ArticleBiophysical journal2009
Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 37 citations in OpenAlex.
- Cyanovirin-N Binding toBiochemistry · 2024Article
- Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations.eLife · 2022Article
- A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations.Glycobiology · 2021Article
- The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations.Biophysical journal · 2019Article
- Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics.International journal of molecular sciences · 2018Review
- Article
- Article
- Article
- Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins.Biophysical journal · 2014Article
- A flexible docking scheme efficiently captures the energetics of glycan-cyanovirin binding.Biophysical journal · 2014Article
- Dependence of protein crystal stability on residue charge states and ion content of crystal solvent.Biophysical journal · 2014Article
- Linker-extended native cyanovirin-N facilitates PEGylation and potently inhibits HIV-1 by targeting the glycan ligand.PloS one · 2014Article
- Network visualization of conformational sampling during molecular dynamics simulation.Journal of molecular graphics & modelling · 2013Article
- Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field.Journal of computational chemistry · 2013Article
- Carbohydrate force fields.Wiley interdisciplinary reviews. Computational molecular science · 2012Article
- Molecular simulation uncovers the conformational space of the λ Cro dimer in solution.Biophysical journal · 2011Article
- Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics.Biophysical journal · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cyanovirin-N (CVN) is a highly potent anti-HIV carbohydrate-binding agent that establishes its microbicide activity through interaction with mannose-rich glycoprotein gp120 on the virion surface. The m4-CVN and P51G-m4-CVN mutants represent simple models for studying the high-affinity binding site, B(M). A recently determined 1.35 A high-resolution structure of P51G-m4-CVN provided details on the di-mannose binding mechanism, and suggested that the Arg-76 and Glu-41 residues are critical components of high mannose specificity and affinity. We performed molecular-dynamics simulations in solution and a crystal environment to study the role of Arg-76. Network analysis and clustering were used to characterize the dynamics of Arg-76. The results of our explicit solvent solution and crystal simulations showed a significant correlation with conformations of Arg-76 proposed from x-ray crystallographic studies. However, the crystal simulation showed that the crystal environment strongly biases conformational sampling of the Arg-76 residue. The solution simulations demonstrated no conformational preferences for Arg-76, which would support its critical role as the residue that locks the ligand in the bound state. Instead, a comparative analysis of trajectories from >50 ns of simulation for two mutants revealed the existence of a very stable eight-hydrogen-bond network between the di-mannose ligand and predominantly main-chain atoms. This network may play a key role in the specific recognition and strong binding of mannose oligomers in CVN and its homologs.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.