THE APPARENT DISSOCIATION CONSTANTS OF PHENYLALANINE AND OF DIHYDROXYPHENYLALANINE AND THE APPARENT FREE ENERGY AND ENTROPY CHANGES OF CERTAIN AMINO ACIDS DUE TO IONIZATION

Cotranslational translocon-mediated insertion of membrane proteins into the endoplasmic reticulum is a key process in membrane protein biogenesis. Although the mechanism is understood in outline, quantitative data on the energetics of the process is scarce. Here, we have measured the effect on membrane integration efficiency of nonproteinogenic analogs of the positively charged amino acids arginine and lysine incorporated into model transmembrane segments. We provide estimates of the influence on the apparent free energy of membrane integration (ΔGapp) of “snorkeling” of charged amino acids toward the lipid–water interface, and of charge neutralization. We further determine the effect of fluorine atoms and backbone hydrogen bonds (H-bonds) on ΔGapp. These results help establish a quantitative basis for our understanding of membrane protein assembly in eukaryotic cells.

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Correction to the article “Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations”

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21916 ◽

2008 ◽

Vol 70 (4) ◽

pp. 1655-1656 ◽

Cited By ~ 2

Author(s):

Anna C. V. Johansson ◽

Erik Lindahl

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Lipid Membranes ◽

Free Energy Of Solvation ◽

Dynamics Simulations

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CALCULATION OF THE STANDARD GIBBS FREE ENERGY, ENTHALPY, AND ENTROPY CHANGES FOR THE HYDROLYSIS OF ATP AT 0°, 25°, 37°, and 75°

Horizons of Bioenergetics ◽

10.1016/b978-0-12-618940-7.50017-3 ◽

1972 ◽

pp. 135-147 ◽

Cited By ~ 6

Author(s):

Robert A. Alberty

Keyword(s):

Free Energy ◽

Gibbs Free Energy ◽

Standard Gibbs Free Energy ◽

Entropy Changes ◽

Enthalpy And Entropy Changes ◽

Enthalpy And Entropy ◽

Hydrolysis Of

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Thermodynamics of Helix formation in small peptides of varying lengthin vacuo, implicit solvent and explicit solvent: Comparison between AMBER force fields

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633619500159 ◽

2019 ◽

Vol 18 (03) ◽

pp. 1950015

Author(s):

Zhaoxi Sun ◽

Xiaohui Wang

Keyword(s):

Amino Acids ◽

Free Energy ◽

Hydrogen Bonds ◽

Force Fields ◽

Implicit Solvent ◽

Conformational Ensemble ◽

Helix Formation ◽

Solvent Models ◽

Explicit Solvent ◽

Amber Force Fields

Helix formation is of great significance in protein folding. The helix-forming tendencies of amino acids are accumulated along the sequence to determine the helix-forming tendency of peptides. Computer simulation can be used to model this process in atomic details and give structural insights. In the current work, we employ equilibrate-state free energy simulation to systematically study the folding/unfolding thermodynamics of a series of mutated peptides. Two AMBER force fields including AMBER99SB and AMBER14SB are compared. The new 14SB force field uses refitted torsion parameters compared with 99SB and they share the same atomic charge scheme. We find that in vacuo the helix formation is mutation dependent, which reflects the different helix propensities of different amino acids. In general, there are helix formers, helix indifferent groups and helix breakers. The helical structure becomes more favored when the length of the sequence becomes longer, which arises from the formation of additional backbone hydrogen bonds in the lengthened sequence. Therefore, the helix indifferent groups and helix breakers will become helix formers in long sequences. Also, protonation-dependent helix formation is observed for ionizable groups. In 14SB, the helical structures are more stable than in 99SB and differences can be observed in their grouping schemes, especially in the helix indifferent group. In solvents, all mutations are helix indifferent due to protein–solvent interactions. The decrease in the number of backbone hydrogen bonds is the same with the increase in the number of protein–water hydrogen bonds. The 14SB in explicit solvent is able to capture the free energy minima in the helical state while 14SB in implicit solvent, 99SB in explicit solvent and 99SB in implicit solvent cannot. The helix propensities calculated under 14SB agree with the corresponding experimental values, while the 99SB results obviously deviate from the references. Hence, implicit solvent models are unable to correctly describe the thermodynamics even for the simple helix formation in isolated peptides. Well-developed force fields and explicit solvents are needed to correctly describe the protein dynamics. Aside from the free energy, differences in conformational ensemble under different force fields in different solvent models are observed. The numbers of hydrogen bonds formed under different force fields agree and they are mostly determined by the solvent model.

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Chelating polymers. I. The synthesis and acid dissociation behavior of several N-(p-vinylbenzenesulfonyl)-substituted diaminopolyacetic acid monomers, monomeric analogues, and related intermediates

Canadian Journal of Chemistry ◽

10.1139/v70-023 ◽

1970 ◽

Vol 48 (1) ◽

pp. 163-175 ◽

Cited By ~ 13

Author(s):

R. M. Genik-Sas-Berezowsky ◽

I. H. Spinner

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Dissociation Constants ◽

Acid Dissociation ◽

Inductive Effects ◽

Cyclic Amide ◽

Amino Acid Analogues ◽

Related Compounds ◽

Chelating Polymers ◽

Made In

Two new chelating monomers, N-(p-vinylbenzenesulfonyl)1,2-diaminoethane-N′,N′-diacetic (SS-EDDA) and -N,N′,N′-triacetic (SS-ED3A) acids, as well as several monomeric analogues and related intermediates have been prepared. In addition, 2-oxo-1-piperazine acetic (S-KP), 3-oxo-1-piperazine acetic (U-KP), and 2-oxo-1,4-piperazine diacetic (3-KP) acids have been synthesized and the interconvertibility between these cyclic amides and their unsubstituted linear amino acid analogues, ethylene-diamine-N,N′-diacetic (S-EDDA), -N,N-diacetic (U-EDDA), and -N,N,N′-triacetic (ED3A) acids respectively, was demonstrated.The acid dissociation constants of the various amino acids were determined potentiometrically at 25° and μ = 0.1 M(KNO3) and the results were compared with the hydrogen ion affinities of related compounds. Dissociation schemes were proposed for all the compounds based on these results. Rationalizations of the linear amino acid and the cyclic amide dissociation constants were made in terms of the effects of cyclization and the inductive effects of neighboring groups. These rationalizations were found to be helpful in clarifying the dissociation schemes previously proposed for several of the linear amino acids.

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