X-ray Structures of the Leucine-binding Protein Illustrate Conformational Changes and the Basis of Ligand Specificity

Magnusson, Ulrika; Salopek‐Sondi, Branka; Luck, Linda A.; Mowbray, Sherry L.

doi:10.1074/jbc.m311890200

Cited by 76 publications

(74 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Fig. 1 illustrates our first example, the L-leucine binding protein [Protein Data Bank (PDB) IDs 1usg and 1usi], which experiences large conformational changes upon binding to L-leucine (30). …”

Section: Resultsmentioning

confidence: 99%

Coevolutionary signals across protein lineages help capture multiple protein conformations

Morcos

Jana

Hwa

et al. 2013

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

175

195

View full text Add to dashboard Cite

A long-standing problem in molecular biology is the determination of a complete functional conformational landscape of proteins. This includes not only proteins' native structures, but also all their respective functional states, including functionally important intermediates. Here, we reveal a signature of functionally important states in several protein families, using direct coupling analysis, which detects residue pair coevolution of protein sequence composition. This signature is exploited in a protein structure-based model to uncover conformational diversity, including hidden functional configurations. We uncovered, with high resolution (mean ∼1.9 Å rmsd for nonapo structures), different functional structural states for medium to large proteins (200-450 aa) belonging to several distinct families. The combination of direct coupling analysis and the structure-based model also predicts several intermediates or hidden states that are of functional importance. This enhanced sampling is broadly applicable and has direct implications in protein structure determination and the design of ligands or drugs to trap intermediate states.A s demonstrated by Anfinsen in 1973 (1) for small and intermediate-size proteins, amino acid sequences contain all of the necessary information to determine their native structure and function. In principle, a complete physical understanding of all molecular interactions should be sufficient to uncover not only the proteins' native structures, but also all their respective functional states, including functionally important intermediates. This landscape is required for a complete knowledge of functional mechanisms and therefore it has implications for drug discovery. Advances in computational approaches have been promising in sampling such conformational intermediates (2, 3). However, in general, computational methods are limited by uncertainties in protein models as well as insufficient computational resources to achieve proper sampling. Experimental techniques such as crystallography or NMR spectroscopy have been successful in identifying functional protein structures but only for a fraction of the complete set of known protein sequences (4, 5). Additionally, the determination of functionally important intermediate states using such methods has been challenging due to their transient nature. One idea to confront this challenge is to search for clues in genomic data (6-10). Functional states under conformational selection should leave a trace in the evolutionary history of proteins. Recent results inspired by this hypothesis have led to the development of the powerful "direct coupling analysis" (DCA), which was able to predict a large number of direct structural contacts between residues from sequences alone (11). Other useful methods have been developed to define coupling among residue pairs (12, 13). Others have also looked into correlated electrostatic mutations to study the evolution of protein topology toward minimized interaction frustration (14). Integrating the DCA-predicted co...

show abstract

Section: Resultsmentioning

confidence: 99%

Coevolutionary signals across protein lineages help capture multiple protein conformations

Morcos

Jana

Hwa

et al. 2013

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

175

195

View full text Add to dashboard Cite

show abstract

“…Conformational changes of periplasmic SBPs, such as ribose-binding protein, allose-binding protein, leucine/isoleucine/￦ valine-binding protein, and leucine-binding protein, were intensively studied by X-ray crystallography (22)(23)(24)(25). These SBPs adopt a similar fold made of two lobes, which are connected by one or more polypeptide chains, forming a hinge.…”

Section: Discussionmentioning

confidence: 99%

Structure and function of a novel periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria

Suginta

Sritho

Ranok

et al. 2018

Journal of Biological Chemistry

View full text Add to dashboard Cite

Periplasmic solute-binding proteins (SBPs) in bacteria are involved in the active transport of nutrients into the cytoplasm. In marine bacteria of the genus Vibrio, a chitooligosaccharide-binding protein (CBP) is thought to be the major SBP controlling the rate of chitin uptake in these bacteria. However, the molecular mechanism of the CBP involvement in chitin metabolism has not been elucidated. Here, we report the structure and function of a recombinant chitooligosaccharide-binding protein from Vibrio harveyi, namely VhCBP, expressed in Escherichia coli. Isothermal titration calorimetry (ITC) revealed that VhCBP strongly binds shorter chitooligosaccharides [(GlcNAc) n , n = 2, 3, and 4] with affinities that are considerably greater than those for glycoside hydrolase family 18 (GH18) and GH19 chitinases, but does not bind longer ones, including insoluble chitin polysaccharides. We also found that VhCBP comprises two domains with flexible linkers and that the domain-domain interface forms the sugar-binding cleft, which is not long extended but forms a small cavity. (GlcNAc) 2 bound to this cavity, apparently triggering a closed conformation of VhCBP. Trp-363 and Trp-513, which stack against the two individual GlcNAc rings, likely make a major contribution to the high affinity of VhCBP for (GlcNAc) 2 . The strong chitobiose binding, followed by the conformational change of VhCBP, may facilitate its interaction with an active-transport system in the inner membrane of Vibrio species.Vibrio harveyi is a Gram-negative bioluminescent marine bacterium found in tropical marine waters, and is a serious pathogen of aquatic fish and invertebrates, including crustacean and zooplankton (1). Chitin, -1,4-linked polysaccharide of N-acetylglucosamine (GlcNAc), is an important marine biomass, which is efficiently converted by Vibrios. Thus, V. harveyi has an efficient chitin degradation system, including a chitinase A (2-5) belonging to glycoside hydrolase family 18 (GH18), a -N-acetylglucosaminidase (6,7) belonging to the GH20 family, and a chitin-oligosaccharide deacetylase (8,9) belonging to carbohydrate esterase family 4 (CE4).GH18 chitinases hydrolyze -1,4-glycosidic linkages of chitin in an endo-splitting mode, producing chitin oligosaccharides (GlcNAc) n (n=2, 3, 4, and http://www.jbc.org/cgi

show abstract

“…A conformational change to either a larger or a smaller size plays an important role in the ligandbinding mechanism. In fact, conformational changes of the side chains of a binding site (Najmanovich et al 2000;Zavodszky and Kuhn 2005), small movements and/or deformation of loops (Malkowski et al 1997;Karthikeyan et al 2003), large-scale domain motions (Kraft et al 2002;Magnusson et al 2004;Amemiya et al 2012), and quaternary movements of subunits (Xiong et al 2002;Benison et al 2008) have been observed during the binding of a ligand to proteins. The intrinsic thermal motion of proteins is considered responsible for the conformational changes upon ligand binding.…”

Section: Ligand-induced Conformational Changementioning

confidence: 99%

Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank

Wako

Endo

2017

Biophys Rev

View full text Add to dashboard Cite

Normal mode analysis (NMA) can facilitate quick and systematic investigation of protein dynamics using data from the Protein Data Bank (PDB). We developed an elastic network model-based NMA program using dihedral angles as independent variables. Compared to the NMA programs that use Cartesian coordinates as independent variables, key attributes of the proposed program are as follows: (1) chain connectivity related to the folding pattern of a polypeptide chain is naturally embedded in the model; (2) the full-atom system is acceptable, and owing to a considerably smaller number of independent variables, the PDB data can be used without further manipulation; (3) the number of variables can be easily reduced by some of the rotatable dihedral angles; (4) the PDB data for any molecule besides proteins can be considered without coarse-graining; and (5) individual motions of constituent subunits and ligand molecules can be easily decomposed into external and internal motions to examine their mutual and intrinsic motions. Its performance is illustrated with an example of a DNA-binding allosteric protein, a catabolite activator protein. In particular, the focus is on the conformational change upon cAMP and DNA binding, and on the communication between their binding sites remotely located from each other. In this illustration, NMA creates a vivid picture of the protein dynamics at various levels of the structures, i.e., atoms, residues, secondary structures, domains, subunits, and the complete system, including DNA and cAMP. Comparative studies of the specific protein in different states, e.g., apo-and holo-conformations, and free and complexed configurations, provide useful information for studying structurally and functionally important aspects of the protein.

show abstract

X-ray Structures of the Leucine-binding Protein Illustrate Conformational Changes and the Basis of Ligand Specificity

Cited by 76 publications

References 38 publications

Coevolutionary signals across protein lineages help capture multiple protein conformations

Coevolutionary signals across protein lineages help capture multiple protein conformations

Structure and function of a novel periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria

Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank

Contact Info

Product

Resources

About