ArticleBiophysical journal2000
Backbone dipoles generate positive potentials in all proteins: origins and implications of the effect.
Article in Biophysical journal, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 79 citations in OpenAlex.
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- Marginal protein stability drives subcellular proteome isoelectric point.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes.Journal of computer-aided molecular design · 2018Article
- Model for screened, charge-regulated electrostatics of an eye lens protein: Bovine gammaB-crystallin.Physical review. E · 2017Article
- On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps.Protein science : a publication of the Protein Society · 2017Article
- Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.Methods in enzymology · 2016Review
- pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa.Proteins · 2015Article
- Stigmatellin probes the electrostatic potential in the QB site of the photosynthetic reaction center.Biophysical journal · 2015Article
- Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality.Protein engineering, design & selection : PEDS · 2014Article
- On the mechanism of respiratory complex I.Journal of bioenergetics and biomembranes · 2014Review
- Protons as second messenger regulators of G protein signaling.Molecular cell · 2013Article
- Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.The Journal of chemical physics · 2012Article
- A novel mechanism by which small molecule inhibitors induce the DFG flip in Aurora A.ACS chemical biology · 2012Article
- Multiconformation continuum electrostatics analysis of the effects of a buried Asp introduced near heme a in Rhodobacter sphaeroides cytochrome c oxidase.Biochemistry · 2010Article
- MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling.Journal of computational chemistry · 2009Article
- Article
- Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer.The journal of physical chemistry. B · 2008Article
- Protein denaturation by urea: slash and bond.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Semi-continuum electrostatic calculations of redox potentials in photosystem I.Photosynthesis research · 2008Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Asymmetry in packing the peptide amide dipole results in larger positive than negative regions in proteins of all folding motifs. The average side chain potential in 305 proteins is 109 +/- 30 mV (2. 5 +/- 0.7 kcal/mol/e). Because the backbone has zero net charge, the non-zero potential is unexpected. The larger oxygen at the negative and smaller proton at the positive end of the amide dipole yield positive potentials because: 1) at allowed phi and psi angles residues come off the backbone into the positive end of their own amide dipole, avoiding the large oxygen; and 2) amide dipoles with their carbonyl oxygen surface exposed and amine proton buried make the protein interior more positive. Twice as many amides have their oxygens exposed than their amine protons. The distribution of acidic and basic residues shows the importance of the bias toward positive backbone potentials. Thirty percent of the Asp, Glu, Lys, and Arg are buried. Sixty percent of buried residues are acids, only 40% bases. The positive backbone potential stabilizes ionization of 20% of the acids by >3 pH units (-4.1 kcal/mol). Only 6.5% of the bases are equivalently stabilized by negative regions. The backbone stabilizes bound anions such as phosphates and rarely stabilizes bound cations.
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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.