Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification

Klapper, Isaac; Hagstrom, Ray; Fine, Richard M.; Sharp, Kim A.; Honig, Barry

doi:10.1002/prot.340010109

Cited by 750 publications

(620 citation statements)

References 19 publications

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“…Qualitative electrostatic surface potentials can be calculated, e.g., with the program PyMOL [DeLano, 2002] or Delphi [Klapper et al, 1986;. In addition to the shape, also charge properties are important, e.g., for ligand (substrate, cofactor, inhibitor, etc.)…”

Section: Discussionmentioning

confidence: 99%

Bioinformatic analysis of protein structure–function relationships: case study of leukocyte elastase (ELA2) missense mutations

Thusberg

Vihinen

2006

Hum. Mutat.

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For the Immunogenetics Special IssueCyclic and congenital neutropenia are caused by mutations in the human neutrophil elastase (HNE) gene (ELA2), leading to an immunodeficiency characterized by decreased or oscillating levels of neutrophils in the blood. The HNE mutations presumably cause loss of enzyme activity, consequently leading to compromised immune system function. To understand the structural basis for the disease, we implemented methods from bioinformatics to analyze all the known HNE missense mutations at both the sequence and structural level. Our results demonstrate that the 32 different mutations have diverse effects on HNE structure and function, affecting structural disorder and aggregation tendencies, stability maintaining contacts, and electrostatic properties. A large proportion of the mutations are located at conserved amino acids, which are usually essential in determining protein structure and function. The majority of the disease-causing HNE missense mutations lead to major structural changes and loss of stability in the protein. A few mutations also affect functional residues, leading into decreased catalytic activity or altered ligand binding. Our analysis reveals the putative effects of all known missense mutations in HNE, thus allowing the structural basis of cyclic and congenital neutropenia to be elucidated. We have employed and analyzed a set of some 30 different methods for predicting the effects of amino acid substitutions. We present results and experience from the analysis of the applicability of these methods in the analysis of numerous genes, proteins, and diseases to reveal protein structure-function relationships and disease genotype-phenotype correlations.

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Section: Discussionmentioning

confidence: 99%

Bioinformatic analysis of protein structure–function relationships: case study of leukocyte elastase (ELA2) missense mutations

Thusberg

Vihinen

2006

Hum. Mutat.

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“…We made use of finite difference "focusing" [38] in order to improve accuracy of our electrostatic calculations. The first grid always encompassed the entire molecule(s) plus an adequate solvent region (135 3 cubic grid with a…”

Section: Computational Proceduresmentioning

confidence: 99%

Poisson–Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E

Szklarczyk

Zuberek

Antosiewicz

2009

Biophysical Chemistry

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT AbstractThe electrostatic free energy of binding of two analogues of the 5'-mRNA cap, differing in size and electric charge, to the wild type and mutated eukaryotic initiation factor eIF4E was computed using the finite difference solutions to the Poisson-Boltzmann equation. Two definitions of the solute-solvent dielectric boundary were used: van der Waals model, solvent exclusion (SE) model. The computed electrostatic energies were supplemented by estimations of the non polar and entropic contributions. A comparison with experimental data for the investigated systems was done. It appears that the SE model with additional contribution fits experimental findings better than the van der Waals model does.

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“…Partial charges have been assigned to the atomic coordinates, including all hydrogen atoms, according to the CHARMM force field (Brooks et al, 1983). To simulate the finite radius of the solvent ions an ion exclusion layer (Klapper et al, 1986) of 2 8, was used in the calculations.…”

Section: Brownian Dynamics Simulations and Electrostatic Potential Camentioning

confidence: 99%

Role of the electrostatic loop charged residues in Cu, Zn superoxide dismutase

et al. 1998

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We have expressed and characterized a mutant of Xenopus laevis Cu,Zn superoxide dismutase in which four highly conserved charged residues belonging to the electrostatic loop have been replaced by neutral side chains: Lysl20 + Leu, Asp130 + Gln, Glu131 + Gln, and Lys134 -+ Thr. At low ionic strength, the mutant enzyme is one of the fastest superoxide dismutases ever assayed (k = 6.7 X 10' M" s-' , at pH 7 and p = 0.02 M). Brownian dynamics simulations give rise to identical enzyme-substrate association rates for both wild-type and mutant enzymes, ruling out the possibility that enhancement of the activity is due to pure electrostatic factors. Comparative analysis of the experimental catalytic rate of the quadruple and single mutants reveals the nonadditivity of the mutation effects, indicating that the hyperefficiency of the mutant is due to a decrease of the energy barrier and/or to an alternative pathway for the diffusion of superoxide within the active site channel. At physiological ionic strength the catalytic rate of the mutant at neutral pH is similar to that of the wild-type enzyme as it is to the catalytic rate pH dependence. Moreover, mutation effects are additive. These results show that, at physiological salt conditions, electrostatic loop charged residues do not influence the diffusion pathway of the substrate and, if concomitantly neutralized, are not essential for high catalytic efficiency of the enzyme, pointing out the role of the metal cluster and of the invariant Arg 141 in determining the local electrostatic forces facilitating the diffusion of the substrate towards the active site.

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Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification

Cited by 750 publications

References 19 publications

Bioinformatic analysis of protein structure–function relationships: case study of leukocyte elastase (ELA2) missense mutations

Bioinformatic analysis of protein structure–function relationships: case study of leukocyte elastase (ELA2) missense mutations

Poisson–Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E

Role of the electrostatic loop charged residues in Cu, Zn superoxide dismutase

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