Computation of electrostatic complements to proteins: A case of charge stabilized binding

Chong, Lillian T.; Dempster, Sara E.; Hendsch, Zachary S.; Lee, Lee‐Peng; Tidor, Bruce

doi:10.1002/pro.5560070122

Cited by 74 publications

(90 citation statements)

References 27 publications

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“…One possibility is that the receptor binding epitope of the CD loop in the wild type sequence normally provides an electrostatic balance of one net positive charge 88 EERRR 92 that is mimicked by the mutant sequence with Arg 90 . The importance of charge distribution in protein binding is recognized generally (35). Its role in IL-5 receptor recognition merits further investigation through an 4 S. Chen, S.-J.…”

Section: Discussionmentioning

confidence: 99%

Randomization of the Receptor α Chain Recruitment Epitope Reveals a Functional Interleukin-5 with Charge Depletion in the CD Loop

Wu¹,

Tsui

et al. 1999

Journal of Biological Chemistry

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1 is a T cell-derived cytokine that specifically stimulates differentiation, proliferation, and activation of eosinophils (1) and appears to play an important role in the pathogenesis of asthma. IL-5 is a homodimer that folds into a cylindrical molecule containing two four-helix bundles (2), each of which resembles the four-helix bundle seen in the monomeric cytokines IL-3, IL-4, granulocyte-macrophage colony-stimulating factor, and growth hormone.The cell receptor for IL-5 is composed of two subunits, ␣ and ␤ c . The ␣ chain is cytokine-specific and by itself can bind IL-5 with high affinity (3). Extensive site-directed mutagenesis studies have shown that residues clustered near the helix bundle interface, in the CD loop, including Glu 89 and Arg 91 , and at the carboxyl-terminal end of helix D, notably Glu 110 , engage in receptor ␣ chain binding (4 -6). Glu 13 , which is at each of the distal ends of the IL-5 cylinder away from the interface between the two four-helix bundles and is not involved directly in ␣ chain interaction, is a key residue mediating productive interaction of the ␤ c chain of IL-5 receptor (4, 5). It is the ␤ c recruitment into ␣␤ c that leads to triggering of the intracellular signaling cascade.Although site-directed mutagenesis studies have identified important residues for receptor binding, the one-residue-at-atime substitution allowed by this technique limits a full mechanistic understanding of the specific structural and electrostatic features of the IL-5 surface required for receptor-ligand interaction. However, through the use of randomly generated side chain libraries, it should be possible to measure the effect of replacing individual side chains or sets of side chains in local regions on the IL-5 surface and hence determine which combinations allow productive binding. Such random epitope mutagenesis can be achieved with sequence libraries formed by phage display. This technique has been applied successfully to in vitro antibody maturation and protein engineering (7). Typically a foreign gene is fused in frame with phage coat protein pIII encoded by a phagemid vector, and the surface-displayed recombinant foreign protein selected by affinity selection procedures (biopanning). Human growth hormone has been displayed on phage and higher receptor affinity variants selected through random mutagenesis and phage panning (8). Phage display of multichain proteins also has been achieved, for example for antibody Fab fragments (9) and vascular epidermal growth factor (10). Nonetheless, in our hands, phage display of the dimeric wild type IL-5 has proven difficult, perhaps reflecting folding difficulties that previously have led to insoluble inclusion bodies in intracellular Escherichia coli expression (11).We have sought to overcome limitations in phage display of IL-5 by using a single chain form of human IL-5 (scIL-5), in which two IL-5 molecules are tandemly linked by a Gly-Gly dipeptide linker (12). Single chain IL-5 and wtIL-5 have virtually identical biological activities and bindin...

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Section: Discussionmentioning

confidence: 99%

Randomization of the Receptor α Chain Recruitment Epitope Reveals a Functional Interleukin-5 with Charge Depletion in the CD Loop

Wu¹,

Tsui

et al. 1999

Journal of Biological Chemistry

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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%

“…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). However, at the same time, charges on the molecular binding surface must shed their bound water in order to allow close binding.…”

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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“…The indirect interaction between the two members of this hydrogen bond would favor complex formation, since solvent would screen their favorable electrostatic interaction less in the bound state than in the unbound state. An important result of the work reported here is that energetics due to indirect effects are significant, though the importance of this term has generally not been recognized~Elcock & McCammon, 1996;Oberoi et al, 1996;Chong et al, 1998;Kangas & Tidor, 1998!. Summing each type of term for every group in the GCN4 leucine zipper~in a manner that counts each interaction once! showed that the electrostatic effect of complex formation is destabilizing because the unfavorable solvation term~24.0 kcal0mol!…”

Section: Resultsmentioning

confidence: 99%

Untitled

1999

Protein Science

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The GCN4 leucine zipper is a peptide homodimer that has been the subject of a number of experimental and theoretical investigations into the determinants of affinity and specificity. Here, we utilize this model system to investigate electrostatic effects in protein binding using continuum calculations. A particularly novel feature of the computations made here is that they provide an interaction-by-interaction breakdown of the electrostatic contributions to the free energy of docking that includes changes in the interaction of each functional group with solvent and changes in interactions between all pairs of functional groups on binding. The results show that~1! electrostatic effects disfavor binding by roughly 15 kcal0mol due to desolvation effects that are incompletely compensated in the bound state,~2! while no groups strongly stabilize binding, the groups that are most destabilizing are charged and polar side chains at the interface that have been implicated in determining binding specificity, and~3! attractive intramolecular interactions e.g., backbone hydrogen bonds! that are enhanced on binding due to reduced solvent screening in the bound state contribute significantly to affinity and are likely to be a general effect in other complexes. A comparison is made between the results obtained in an electrostatic analysis carried out calculationally and simulated results corresponding to idealized data from a scanning mutagenesis experiment. It is shown that scanning experiments provide incomplete information on interactions and, if overinterpreted, tend to overestimate the energetic effect of individual side chains that make attractive interactions. Finally, a comparison is made between the results available from a continuum electrostatic model and from a simpler surface-area dependent solvation model. In this case, although the simpler model neglects certain interactions, on average it performs rather well.

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Computation of electrostatic complements to proteins: A case of charge stabilized binding

Cited by 74 publications

References 27 publications

Randomization of the Receptor α Chain Recruitment Epitope Reveals a Functional Interleukin-5 with Charge Depletion in the CD Loop

Randomization of the Receptor α Chain Recruitment Epitope Reveals a Functional Interleukin-5 with Charge Depletion in the CD Loop

Computational Methods for Biomolecular Electrostatics

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