidative stress (OS). This study aims to identify and validate potential OS-related genes associated with OSA through bioinformatics methods. We successfully identified OS-related differentially expressed genes (OS-DEGs) by combining the limma test, weighted correlation network analysis (WGCNA), and OS-related genes from the GeneCards database. Key genes and potential biological roles were further identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), enrichment analysis, protein-protein interaction (PPI) network analysis, Lasso regression analysis, random forest algorithm, and support vector machine recursive feature elimination (SVM-RFE) method. Evaluate and validate the accuracy of key genes through receiver operating characteristic (ROC) curve analysis. The human single-cell RNA sequencing (scRNA-seq) dataset is used for cell classification annotation, analysis of key gene single-cell expression profiles, and virtual gene knockout experiments based on the scTenifoldKnk algorithm. Integrating scRNA-seq sequencing, pseudotime trajectory inference, cell-cell communication analysis, and bulk immune infiltration deconvolution reveals monocyte subtype remodeling in OSA. Finally, the expression levels of key genes in clinical samples were validated using real-time quantitative PCR (RT-qPCR) and Western blotting. A total of 57 common DEGs, indicating significant enrichment in OS, inflammation, and tumor pathways, particularly prominent in the immunometabolism pathway. By integrating DEGs, WGCNA, PPI results, and machine learning methods, key genes Janus kinase 2 (JAK2) and ANXA5 were screened out. JAK2 was significantly upregulated under disease conditions, while ANXA5 was significantly downregulated. ROC curve exhibited high accuracy (area under the curve [AUC] > 0.85). Human scRNA-seq analysis revealed that key genes were predominantly highly expressed in monocytes. Virtual knockout experiments demonstrated that these key genes play a crucial role in regulating immune responses and inflammatory reactions. PPI networks and enrichment analysis verified that downstream genes S100P, ALOX5AP, PROK2, and PADI4 may collaboratively participate in immune response and inflammation regulation. Finally, clinical sample experiment further validated the results of bioinformatics analysis. This study provides new research insights for the diagnosis, mechanism research, and treatment development of OSA in the future by integrating multilayer transcriptomic and machine learning techniques.

Humans↗

PubMed2004

Physical aggression during early childhood: trajectories and predictors.

OBJECTIVES: Physical aggression in children is a major public health problem. Not only is childhood physical aggression a precursor of the physical and mental health problems that will be visited on victims, but also aggressive children themselves are at higher risk of alcohol and drug abuse, accidents, violent crimes, depression, suicide attempts, spouse abuse, and neglectful and abusive parenting. Furthermore, violence commonly results in serious injuries to the perpetrators themselves. Although it is unusual for young children to harm seriously the targets of their physical aggression, studies of physical aggression during infancy indicate that by 17 months of age, the large majority of children are physically aggressive toward siblings, peers, and adults. This study aimed, first, to identify the trajectories of physical aggression during early childhood and, second, to identify antecedents of high levels of physical aggression early in life. Such antecedents could help to understand better the developmental origins of violence later in life and to identify targets for preventive interventions. METHODS: A random population sample of 572 families with a 5-month-old newborn was recruited. Assessments of physical aggression frequency were obtained from mothers at 17, 30, and 42 months after birth. Using a semiparametric, mixture model, distinct clusters of physical aggression trajectories were identified. Multivariate logit regression analysis was then used to identify which family and child characteristics, before 5 months of age, predict individuals on a high-level physical aggression trajectory from 17 to 42 months after birth. RESULTS: Three trajectories of physical aggression were identified. The first was composed of children who displayed little or no physical aggression. These individuals were estimated to account for approximately 28% of the sample. The largest group, estimated at approximately 58% of the sample, followed a rising trajectory of modest aggression. Finally, a group, estimated to comprise approximately 14% of the sample, followed a rising trajectory of high physical aggression. Best predictors before or at birth of the high physical aggression trajectory group, controlling for the levels of the other risk factors, were having young siblings (odds ratio [OR]: 4.00; confidence interval [CI]: 2.2-7.4), mothers with high levels of antisocial behavior before the end of high school (OR: 3.1; CI: 1.1-8.6), mothers who started having children early (OR: 3.1; CI: 1.4-6.8), families with low income (OR: 2.6; CI: 1.3-5.2), and mothers who smoked during pregnancy (OR: 2.2; CI: 1.1-4.1). Best predictors at 5 months of age were mothers' coercive parenting behavior (OR: 2.3; CI: 1.1-4.7) and family dysfunction (OR: 2.2; CI: 1.2-4.1). The OR for a high-aggression trajectory was 10.9 for children whose mother reported both high levels of antisocial behavior and early childbearing. CONCLUSIONS: Most children have initiated the use of physical aggression during infancy, and most will learn to use alternatives in the following years before they enter primary school. Humans seem to learn to regulate the use of physical aggression during the preschool years. Those who do not, seem to be at highest risk of serious violent behavior during adolescence and adulthood. Results from the present study indicate that children who are at highest risk of not learning to regulate physical aggression in early childhood have mothers with a history of antisocial behavior during their school years, mothers who start childbearing early and who smoke during pregnancy, and parents who have low income and have serious problems living together. All of these variables are relatively easy to measure during pregnancy. Preventive interventions should target families with high-risk profiles on these variables. Experiments with such programs have shown long-term impacts on child abuse and child antisocial behavior. However, these impacts were not observed in families with physical violence. The problem may be that the prevention programs that were provided did not specifically target the parents' control over their physical aggression and their skills in teaching their infant not to be physically aggressive. Most intervention programs to prevent youth physical aggression have targeted school-age children. If children normally learn not to be physically aggressive during the preschool years, then one would expect that interventions that target infants who are at high risk of chronic physical aggression would have more of an impact than interventions 5 to 10 years later, when physical aggression has become a way of life.

Aggression↗

PubMed1993

Lymphocyte locomotion in three-dimensional collagen gels. Comparison of three quantitative methods for analysing cell trajectories.

We evaluated three different quantitative evaluation methods for lymphocyte locomotion in three-dimensional collagen gels: (1) the length of the two-dimensional migration path (distance migrated) was compared to (2) the resulting average displacement from the starting to the end point and (3) the displacement of the furthest migrating population (cells with high displacement). Locomotion of immunomagnetically isolated human CD4+ and CD8+ peripheral blood lymphocytes suspended in type I collagen gels was recorded using time-lapse videomicroscopy. Paths of randomly selected locomoting cells were digitized, reconstructed and quantitatively analysed. For spontaneously locomoting CD4+ and CD8+ lymphocytes (90 min observation period) the mean total distance migrated was 10.0 +/- 3.7 microns/min (CD4+; n = 114 cells) and 5.6 +/- 3.3 microns/min (CD8+; n = 90 cells). The mean displacement from the individual starting point amounted to 1.3 +/- 0.7 micron/min for CD4+ and 1.1 +/- 0.7 micron/min for CD8+ cells, thus representing only 5-25% of the total migration path (index range displacement/distance migrated: 0.13-50%). Incubation with interleukin-8 and/or receptor blocking by monoclonal antibodies against VLA-2 (Gi9) or VLA-4 (HP2/1) integrins significantly altered the mean length of the migration paths for six out of ten different experimental conditions. Average displacement or displacement of the most active cells detected significant changes in two and three out of ten samples. Whereas the interleukin-8 induced locomotory changes were correctly represented by end point determination, relatively slight but significant modulation in lymphocyte behaviour by anti-integrin antibodies was revealed solely by analysis of the complete cell trajectory. In conclusion, the cell trajectory may represent a sensitive method for evaluating induced subtle changes in lymphocyte locomotory characteristics.

CD4-Positive T-Lymphocytes↗

PubMed2005

On-line multi-analyzer monitoring of biomass, glucose and acetate for growth rate control of a Vibrio cholerae fed-batch cultivation.

In situ near-infrared (NIR) spectroscopy and in-line electronic nose (EN) mapping were used to monitor and control a cholera-toxin producing Vibrio cholerae fed-batch cultivation carried out with a laboratory method as well as with a production method. Prediction models for biomass, glucose and acetate using NIR spectroscopy were developed based on spectral identification and partial-least squares (PLS) regression resulting in high correlation to reference data (standard errors of prediction for biomass, glucose and acetate were 0.20 gl(-1), 0.26 gl(-1) and 0.28 gl(-1)). A compensation algorithm for aerated bioreactor disturbances was integrated in the model computation, which in particular improved the prediction by the biomass model. First, the NIR data were applied together with EN in-line data selected by principal component analysis (PCA) for generating a trajectory representation of the fed-batch cultivation. A correlation between the culture progression and EN signals was demonstrated, which proved to be beneficial in monitoring the culture quality. It was shown that a deviation from a normal cultivation behavior could easily be recognized and that the trajectory was able to alarm a bacterial contamination. Second, the NIR data indicated the potential of predicting the concentration of formed cholera toxin with a model prediction error of 0.020 gl(-1). Third, the on-line biomass prediction based on the NIR model was used to control the overflow metabolism acetate formation of the V. cholerae culture. The controller compared actual specific growth rate as estimated from the prediction with the critical acetate formation growth rate, and from that difference adjusted the glucose feed rate.

Acetates↗

PubMed2004

Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: an analysis of configurational entropy changes upon complexation.

The HIV-1 gp120/CD4 interaction shows a large, unprecedented entropy/enthalpy compensation, with the capacity to fine-tune recognition over a broad range of affinity. The intermolecular interaction involves stable hydrophobic contacts with a unique protruding CD4-Phe43 structure surrounded by an intermolecular hydrogen-bond network that covers the hemisphere of the CD4 D1 domain. We have applied a heuristic formula based on the covariance matrix of atom-positional fluctuations to assess the configurational entropy of the gp120/CD4 complex at different levels. The system was dissected into various subsets of atoms to evaluate the entropic contributions of different functional elements. By combining the trajectories of the free and complex forms, further insight into the conformational sampling was extracted. Despite the limited sampling time of 10 ns, the theoretically derived changes in configurational entropy are in fair agreement with the experimentally determined data. The simultaneous evaluation of different interaction modes through a decomposition approach is only feasible with the knowledge of the atomic trajectory of the system. The configurational entropy analysis in terms of combined trajectories presented here shall potentially provide accurate estimations of thermodynamic properties of biomolecules given sufficient sampling of conformational space.

Biophysics↗

PubMed1998

XOR has no local minima: A case study in neural network error surface analysis.

This paper presents a case study of the analysis of local minima in feedforward neural networks. Firstly, a new methodology for analysis is presented, based upon consideration of trajectories through weight space by which a training algorithm might escape a hypothesized local minimum. This analysis method is then applied to the well known XOR (exclusive-or) problem, which has previously been considered to exhibit local minima. The analysis proves the absence of local minima, eliciting significant aspects of the structure of the error surface. The present work is important for the study of the existence of local minima in feedforward neural networks, and also for the development of training algorithms which avoid or escape entrapment in local minima.

Journal Article↗

PubMed2005

On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations.

The way in which enzymes influence the rate of chemical processes is still a question of debate. The protein promotes the catalysis of biochemical processes by lowering the free energy barrier in comparison with the reference uncatalyzed reaction in solution. In this article we are reporting static and dynamic aspects of the enzyme catalysis in a bimolecular reaction, namely a methyl transfer from S-adenosylmethionine to the hydroxylate oxygen of a substituted catechol catalyzed by catechol O-methyltransferase. From QM/MM optimizations, we will first analyze the participation of the environment on the transition vector. The study of molecular dynamics trajectories will allow us to estimate the transmission coefficient from a previously localized transition state as the maximum in the potential of mean force profile. The analysis of the reactive and nonreactive trajectories in the enzyme environment and in solution will also allow studying the geometrical and electronic changes, with special attention to the chemical system movements and the coupling with the environment. The main result, coming from both analyses, is the approximation of the magnesium cation to the nucleophilic and the hydroxyl group of the catecholate as a result of a general movement of the protein, stabilizing in this way the transition state. Consequently, the free energy barrier of the enzyme reaction is dramatically decreased with respect to the reaction in solution.

Catechol O-Methyltransferase↗

PubMed1999

The potential for long-range transport of air-pollutants into Greece: a climatological analysis.

A flow climatology using 5 years (1983-1987) of back trajectories has been created for the Aliartos meteorological-chemical station (Greece's EMEP-station phi = 38 degrees 13'N, lambda = 23 degrees 00'E) using the Air Resources Laboratory (ARL) trajectory model. Air mass back trajectories were analysed to quantify the contributions of major source areas to the air pollution concentration in the area of Greece. The trajectories were produced two times a day at the 850-hPa and 700-hPa pressure surface. The trajectories were classified and summarised in order to produce a long range trajectory climatology. The purpose of this paper is to use the above flow climatology to improve understanding to atmospheric transport pathways to Greece (and to the greater south-eastern area of Europe) and to evaluate the polluting potential of distant source regions outside the country. The limited chemical concentration data available from Aliartos are used to evaluate the conclusions reached from the flow climatology and emissions analysis. The results show that trajectories reach Greece from five major source areas: (i) Northwest Europe, (ii) west Europe, (iii) north Europe, (iv) Northwest Asia, and (v) Northwest Africa. Sector analysis of air pollution concentrations and emissions also showed that: (i) Most air pollutants transport from distances beyond 1800 km takes place, and the most probable source areas are the industrialised countries of Europe. (ii) Countries of west and north-central Europe emit the greater amounts of air pollutants (S and N). (iii) Sulphate and nitrate concentrations are similar among transport sectors.

Air Pollutants↗

PubMed2006

CAVER: a new tool to explore routes from protein clefts, pockets and cavities.

BACKGROUND: The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. RESULTS: The algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. The fully functional program is available as a stand-alone version and as plug-in for the molecular modeling program PyMol. Additionally, selected functions are accessible in an online version. CONCLUSION: The algorithm developed automatically finds the path from a starting point located within the interior of a protein. The algorithm is sufficiently rapid and robust to enable routine analysis of molecular dynamics trajectories containing thousands of snapshots. The algorithm is based on reciprocal metrics and provides an easy method to find a centerline, i.e. the spine, of complicated objects such as a protein tunnel. It can also be applied to many other molecules. CAVER is freely available from the web site http://loschmidt.chemi.muni.cz/caver/.

Algorithms↗

PubMed1994

Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis.

A comparison is made between a 200-ps molecular dynamics simulation in vacuum and a normal mode analysis on the protein bovine pancreatic trypsin inhibitor (BPTI) in order to elucidate the dual aspects of harmonicity and anharmonicity in the dynamics of proteins. The molecular dynamics trajectory is analyzed using principal component analysis, an effective harmonic analysis suited for comparison with the results from the normal mode analysis. The results suggest that the first principal component shows qualitatively different behavior from higher principal components and is associated with apparent barrier crossing events on an anharmonic conformational energy surface. The higher principal components appear to have probability distributions that are well approximated by Gaussians, indicating harmonicity. Eliminating the contribution from the first principal component reveals a great deal of correspondence between the 2 methods. This correspondence, however, involves a factor of 2, as the variances of the distribution of the higher principal components are, on average, roughly twice those found from the normal mode analysis. A model is proposed to reconcile these results with those from previous analyses.

Aprotinin↗

PubMed1992

Conformational properties of oxytocin in dimethyl sulfoxide solution: NMR and restrained molecular dynamics studies.

The conformation of oxytocin, the neurohypophyseal nonapeptide hormone, in solution in deuterated dimethyl sulfoxide has been determined by 1H-nmr. The structural determination is based on the experimental data set of nuclear Overhauser effect restraints. Obtained after the restrained molecular dynamics simulation on an initial structure of extended conformation, five resultant structures satisfy the experimental restraints well. These structures resemble that of the crystal structure of deamino-oxytocin, an analogue of oxytocin, in terms of a close correlation observed both at two beta-turn regions of the 20-membered tocin ring and at the tripeptide tail end. Based on this comparison and analysis of restrained molecular dynamics trajectories, we found that, although the turns are stabilized by the formation of hydrogen bonds, the oxytocin molecule possesses a slight twist in DMSO solution relative to the orientation of deamino-oxytocin in the crystalline state. Analyses of oxytocin conformation indicate that the tripeptide tail is more flexible than the tocin ring.

Amino Acid Sequence↗

PubMed1992

Predicting the product specificity and coupling of cytochrome P450cam.

We present an analysis of several molecular dynamics trajectories of substrate-bound cytochrome P450cam. Trajectories were calculated for the native substrate, camphor, as well as for the alternative substrates, norcamphor and thiocamphor. The system modeled consisted of the crystallographically resolved amino acids, the heme group with a single oxygen atom as the distal ligand, the bound substrate, and the crystallographic waters. These trajectories of the presumptive ferryl oxygen intermediate were used to predict regiospecificity of hydroxylation and coupling between NADH consumption and product formation. Simple geometric criteria in combination with electronic considerations were used to calculate the probability of hydroxylation at specific sites on the substrate. We found that for all the cases examined, the predicted product ratios were in good agreement with the experimentally observed values. We also determined that these simple geometric criteria can be used to predict the degree of coupling between NADH consumption and product formation for a given substrate, which was in good agreement with the experimental values.

Camphor↗

PubMed1992

Common principle of guidance by echolocation and vision.

1. Using echolocation, bats move as gracefully as birds through the cluttered environment, suggesting common principles of optic and acoustic guidance. We tested the idea by analysing braking control of bats (Macroderma gigas) flying through a narrow aperture with eyes covered and uncovered. 2. Though braking control would seem to require rapid detection of distance and velocity and computation of deceleration, simpler control is possible using the tau function of any sensory variable S that is a power function of distance to aperture. Tau function of S is tau (S) = S/S (the dot means time derivative). Controlled braking is achievable by keeping tau (S) constant. 3. Previous experiments indicated the tau (S) constant procedure is followed by humans and birds in visually controlling braking. Analysis of the bats' flight trajectories indicated they too followed the braking procedure using echolocation. 4. The tau function of echo-delay or of echo-intensity or of angle subtended by directions of echoes from two points on the approach surface could be used to control braking. Aperture size was modulated during flight on some trials in an attempt to test between these possibilities, but the results were inconclusive.

Animals↗

PubMed2006

Single particle tracking across sequences of microscopical images: application to platelet adhesion under flow.

A versatile and automated image processing technique and data extraction procedure from videomicroscopic data is presented. The motivation is a detailed quantification of blood platelet adhesion from laminar flow onto a surface. The characteristics of the system under observation (type of cells, their speed of movement, and the quality of the optical image to analyze) provided the criteria for developing a new procedure enabling tracking for long image sequences. Specific features of the novel method include: automatic segmentation methodology which removes operator bias; platelet recognition across the series of images based on a probability density function (two-dimensional, Gaussian-like) tailored to the physics of platelet motion on the surface; options to automatically tune the procedure parameters to explore different applications; integrated analysis of the results (platelet trajectories) to obtain relevant information, such as deposition and removal rates, displacement distributions, pause times and rolling velocities. Synthetic images, providing known reference conditions, are used to test the method. The algorithm operation is illustrated by application to images obtained by fluorescence microscopy of the interaction between platelets and von Willebrand factor-coated surfaces in parallel-plate flow chambers. Potentials and limits are discussed, together with evaluation of errors resulting from an inaccurate tracking.

Algorithms↗

PubMed2026

Mechanistic insights into Claudin-14 dysfunction implicated in veins of Galen malformation.

Claudin-14 (CLDN14) is a key component of tight junctions (TJs) critical for maintaining paracellular barrier function. Variants of CLDN14 have been linked to Vein of Galen malformations (VOGMs), a rare cerebrovascular disorder; however, the molecular mechanisms underlying their pathogenicity remain unknown. Here, we investigate the mechanistic effects of two VOGM-associated mutations, A113P and V143M, using reinforcement-learning driven enhanced sampling molecular dynamics simulations combined with DiffNets-based deep learning and independent trajectory-wide structural analyses. Our analysis reveals that A113P induces broader structural disruption of CLDN14, perturbing paracellular sealing, pore symmetry, and inter-protomer communication, whereas V143M induces structural rearrangements centred around TM3 and the TM3-ECL2 region. In both cases, mutation-specific alterations are observed in structural stability and interfacial organization across oligomeric assemblies. Notably, these effects are qualitatively consistent across different modelled architectures, despite variability in local responses. In the absence of experimentally resolved structures, the structural perturbations reported here provide a mechanistic understanding of how VOGM-associated variants may influence CLDN14 structure and dynamics.

Aneurysm↗

PubMed2006

Molecular dynamics and circular dichroism studies of human and rat C-peptides.

Proinsulin C-peptide has been recently described as an endogenous peptide hormone, responsible for important physiological functions others than its role in proinsulin processing. Accumulating evidences that C-peptide exerts beneficial effects in the treatment of long term complications of patients with type 1 diabetes mellitus indicate that this molecule may be administered together with insulin in future therapies. Despite its clear pharmacological interest, the secondary and three-dimensional (3D) structures of human C-peptide are still points of controversy. In the present work we report molecular dynamics (MD) simulations of human, rat I and rat II C-peptides. A common experimental strategy applied to all peptides consisted of homology building followed by multinanosecond MD simulations in vacuum and water. Circular dichroism (CD) experiments of each peptide in the absence and presence of 2,2,2-trifluoroethanol (TFE) were performed to support validation of the theoretical models. A multiple sequence alignment of 23 known mammalian C-peptides was constructed to identify significant conserved sites that would be important for the maintenance of secondary and tertiary structures. The analysis of the molecular dynamics trajectories for the human, rat I and rat II molecules have shown quite different general behavior, being the human C-peptide more flexible than the two others. Human and rat C-peptides exhibit very stable turn-like structures at the middle and C-terminal regions, which have been described as potential active sites of C-peptides. Human C-peptide also presented a short alpha-helix throughout the MD, which was not found in the rat molecules. CD data is in very good agreement with the MD results and both methods were able to identify a greater structural stability and potential in rat C-peptides when compared to the human C-peptide. The simulation results are discussed and validated in the light of multiple sequence alignment, recent experimental data from the literature and our own CD experiments.

Amino Acid Sequence↗

PubMed2025

Unusual relapse dynamics in EGFR-mutated lung adenocarcinoma uncovered by genomic profiling: Insights from a case report.

Synchronous or metachronous multiple NSCLCs challenge clinical practice, particularly in distinguishing multiple separate primary lung cancers (SPLC) from intrapulmonary metastasis (IPM) for accurate staging and management. Here, we present a unique case of three resected lung adenocarcinomas (LUAD) from a single patient collected at different time points, all harboring the same EGFR p.L858R somatic driver mutation but exhibiting distinct clonal trajectories. Whole exome sequencing (WES) analysis revealed that the first tumor was an independent primary tumor, while the latter two tumors were clonally related. Our findings highlight the complexity of tumor progression and provide insights into clonal heterogeneity. This report underscores the importance of genomic profiling for discriminating SPLC from IPM and emphasizes that the detection of a single shared driver mutation is not sufficient to prove metastasis.

Humans↗

PubMed2005

Structure and dynamics of an RNA tetraloop: a joint molecular dynamics and NMR study.

Molecular dynamics simulations of the RNA tetraloop 5'-CGCUUUUGCG-3' with high melting temperature and significant conformational heterogeneity in explicit water solvent are presented and compared to NMR studies. The NMR data allow for a detailed test of the theoretical model, including the quality of the force field and the conformational sampling. Due to the conformational heterogeneity of the tetraloop, high temperature (350 K) and locally enhanced sampling simulations need to be invoked. The Amber98 force field leads to a good overall agreement with experimental data. Based on NMR data and a principal component analysis of the 350 K trajectory, the dynamic structure of the tetraloop is revealed. The principal component free energy surface exhibits four minima, which correspond to well-defined conformational structures that differ mainly by their base stacking in the loop region. No correlation between the motion of the sugar rings and the stacking dynamics of the loop bases is found.

Nuclear Magnetic Resonance, Biomolecular↗