The distribution of charged groups in proteins

Barlow, D. J.; Thornton, Janet M.

doi:10.1002/bip.360250913

Cited by 131 publications

(78 citation statements)

References 24 publications

(3 reference statements)

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“…An explanation might be that the charge density is not distributed homogeneously over the surface and can differ between proteins. This hypothesis was checked with the data presented by Barlow and Thornton [43], who calculated local and overall charge densities at pH 7.0 for several proteins on the basis of their crystal structures. They found Table 1 overall surface charge densities to be rather similar.…”

Section: Resultsmentioning

confidence: 94%

Protein transfer from an aqueous phase into reversed micelles

Wolbert¹,

Hilhorst²,

Voskuilen³

et al. 1989

European Journal of Biochemistry

113

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Proteins are spontaneously transferred from an aqueous solution into reversed micelles, provided the aqueous phase has the proper composition. Besides the composition of the aqueous phase, the composition of the organic phase and the properties of the proteins also play a role. We studied uptake profiles of 19 proteins as a function of pH of the aqueous solution. The organic phase consisted of trioctylmethylammonium chloride and nonylphenol pentaethoxylate (Rewopal HV5) as surfactant, octanol as cosurfactant and isooctane as continuous phase. In all cases, except for rubredoxin, proteins were transferred at pH values above their isoelectric point. The pH where maximal solubilization takes place can be described by the relationship: pHoptimum = isoelectric point f0.11 x 1O-j M , -0.97. So, the larger the protein, the more charge is needed to provide the energy required for the adaptation of the micellar size to the protein size. For protein transfer into sodium di-(2-ethylhexyl)sulphosuccinate Several fields of application for reversed micelles in biotechnology have been suggested (for reviews see [l -41). One of the potential applications is the extraction of proteins from an aqueous or solid phase via a reversed micellar phase into a second aqueous phase. This double transfer process is based on the ability of reversed micelles to extract proteins from an aqueous solution into their aqueous core. Most proteins retain their native conformation during the transfer process and remain in an active form when incorporated into reversed micelles [ 1 -61.Hatton and coworkers have shown that this technique is feasible for the extraction of proteins from a fermentation broth [7] and Leser et al. [8] demonstrated its applicability for the extraction of proteins from the solid phase. Previously [9] we reported that a-amylase could be extracted from an aqueous solution into a reversed micellar medium and re-extracted into a second aqueous phase in a continuous process with a yield of 45% and a concentration factor of eight with respect to enzyme activity. Addition of the nonionic surfactant nonylphenol pentaethoxylate (Rewopal HV5) to the organic phase, led to an increase both in the degree of solubilization of the enzyme and in the pH range in which solubilization occurs [lo]. By increasing the rate of mass transfer and the distribution coefficient of the enzyme during forward extraction, the yield has been improved to 85% and the concentration factor to 17 [ll].From the results published to date, it becomes evident that protein partitioning depends on the pH, ionic strength and type of ions present in the aqueous phase, on the type of surfactant, cosurfactant and organic solvent used, on micellar size, on the temperature and on properties of the protein [ 5 , 12 -161. However, no information is available on the mechanisms by which these variables affect protein partitioning. In this study the partitioning behaviour is related to such protein properties as size, isoelectric point and distribution of charged groups over th...

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Section: Resultsmentioning

confidence: 94%

Protein transfer from an aqueous phase into reversed micelles

Wolbert¹,

Hilhorst²,

Voskuilen³

et al. 1989

European Journal of Biochemistry

113

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“…There are 26 basic amino acids and only three acidic residues per 100-residue subunit. Whereas 29͞100 is not unusual for the number of charged residues in a protein (25), it is common that the charge is more evenly distributed between acidic and basic residues so that the net charge is considerably smaller in magnitude (26). Moreover, the spatial charge distribution of the DEN2C dimer is remarkably nonuniform.…”

Section: Resultsmentioning

confidence: 99%

Solution structure of dengue virus capsid protein reveals another fold

Jones

Groesch

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

308

421

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Dengue virus is responsible for Ϸ50 -100 million infections, resulting in nearly 24,000 deaths annually. The capsid (C) protein of dengue virus is essential for specific encapsidation of the RNA genome, but little structural information on the C protein is available. We report the solution structure of the 200-residue homodimer of dengue 2 C protein. The structure provides, to our knowledge, the first 3D picture of a flavivirus C protein and identifies a fold that includes a large dimerization surface contributed by two pairs of helices, one of which has characteristics of a coiled-coil. NMR structure determination involved a secondary structure sorting approach to facilitate assignment of the intersubunit nuclear Overhauser effect interactions. The dimer of dengue C protein has an unusually high net charge, and the structure reveals an asymmetric distribution of basic residues over the surface of the protein. Nearly half of the basic residues lie along one face of the dimer. In contrast, the conserved hydrophobic region forms an extensive apolar surface at a dimer interface on the opposite side of the molecule. We propose a model for the interaction of dengue C protein with RNA and the viral membrane that is based on the asymmetric charge distribution of the protein and is consistent with previously reported results.D engue virus, a member of the flavivirus genus of enveloped RNA viruses, is one of the most significant mosquito-borne viral pathogens, given the impact of the recent resurgence of dengue fever and dengue hemorrhagic fever (1). Other members of the flavivirus genus are also important human pathogens and include such viruses as yellow fever, West Nile virus, and Japanese encephalitis (2). The structure of dengue virus was recently described by using cryo-electron microscopy, which permitted visualization of certain viral protein components (3). The organization of the major envelope glycoprotein (E) in the virion was obtained by fitting the atomic structure of the ectodomain from the related tick-borne encephalitis (TBE) E protein into the outermost layer of density (4). Density internal to the E ectodomain demonstrated a host-derived lipid bilayer with transmembrane helices from E and the small structural protein M (5). Interior to the bilayer is the nucleocapsid core that comprises multiple copies of the capsid, or core, protein (C) and a single 10.7-kb genome RNA. Surprisingly, the organization of the C protein within the nucleocapsid core layer is not discernable. The lack of strong density for C may suggest a rather unique architecture of the flavivirus nucleocapsid core that is distinct from the structural organization of morphologically related viruses such as alphaviruses, a genus in the Togaviridae family of mosquito-borne viruses.The dengue C protein is essential in virus assembly to ensure specific encapsidation of the viral genome. The critical role of C is evident from the existence of subviral particles that are released from infected cells but lack C protein and genome RNA (6). The me...

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“…, NR), of the coordinates of NG charges are extracted from the set of surface atoms ( R S ) using an integer-number Monte Carlo algorithm (Spassov & Atanasov, 1994). A similar approach was used by Barlow and Thornton (1986) for analysis of charge asymmetry. The frequencies, f(AGei,rnd), of a random constellation in the intervals of AGei are very similar to the normal (Gaussian) distribution, p(AC,,), indicating that Rmd,i is sufficiently large for a statistical investigation.…”

Section: Monte Carlo Simulationsmentioning

confidence: 99%

Optimization of the electrostatic interactions in proteins of different functional and folding type

1994

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The 3-dimensional optimization of the electrostatic interactions between the charged amino acid residues was studied by Monte Carlo simulations on an extended representative set of 141 protein structures with known atomic coordinates. The proteins were classified by different functional and structural criteria, and the optimization of the electrostatic interactions was analyzed. The optimization parameters were obtained by comparison of the contribution of charge-charge interactions to the free energy of the native protein structures and for a large number of randomly distributed charge constellations obtained by the Monte Carlo technique. On the basis of the results obtained, one can conclude that the charge-charge interactions are better optimized in the enzymes than in the proteins without enzymatic functions. Proteins that belong to the mixed cr/3 folding type are electrostatically better optimized than pure cu-helical or /3-strand structures. Proteins that are stabilized by disulfide bonds show a lower degree of electrostatic optimization. The electrostatic interactions in a native protein are effectively optimized by rejection of the conformers that lead to repulsive charge-charge interactions. Particularly, the rejection of the repulsive contacts seems to be a major goal in the protein folding process. The dependence of the optimization parameters on the choice of the potential function was tested. The majority of the potential functions gave practically identical results. Keywords: energy calculations; ion pairs; Monte Carlo simulations; potential functions; protein electrostatics; protein foldingThe nature and spatial distribution of charged residues in a folded protein can be considered as an evolutionary solution of 2 different tasks: first, the stabilization of the native structure by the contribution of the electrostatic interactions to the free energy and, second, the display of a functional role by creating a specific electrostatic field, necessary for the enhancement of the enzymatic reactions, intermolecular recognition, and assembly. In principle, the solution of the second task could be opposite to the stabilization effect. The magnitude of the stabilization effect of the other forces governing protein folding could counteract the necessity of significant electrostatic interactions.

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The distribution of charged groups in proteins

Cited by 131 publications

References 24 publications

Protein transfer from an aqueous phase into reversed micelles

Protein transfer from an aqueous phase into reversed micelles

Solution structure of dengue virus capsid protein reveals another fold

Optimization of the electrostatic interactions in proteins of different functional and folding type

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