ArticleBiophysical journal2014
3D hydrophobic moment vectors as a tool to characterize the surface polarity of amphiphilic peptides.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 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
43 citing papers in PubMed, 82 citations in OpenAlex.
- Optimization strategies for antimicrobial peptides in dental caries prevention and management: from emerging mechanisms of action to clinical translation.Frontiers in microbiology · 2026Review
- Structure-Antimicrobial Activity Relationships of Recombinant Host Defence Peptides Against Drug-Resistant Bacteria.Microbial biotechnology · 2025Article
- Amino acids hydrophobic properties in proteins are derived from their atomic polarities.European biophysics journal : EBJ · 2025Article
- Molecular dynamics study of the helix-to-disorder transition in short antimicrobial peptides from Urodacus yaschenkoi.European biophysics journal : EBJ · 2025Article
- Specifically targeted antimicrobial peptides synergize with bacterial-entrapping peptide against systemic MRSA infections.Journal of advanced research · 2025Article
- Correlation Between Antimicrobial Structural Classes and Membrane Partitioning: Role of Emerging Lipid Packing Defects.The Journal of membrane biology · 2024Article
- Role of Peptide Associations in Enhancing the Antimicrobial Activity of Adepantins: Comparative Molecular Dynamics Simulations and Design Assessments.International journal of molecular sciences · 2024Article
- Modifying Membranotropic Action of Antimicrobial Peptide Gramicidin S by Star-like Polyacrylamide and Lipid Composition of Nanocontainers.International journal of molecular sciences · 2024Article
- A Critical Review of Short Antimicrobial Peptides from Scorpion Venoms, Their Physicochemical Attributes, and Potential for the Development of New Drugs.The Journal of membrane biology · 2024Review
- Accelerating Antimicrobial Peptide Discovery for WHO Priority Pathogens through Predictive and Interpretable Machine Learning Models.ACS omega · 2024Article
- Peptide Flexibility and the Hydrophobic Moment are Determinants to Evaluate the Clinical Potential of Magainins.The Journal of membrane biology · 2023Article
- Mechanistic Insights into Bioengineered Antibiofilm Enamel Pellicles.Journal of dental research · 2023Article
- Relating Molecular Dynamics Simulations to Functional Activity for Gly-Rich Membranolytic Helical Kiadin Peptides.Pharmaceutics · 2023Article
- The Amphipathic Helix in Visual Cycle Proteins: A Review.Advances in experimental medicine and biology · 2023Review
- Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes.Membranes · 2022Article
- Membrane fluidity, composition, and charge affect the activity and selectivity of the AMP ascaphin-8.Biophysical journal · 2022Article
- Improving the Therapeutic Index of Smp24, a Venom-Derived Antimicrobial Peptide: Increased Activity against Gram-Negative Bacteria.International journal of molecular sciences · 2022Article
- Antibacterial Activity of T22, a Specific Peptidic Ligand of the Tumoral Marker CXCR4.Pharmaceutics · 2021Article
- Membrane partitioning and lipid selectivity of the N-terminal amphipathic H0 helices of endophilin isoforms.Biochimica et biophysica acta. Biomembranes · 2021Article
- The importance of hydrophobic interactions in the structure of transcription systems.European biophysics journal : EBJ · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The interaction of membranes with peptides and proteins is largely determined by their amphiphilic character. Hydrophobic moments of helical segments are commonly derived from their two-dimensional helical wheel projections, and the same is true for β-sheets. However, to the best of our knowledge, there exists no method to describe structures in three dimensions or molecules with irregular shape. Here, we define the hydrophobic moment of a molecule as a vector in three dimensions by evaluating the surface distribution of all hydrophilic and lipophilic regions over any given shape. The electrostatic potential on the molecular surface is calculated based on the atomic point charges. The resulting hydrophobic moment vector is specific for the instantaneous conformation, and it takes into account all structural characteristics of the molecule, e.g., partial unfolding, bending, and side-chain torsion angles. Extended all-atom molecular dynamics simulations are then used to calculate the equilibrium hydrophobic moments for two antimicrobial peptides, gramicidin S and PGLa, under different conditions. We show that their effective hydrophobic moment vectors reflect the distribution of polar and nonpolar patches on the molecular surface and the calculated electrostatic surface potential. A comparison of simulations in solution and in lipid membranes shows how the peptides undergo internal conformational rearrangement upon binding to the bilayer surface. A good correlation with solid-state NMR data indicates that the hydrophobic moment vector can be used to predict the membrane binding geometry of peptides. This method is available as a web application on http://www.ibg.kit.edu/HM/.
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.