Clusters of charged residues in protein three-dimensional structures.

Zhu, Zhanyang; Karlin, Samuel

doi:10.1073/pnas.93.16.8350

Cited by 68 publications

(61 citation statements)

References 34 publications

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“…Electrostatic interactions also play an important role in determining thermodynamics of binding; i.e., binding affinity (Novotny and Sharp, 1992;Fersht, 1993, 1995;Zhu and Karlin, 1996;Chong et al, 1998;Sheinerman et al, 2000;Norel et al, 2001;Rauch et al, 2002). Substrate binding allows the formation of (potentially) favorable charge-charge interactions between the substrate and target, as well as stabilizing specific salt-bridges and hydrogen bonds Fersht, 1993, 1995;Chong et al, 1998).…”

Section: Iib Biomolecule-ligand and -Biomolecule Interactionsmentioning

confidence: 99%

Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Methods in Cell Biology

116

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An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions.

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Section: Iib Biomolecule-ligand and -Biomolecule Interactionsmentioning

confidence: 99%

Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Methods in Cell Biology

116

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“…In order to find possible Ca 2+ -binding sites, we examined the HA from the influenza X-31 strain (PDB entry code 1EO8 [41]) using the program WebFEATURE (web-accessible structural analysis software that permits the identification of calcium-binding sites in three-dimensional protein structures [42]); the three-dimensional protein structure of HA of the Udorn strain is not available. Although WebFEATURE suggests that the binding affinity of Ca 2+ to HA2 is low, a potential Ca 2+ -binding site within the vestigial esterase domain of HA1 [43] was revealed close to residues Asp 68 -Val 78 and Ser 95 -Tyr 100 (not far from the charge cluster in the HA1 subunit described in [40]), see Fig. 5.…”

Section: Identification Of a Putative Ca 2+ -Binding Sites In Hamentioning

confidence: 95%

“…However, there are many types of calcium-binding sites that are different from the EF-hand motif. For example, charge clusters often bind calcium [40]. In [40], two mixed charge clusters in the three-dimensional structure of hemagglutinin were described, one in the HA1 subunit and another in the HA2 subunit.…”

Section: Identification Of a Putative Ca 2+ -Binding Sites In Hamentioning

confidence: 99%

“…For example, charge clusters often bind calcium [40]. In [40], two mixed charge clusters in the three-dimensional structure of hemagglutinin were described, one in the HA1 subunit and another in the HA2 subunit. In order to find possible Ca 2+ -binding sites, we examined the HA from the influenza X-31 strain (PDB entry code 1EO8 [41]) using the program WebFEATURE (web-accessible structural analysis software that permits the identification of calcium-binding sites in three-dimensional protein structures [42]); the three-dimensional protein structure of HA of the Udorn strain is not available.…”

Section: Identification Of a Putative Ca 2+ -Binding Sites In Hamentioning

confidence: 99%

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Influence of calcium on lipid mixing mediated by influenza hemagglutinin

Zhukovsky

Markovic

Bailey

2007

Archives of Biochemistry and Biophysics

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We studied the influence of calcium on lipid mixing mediated by influenza hemagglutinin (HA). Lipid mixing between HA-expressing cells and liposomes containing disialoganglioside, influenza virus receptor, was studied at 37°C and neutral pH after a low-pH pulse at 4°C. With DSPC/ cholesterol liposomes, calcium present after raising the temperature significantly promoted lipid mixing only when it was triggered by a short low-pH application. In case of DOPC/cholesterol liposomes, calcium promotion was observed regardless of the duration of the low-pH pulse. Calcium present during a short, but not long, low-pH application to HA-expressing cells with bound DSPC/ cholesterol liposomes at 4°C inhibited subsequent lipid mixing. We hypothesize that calcium influences lipid mixing because it binds to a vestigial esterase domain of hemagglutinin or causes expulsion of the fusion peptide from an electronegative cavity. We suggest that calcium promotes the transition from early and reversible conformation(s) of low pH-activated HA towards an irreversible conformation that underlies both HA-mediated lipid mixing and HA inactivation.

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“…Some effort has also been made to pursue more "informatics"-based approaches to the interpretation of electrostatic properties. Much of this work includes identification of functionally-relevant residues in biomolecules by looking at electrostatic destabilization of conserved residues [18], highly shifted pK a values [44], clusters of charged residues [59], protein-membrane interactions [40], and other structural characteristics [55]. Other research has focused on comparisons of electrostatic potentials including global analyses of the biomolecular structure [38,9,40,51,37,30,36,47,43,8,53,34,46,35,52] both in threedimensional space over the entire biomolecular structure and at localized regions such as active sites [52,6,22].…”

Section: Introductionmentioning

confidence: 99%

Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity

Zhang¹,

Bajaj²,

Kwon³

et al. 2006

Multiscale Model. Simul.

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In this paper we present a method for the multi-resolution comparison of biomolecular electrostatic potentials without the need for global structural alignment of the biomolecules. The underlying computational geometry algorithm uses multi-resolution attributed contour trees (MACTs) to compare the topological features of volumetric scalar fields. We apply the MACTs to compute electrostatic similarity metrics for a large set of protein chains with varying degrees of sequence, structure, and function similarity. For calibration, we also compute similarity metrics for these chains by a more traditional approach based upon 3D structural alignment and analysis of Carbo similarity indices. Moreover, because the MACT approach does not rely upon pairwise structural alignment, its accuracy and efficiency promises to perform well on future large-scale classification efforts across groups of structurally-diverse proteins. The MACT method discriminates between protein chains at a level comparable to the Carbo similarity index method; i.e., it is able to accurately cluster proteins into functionally-relevant groups which demonstrate strong dependence on ligand binding sites. The results of the analyses are available from the linked web databases

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Clusters of charged residues in protein three-dimensional structures.

Cited by 68 publications

References 34 publications

Computational Methods for Biomolecular Electrostatics

Computational Methods for Biomolecular Electrostatics

Influence of calcium on lipid mixing mediated by influenza hemagglutinin

Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity

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