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Biomedical subjects

B Honig

Publications and source records attributed to B Honig.

At least 91 records · Page 5Linked to original sources
PubMed1988

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis.

In this report we describe an accurate numerical method for calculating the total electrostatic energy of molecules of arbitrary shape and charge distribution, accounting for both Coulombic and solvent polarization terms. In addition to the solvation energies of individual molecules, the method can be used to calculate the electrostatic energy associated with conformational changes in proteins as well as changes in solvation energy that accompany the binding of charged substrates. The validity of the method is examined by calculating the hydration energies of acetate, methyl ammonium, ammonium, and methanol. The method is then used to study the relationship between the depth of a charge within a protein and its interaction with the solvent. Calculations of the relative electrostatic energies of crystal and misfolded conformations of Themiste dyscritum hemerythrin and the VL domain of an antibody are also presented. The results indicate that electrostatic charge-solvent interactions strongly favor the crystal structures. More generally, it is found that charge-solvent interactions, which are frequently neglected in protein structure analysis, can make large contributions to the total energy of a macromolecular system.

Binding, Competitive↗
PubMed1988

Chromophore/protein and chromophore/anion interactions in halorhodopsin.

Halorhodopsin (HR), the light-driven chloride transport pigment of Halobacterium halobium, was bleached and reconstituted with retinal analogues with the pi electron system interrupted at different locations (dihydroretinals). The absorption maxima of the artificial pigments formed with the dihydroretinals are found to be very similar to those of the corresponding pigments formed by reconstitution of bacteriorhodopsin (BR) and sensory rhodopsin (SR). This strongly suggests that the distribution of charges around the retinal is similar in all three bacterial rhodopsins. Comparison of the primary, and proposed secondary, structures for HR and BR reveal conserved asparagine (asp) and arginine (arg) residues, which are likely candidates for the ionizable amino acids that interact with the retinal. In a second set of experiments absorption shifts due to the binding of anions to Sites I and II in HR, reconstituted with different retinal analogues, were used to estimate the locations of these binding sites relative to the retinal. Site I is localized near the Schiff base, and Site II near the ionone ring. On the basis of these results a structural model for HR is proposed, which accounts for the spectroscopic properties of HR in terms of the three buried arg residues and two of the buried asp residues in the protein.

Bacteriorhodopsins↗
PubMed1987

Computer simulations of the diffusion of a substrate to an active site of an enzyme.

Computer simulations of the diffusion of a substrate to an enzyme active site were performed. They included the detailed shape of the protein and an accurate description of its electrostatic potential. Application of the method to the diffusion of the superoxide anion to the protein superoxide dismutase revealed that the electric field of the enzyme enhances the association rate of the anion by a factor of 30 or more. Calculated changes in the association rate as a function of ionic strength and amino acid modification paralleled the observed behavior. Design principles of superoxide dismutase are considered with respect to insights provided by the simulations. A possible means of enhancing the enzyme turnover rate through site-directed mutagenesis is proposed.

Binding Sites↗
PubMed1986

Internal cavities and buried waters in globular proteins.

A fast algorithm that detects internal cavities in proteins and predicts the positions of buried water molecules is described. The cavities are characterized in terms of volume, surface area, polarity, and the presence of bound waters. The algorithm is applied to 12 proteins whose structures are known to high resolution and successfully predicts the locations of over 80% of internal water molecules. Most proteins are found to have a number of internal cavities ranging in volume from 10 to 180 A3. Some of these cavities contain water and some do not, with the probability of containing a buried water increasing with cavity size. However, many large cavities are found to be empty (i.e., they do not contain a crystallographically determined water). For multidomain proteins over half of the total cavity volume is at the interdomain interface. Possible implications for the energetics of cavity formation and for the functional role of internal cavities are discussed.

Hydrogen Bonding↗
PubMed1986

Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification.

In this paper we report the implementation of a finite-difference algorithm which solves the linearized Poisson-Boltzmann equation for molecules of arbitrary shape and charge distribution and which includes the screening effects of electrolytes. The microcoding of the algorithm on an ST-100 array processor allows us to obtain electrostatic potential maps in and around a protein, including the effects of ionic strength, in about 30 minutes. We have applied the algorithm to a dimer of the protein Cu-Zn superoxide dismutase (SOD) and compared our results to those obtained from uniform dielectric models based on coulombic potentials. We find that both the shape of the protein-solvent boundary and the ionic strength of the solvent have a profound effect on the potentials in the solvent. For the case of SOD, the cluster of positive charge at the bottom of the active site channel produces a strongly enhanced positive potential due to the focusing of field lines in the channel-a result that cannot be obtained with any uniform dielectric model. The remainder of the protein is surrounded by a weak negative potential. The electrostatic potential of the enzyme seems designed to provide a large cross-sectional area for productive collisions. Based on the ionic strength dependence of the size of the positive potential region emanating from the active site and the repulsive negative potential barrier surrounding the protein, we are able to suggest an explanation for the ionic strength dependence of the activity of the native and chemically modified forms of the enzyme.

Amino Acids↗
PubMed1986

The influence of short-term estrogen replacement therapy (ERT) on the blood pressure and daily urinary catecholamine excretion in a small group of post-menopausal women.

The blood pressure and daily urinary catecholamine excretion were examined in nineteen non-smoking post-menopausal women, receiving estrogen replacement therapy for a period of 4 months. The estrogens administered consisted of 17 beta-estradiol combined with estriol and norethisterone acetate administered sequentially (Trisequens, Novo, Denmark). Before the institution of treatment, the blood pressure and urinary catecholamine excretion were normal. After a period of 4 months, no change in blood pressure was observed. However, a marked and significant increase in daily urinary catecholamine excretion was noticed (72.3 +/- 18.96 micrograms/day to 102.0 +/- 26.0 micrograms: p less than 0.01). The pathogenetic implications of this increase are discussed.

Blood Pressure↗
PubMed1986

Chromophore/protein interaction in bacterial sensory rhodopsin and bacteriorhodopsin.

Retinal analogues with altered conjugated double bond systems or altered stereochemistry were incorporated into the phototaxis receptor sensory rhodopsin (SR) and the light-driven proton pump bacteriorhodopsin (BR) from Halobacterium halobium. Wavelength shifts in absorption ("opsin shifts") due to analogue interaction with the protein microenvironment demonstrate that the same overall electrostatic and steric properties of the retinal binding-site structures exist in both proteins despite their different functions. pi-Electron calculations from the opsin shifts lead to a new description of protein charge distribution that applies to the binding sites of both SR and BR. The new data extends the previously proposed external point charge model for BR to include an ion-pair protein/chromophore interaction near the beta-ionone moiety. The new data modifies the previously proposed external point-charge model, the derivation of which involved an experimentally erroneous opsin shift for one of the BR analogues.

Bacteriorhodopsins↗
PubMed1985

On the calculation of electrostatic interactions in proteins.

In this paper we present a classical treatment of electrostatic interactions in proteins. The protein is treated as a region of low dielectric constant with spherical charges embedded within it, surrounded by an aqueous solvent of high dielectric constant, which may contain a simple electrolyte. The complete analysis includes the effects of solvent screening, polarization forces, and self energies, which are related to solvation energies. Formulae, and sample calculations of forces and energies, are given for the special case of a spherical protein. Our analysis and model calculations point out that any consistent treatment of electrostatic interactions in proteins should account for the following. Solvent polarization is an important factor in the calculation of pairwise electrostatic interactions. Solvent polarization substantially affects both electrostatic energies and forces acting upon charges. No simple expression for the effective dielectric constant, Deff, can generally be valid, since Deff is a sensitive function of position. Solvent screening of pairwise interactions involving dipolar groups is less effective than the screening of charges. In fact for many interactions involving dipoles, solvent screening can be essentially ignored. The self energy of charges makes a large contribution to the total electrostatic energy of a protein. This must be compensated by specific interactions with other groups in the protein. Strategies for applying our analysis to proteins whose structures are known are discussed.

Electricity↗
PubMed1984

On the environment of ionizable groups in globular proteins.

The environment of ionizable groups in 36 proteins is characterized in terms of solvent-accessibility, salt-bridge formation and hydrogen-bonding. Possible implications of our results as to the protonation state of buried ionizable groups are considered and patterns useful for model building studies on proteins are derived. The most interesting finding is that there are on average two completely buried ionizable groups per protein of which at least 20% do not form salt-bridges. However, all buried ionizable groups form hydrogen bonds with neutral polar groups.

Amino Acids↗
PubMed1984

Fluorescence quantum yield of visual pigments: evidence for subpicosecond isomerization rates.

The fluorescence quantum yields (phi f) for bovine and squid rhodopsins are determined. Both pigments yield similar results, with an average value for phi f of 1.2 (+/- 0.5) X 10(-5). Since the estimated radiative lifetime of rhodopsin is 5 nsec, the rate constant of the process that competes with fluorescence must be on the order of 0.1 psec. Given the large quantum yield for isomerization of rhodopsin's retinal chromophore, this process is likely to correspond to the motion along retinal's C11-C12 torsional coordinate that leads to cis-trans isomerization. An empirical excited-state potential energy curve along this coordinate is derived. It is shown that subpicosecond torsional motion to highly twisted nonfluorescing regions of the potential is possible and, in fact, likely. Our results require the existence of a barrier-less excited-state potential energy curve and suggest that cis-trans isomerization occurs in less than 1 psec.

Animals↗
PubMed1983

Charged amino acids as spectroscopic determinants for chlorophyll in vivo.

In this paper we propose that the large spectroscopic red shifts observed for chlorophyll (Chl) and bacteriochlorophyll (BChl) in vivo may be due to charged amino acids in the binding site. Molecular orbital calculations of the transition energies of Chl in the field of external charges are carried out. The calculated wavelength shifts induced by these charges are comparable in magnitude to those observed in vivo. Moreover the size of the shifts increases in the order BChl b > BChl a > Chl a, which is the observed trend. The ability of the calculations to account for both the absolute and relative magnitudes of the wavelength shifts argues for the validity of the model. Further indirect support comes from the recent demonstration that charged amino acids are responsible for the colors of visual pigments and bacteriorhodopsin. In addition to their effects on spectra the presence of external charges induces large changes in the ionization potential of Chl molecules and thus might explain the in vivo alteration of the oxidation potentials in reaction centers.

Journal Article↗
PubMed1982

Theoretical studies of the electrochromic response of carotenoids in photosynthetic membranes.

Molecular orbital calculations are carried out on a number of carotenoids in the presence of an external charge and a constant electric field. The external charge is used to represent the strong permanent field that is believed to polarize carotenoids in photosynthetic membranes and thus to account for their linear response to the transmembrane potential. Our calculations show that the in vitro leads to in vivo spectral shifts of carotenoids (approximately 25 nm) can be produced by a charge in close proximity to the molecule. The interaction of the induced dipole moment with a constant field accounts for the observed magnitude of the electrochromic response in photosynthetic bacteria. The existence of a second pool of carotenoids that shows a significant (approximately 20 nm) wavelength shift but no electrochromic response can be explained by an external charge positioned near the center of the molecule that affects its absorption maximum while inducing essentially no dipole moment. The spectral shift for this pool is due to the induction of higher multipoles. These also account for discrepancies that arise when one attempts to account quantitatively for available experimental results on carotenoid band shifts in terms of classical electrochromic theory.

Bacteriorhodopsins↗
PubMed1981

Environmental effects on formation and photoreaction of the M412 photoproduct of bacteriorhodopsin: implications for the mechanism of proton pumping.

Photochemical studies of the effects of temperature, pH, and dehydration on the formation and back photoreaction of the M412 intermediate in the photocycle of light-adapted bacteriorhodopsin (bR570) are carried out. Continuous illumination experiments in the range between -40 and -90 degrees C indicate that at low temperatures branching occurs at the stage of the L550 intermediate in which a back reaction to the parent pigment competes with the formation of M412. At low temperatures the yield of M412 is markedly increased at high pH. The effect is attributed to the catalytic action of a protein group of pK congruent to 10 on the rate of the L550 leads to M412 process. Our results, taken together with previous evidence for deprotonation of a tyrosine during the L550 leads to M412 transition, suggest that the formation of a tyrosinate ion is a prerequisite for deprotonation of the Schiff base. A model is proposed in which both the Schiff base and the tyrosine translocate their protons to two acceptor groups, A1 and A2, accessible to the outside of the cell through a segment of a proton wire. The model accounts for the observation that up to two photons may be pumped per cycle. The proton-pump mechanism is analyzed in terms of a generalized kinetic scheme for pumping. In contrast to current models for proton pumping which are based on a (primary) light-induced accessibility change of the chromophore (class I models), we introduce a new class (II) of models based exclusively on pK changes. We suggest that in bR570 the Schiff base and the tyrosine are accessible to protons on the outside surface of the membrane. An analysis of the back photoreaction from M412 tends to favor class II models over previous class I models.

Bacteriorhodopsins↗
PubMed1981

On the mechanism of hydrogen-deuterium exchange in bacteriorhodopsin.

Continuous-flow resonance Raman experiments carried out in bacteriorhodopsin show that the exchange of a deuteron on the Schiff base with a proton takes place in times shorter than 3 ms. Exchange mechanisms based on a base-catalyzed deprotonation followed by reprotonation of the Schiff base are excluded. A mechanism is suggested in which a water molecule interacts directly with the Schiff base deuteron in a concerted exchange mechanism. It appears that in the dark, the binding site is more accessible to neutral water molecules than to charged protons.

Bacteriorhodopsins↗