Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein

He, Jing

doi:10.1002/pro.5560021010

Cited by 67 publications

(57 citation statements)

References 25 publications

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“…48 Elimination of this interaction in FbpA and SBP greatly reduces anion binding affinity. 58,59 The anion interactions in FbpA are reduced in comparison ( Figure 1) and sulfate and phosphate binding is weaker than that observed for the SBP and PBP anions (i.e K d of apo-FbpA-X on the order of mM) ( Table 1). The presence of Glu57 (Figure 1) in FbpA should play a role similar to that of Asp56 in PBP, resulting in discrimination against sulfate.…”

Section: Structural Analysis Of Fbpa and Synergistic Anion Interactionsmentioning

confidence: 92%

Sulfate as a Synergistic Anion Facilitating Iron Binding by the Bacterial Transferrin FbpA: The Origins and Effects of Anion Promiscuity

et al. 2007

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The ferric binding protein, FbpA, has been demonstrated to facilitate the transport of naked Fe 3+ across the periplasmic space of several gram-negative bacteria. The sequestration of iron by FbpA is facilitated by the presence of a synergistic anion, such as phosphate or sulfate. Here we report the sequestration of Fe 3+ by FbpA in the presence of sulfate, at an assumed periplasmic pH of 6.5 to form FeFbpA-SO 4 with K′ eff = 1.7 × 10 16 M −1 (at 20°C, 50 mM MES, 200 mM KCl). The iron affinity of the FeFbpA-SO 4 protein assembly is two orders of magnitude lower than when bound with phosphate and is the lowest of any of the FeFbpA-X assemblies yet reported. Iron reduction at the cytosolic membrane receptor may be an essential aspect of the periplasmic iron transport process and with an E 1/2 of −158 mV (NHE), FeFbpA-SO 4 is the most easily reduced of all FeFbpA-X assemblies yet studied. The variation of FeFbpA-X assembly stability (K′ eff ) and ease of reduction (E 1/2 ) with differing synergistic anions X n− are correlated over a range of 14 kJ, suggesting that the variations in redox potentials are due to stabilization of Fe 3+ in FeFbpA-X by X n− . Anion promiscuity of FbpA in the diverse composition of the periplasmic space is illustrated by the ex vivo exchange kinetics of FeFbpA-SO 4 with phosphate and arsenate, with first order kinetics with respect to FeFbpA-SO 4 (k = 30 s −1 ) at pH 6.5, independent of entering anion concentration and identity. Anion lability and influence on the iron affinity and reduction potential for FeFbpA-X support the hypothesis that synergistic anion exchange may be an important regulator in iron delivery to the cytosol. This structural and thermodynamic analysis of anion binding in FeFbpA-X provides additional insight into anion promiscuity and importance.

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Section: Structural Analysis Of Fbpa and Synergistic Anion Interactionsmentioning

confidence: 92%

Sulfate as a Synergistic Anion Facilitating Iron Binding by the Bacterial Transferrin FbpA: The Origins and Effects of Anion Promiscuity

et al. 2007

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“…Because the putative ABC transporter system of GL-BP (BL1638 -1640) contains two separate transmembrane components expected to form a heterodimer, it will be also classified in the CUT1 family (36). GL-BP shows modest structural similarity (Dali Z scores Ͼ 10) with bacterial SBPs belonging to the SBP_bac_1 family of Pfam (37), such as thiaminase I (38) and binding proteins for iron (39), polyamines (40), sulfate (41), and molybdate (42).…”

Section: Analysis Of Ligand Specificity By Itc-mentioning

confidence: 99%

Structural and Thermodynamic Analyses of Solute-binding Protein from Bifidobacterium longum Specific for Core 1 Disaccharide and Lacto-N-biose I

Suzuki

Wada

Katayama

et al. 2008

Journal of Biological Chemistry

114

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Recently, a gene cluster involving a phosphorylase specific for lacto-N-biose I (LNB; Gal␤1-3GlcNAc) and galacto-N-biose (GNB; Gal␤1-3GalNAc) has been found in Bifidobacterium longum. We showed that the solute-binding protein of a putative ATP-binding cassette-type transporter encoded in the cluster crystallizes only in the presence of LNB or GNB, and therefore we named it GNB/LNB-binding protein (GL-BP). Isothermal titration calorimetry measurements revealed that GL-BP specifically binds LNB and GNB with K d values of 0.087 and 0.010 M, respectively, and the binding process is enthalpydriven. The crystal structures of GL-BP complexed with LNB, GNB, and lacto-N-tetraose (Gal␤1-3GlcNAc␤1-3Gal␤1-4Glc) were determined. The interactions between GL-BP and the disaccharide ligands mainly occurred through water-mediated hydrogen bonds. In comparison with the LNB complex, one additional hydrogen bond was found in the GNB complex. These structural characteristics of ligand binding are in agreement with the thermodynamic properties. The overall structure of GL-BP was similar to that of maltose-binding protein; however, the mode of ligand binding and the thermodynamic properties of these proteins were significantly different.Bifidobacteria are Gram-positive anaerobes naturally present in the dominant colonic microbiota and have been considered to be beneficial for human health. As probiotic agents, Bifidobacteria can prevent or alleviate infectious diarrhea through their effects on the immune system and promote the host resistance to colonization by pathogens (1). Carbon source compounds, including oligofructose, inulin, and raffinose, are used as food additives (prebiotics) to selectively promote the growth of Bifidobacteria in the gut (2, 3). Bifidobacteria predominate the intestinal flora of breastfed infants (4, 5), whereas bottle-fed infants do not show rapid colonization of these organisms (6). It has been widely accepted that oligosaccharides other than lactose in human milk (human milk oligosaccharides, HMOs) 4 play a key role in the growth of Bifidobacteria in the gut (7,8). However, it remains unknown what structure, in HMOs, constitutes the bifidus factor responsible for increasing the bifidobacterial population. Human milk is reported to contain more than 100 kinds of oligosaccharides, the building blocks of which are the following three basic core disaccharides: lactose (Gal␤1-4Glc), lacto-N-biose I (LNB; Gal␤1-3GlcNAc), and N-acetyllactosamine (LacNAc; Gal␤1-4GlcNAc). These oligosaccharides are often modified by sialic acid and/or L-fucose (7). Lacto-N-tetraose (LNT; Gal␤1-3GlcNAc␤1-3Gal␤1-4Glc), which is formed by a ␤1-3 linkage between LNB and lactose, and fucosylated derivative (Fuc␣1-2Gal␤1-3GlcNAc␤1-3Gal␤1-4Glc) are the major components of HMOs (9 -11).Recently, we found that Bifidobacterium longum JCM1217 has a unique metabolic pathway specific for LNB and galacto-N-biose (GNB, Gal␤1-3GalNAc), and we presented the hypothesis that the LNB residue in HMOs is the bifidus factor in breastfed infants (12). B...

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“…1978) ascribed the binding of anions at helical N-termini to an interaction with the macrodipole of the entire helix. It seems more realistic, however, to regard them (He & Quiocho, 1993) as interacting with the local dipoles of the CONH groups of the first turn or two of the helix.…”

Section: Relevance To Aspects Of Proteinsmentioning

confidence: 99%

The partial charge of the nitrogen atom in peptide bonds

1997

Protein Science

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A majority of the standard texts dealing with proteins portray the peptide link as a mixture of two resonance forms, in one of which the nitrogen atom has a positive charge. As a consequence, it is often believed that the nitrogen atom has a net positive charge. This is in apparent contradiction with the partial negative charge on the nitrogen that is used in force fields for molecular modeling. However, charges on resonance forms are best regarded as formal rather than actual charges and current evidence clearly favors a net negative charge for the nitrogen atom. In the course of the discussion, new ideas about the electronic structure of amides and the peptide bond are presented.Keywords: a-helix; amides; electrostatics; hydrogen bonds; proteins; quantum mechanics This article begins with a listing of some estimates of the partial charges of the atoms of amides. The planarity of amides is typically explained by portraying them as two resonance forms, one of which has a nitrogen atom with a formal positive charge. However, it is chemically unsatisfactory for the nitrogen atom to have a net partial positive charge, and the reasons for this are given. The strongest evidence that the nitrogen is negative rather than positive comes from quantum mechanics. Some recent work on amides and its implications for the electronic structure of the and T orbitals of the CONH group are discussed in some detail. The effect of hydrogen bonding is then considered and, finally, the relevance of these insights for a-helices is addressed. Point charges on individual atoms:The resonance method used commonly to represent the peptide bond as in Figure 1 is often taken to imply that the nitrogen has a partial positive charge. This conflicts with the partial charges used widely in molecular mechanics force fields for modeling biological molecules. A set of calculated partial charges has been collected (Rogers, 1986), and a

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Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein

Cited by 67 publications

References 25 publications

Sulfate as a Synergistic Anion Facilitating Iron Binding by the Bacterial Transferrin FbpA: The Origins and Effects of Anion Promiscuity

Sulfate as a Synergistic Anion Facilitating Iron Binding by the Bacterial Transferrin FbpA: The Origins and Effects of Anion Promiscuity

Structural and Thermodynamic Analyses of Solute-binding Protein from Bifidobacterium longum Specific for Core 1 Disaccharide and Lacto-N-biose I

The partial charge of the nitrogen atom in peptide bonds

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