Geometry, thermodynamics, and protein

Fang, Yi; Jing, Junmei

doi:10.1016/j.jtbi.2009.09.013

Cited by 10 publications

(18 citation statements)

References 31 publications

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“…We note finally that although the notion of protein surface tension is not widely used, the protein surface is undisputedly of the highest importance, and so should the associated Gibbs free energy [20].…”

Section: Capillary Compactionmentioning

confidence: 95%

Why do GroEL Ions Exhibit Two Gas Phase Conformers?

Mora

2012

J. Am. Soc. Mass Spectrom.

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The reasons for the existence of two gas phase conformers for electrosprayed ions of the large tetradecameric protein complex GroEL are considered. Key features are that: (1) both conformers extrapolate to very similar cross sections in the limit of zero charge; (2) both conformers supercharge above the maximum value permitted by the Rayleigh criterion; and (3) one of the conformers supercharges substantially more than the other. We hypothesize that the supercharging observed is associated to the approximately cylindrical shape of GroEL in aqueous solution, enabling accumulation of extra charge on either one or two of its bases when they intersect the evaporating drop surface. The two conformers would then correspond to cases when either one or the two bases of the cylinder carry extra charge. Apparently, the conformer symmetrically (doubly) supercharged on both ends is Coulombically stretched, therefore exhibiting a mobility different from the conformer asymmetrically supercharged only on one end. Several general consequences follow. First, non-spherical proteins may generally be charged above the usual Rayleigh limit. Second, we confirm the previously advanced but contentious notion that gas phase protein ions are readily compacted or stretched away from their crystal structure by capillary and Coulombic forces during the electrospraying process.

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Section: Capillary Compactionmentioning

confidence: 95%

Why do GroEL Ions Exhibit Two Gas Phase Conformers?

Mora

2012

J. Am. Soc. Mass Spectrom.

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“…In [15] a simulation of enlarging the hydrophobic core alone, whose forming is considered the main effect of HOO, not only produced secondrary structures, but also produced the intra-molecular hydrogen bonds. This result shows that HOO should not be dismissed so simply.…”

Section: Thermodynamic Systemmentioning

confidence: 99%

“…Rather, the chemical potentials w ll be constants duri the folding, as the environment is u changed. s i ng kept Formula (10) is not easy to calculate, we can convert it in so al de ed form la appeared n to a geometric form that is not only calculable but al coincident to a mathematic ly riv u in [15,19].…”

Section: The Formulasmentioning

confidence: 99%

Ben-Naim’s “Pitfall”: Don Quixote’s Windmill

Fang¹

2013

OJBIPHY

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Ben-Naim in three articles dismissed and "answered" the Levinthal's paradox. He announces there are pitfalls caused by the "misinterpretation" of thermodynamic hypothesis. He claims no existence of Gibbs free energy formula   G X where the variable is a protein's conformation X . His Gibbs energy functional is     , , ; G T P N P R , where the variable is probability distributions of the conformations. His "minimum distribution " is wrong. By carefully establishing thermodynamic systems, we demonstrate how to apply quantum statistics to derive Gibbs free energy formulaThe formula of the folding force   G  X is given.

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“…The theoretically derived formulas (1) and (2) can explain why the hydrophobic effect is indeed the driving force. A simulation of reducing hydrophobic area alone by Fang and Jing (2010) shows that the result is the appearance of regularly patterned intramolecular hydrogen bonds associated to the secondary structures.…”

Section: Explain Hydrophobic Effect and The Role Played By Hydrogen Bmentioning

confidence: 99%

“…Moreover, a simulation of shrinking hydrophobic surface area alone indeed produced secondary structures and hydrogen bonds. The simulation was reported by Fang and Jing (2010). Without calculating any dihedral angles or electronic charges, without any arbitrary parameter, paying no attention to any particular atom's position, by just reducing hydrophobic surface area (there it was assumed that there are only two kinds of atoms, hydrophobic and hydrophilic), secondary structures and hydrogen bonds duly appeared.…”

Section: Explain Hydrophobic Effect and The Role Played By Hydrogen Bmentioning

confidence: 99%