There is a lack of tools to analyze simulations of protein molecular dynamics quantitatively. Our aim is to use calmodulin, a prototypical calcium-binding protein, to describe a strategy and some tools for extracting relevant information from dynamics calculations. Our main conclusions are as follows: Autocorrelation vectors may be used to represent a 3D conformation in an n-dimensional space, where n is variable (n < or = 20-30). On such a transformation, classic statistical tools (PCA, clustering, etc.) may be used to differentiate or characterize dynamics trajectories quantitatively. TSAR, an integrated package used for quantitative structure-activity relationships, is well suited (after minor modifications) for such a purpose. Finally, this type of strategy is able to point out the effects of the solvent screening parameters of the Amber software on the dynamics trajectories of calmodulin.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/0263-7855(94)00012-h | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age.
Nat Immunol
January 2025
Department of Cardiology, Renji Hospital, School of Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China.
A comprehensive understanding of the evolution of the immune landscape in humans across the entire lifespan at single-cell transcriptional and protein levels, during development, maturation and senescence is currently lacking. We recruited a total of 220 healthy volunteers from the Shanghai Pudong Cohort (NCT05206643), spanning 13 age groups from 0 to over 90 years, and profiled their peripheral immune cells through single-cell RNA-sequencing coupled with single T cell and B cell receptor sequencing, high-throughput mass cytometry, bulk RNA-sequencing and flow cytometry validation experiments. We revealed that T cells were the most strongly affected by age and experienced the most intensive rewiring in cell-cell interactions during specific age.
View Article and Find Full Text PDFAcute effects of voluntary breathing patterns on postural control during walking.
Hum Mov Sci
January 2025
Sports Physical Therapy Laboratory, School of Physical Education and Sports Science, National and Kapodistrian University of Athens, Greece. Electronic address:
Introduction: Breathing and postural control is reported to be both neuromuscularly and mechanically interdependent. To date, the effects of voluntary abdominal and thoracic breathing (VAB and VTB) on the EMG activity of muscles involved in both respiratory and postural functions, as well as gait biomechanics related to these breathing patterns, have not been investigated in young, healthy adults. The aim of the study was to evaluate the EMG responses of neck and trunk muscles, as well as the kinematic, stability, and kinetic parameters of gait induced by VAB and VTB compared to involuntary breathing (INB).
View Article and Find Full Text PDFFlexible electronic brush: Real-time multimodal sensing powered by reservoir computing through whisker dynamics.
Sci Adv
January 2025
Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan.
Article Synopsis
- Multimodal sensing using soft body dynamics is essential for controlling soft robotic movements, particularly through the imitation of whisker dynamics.
- The study introduces a multitasking electronic brush (e-brush) featuring four integrated pressure sensors capable of monitoring motion parameters like speed, force, slip, and surface interactions with low pressure sensitivity.
- A reservoir computing algorithm is employed to accurately extract and analyze these motion parameters, successfully demonstrating the brush's ability to track handwriting movements as a proof of concept.
Sphingolipid metabolism orchestrates establishment of the hair follicle stem cell compartment.
J Cell Biol
April 2025
Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Sphingolipids serve as building blocks of membranes to ensure subcellular compartmentalization and facilitate intercellular communication. How cell type-specific lipid compositions are achieved and what is their functional significance in tissue morphogenesis and maintenance has remained unclear. Here, we identify a stem cell-specific role for ceramide synthase 4 (CerS4) in orchestrating fate decisions in skin epidermis.
View Article and Find Full Text PDFElectronically Nonadiabatic Quenching of Excited States of O by Collisions with O Atoms.
J Phys Chem A
January 2025
Department of Chemistry and Chemical Biology, Center for Computational Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, United States.
The kinetics of electronically inelastic quenching of O(Δ) and O(Σ) by collisions with O(P) have been investigated using mixed quantum-classical trajectories governed by adiabatic potential energy surfaces and state couplings generated from a recently developed diabatic potential energy matrix (DPEM) for the 14 lowest-energy A' states of O. Using the coherent switching with decay of mixing (CSDM) method, dynamics calculations were performed both with 14 coupled electronic states and with 8 coupled electronical states, and similar results were obtained. The calculated thermal quenching rate coefficients are generally small, but they increase with temperature.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!