Structural Evidence for Adaptive Ligand Binding of Glycolipid Transfer Protein

Airenne, Tomi T.; Kidron, Heidi; Nymalm, Yvonne; Nylund, Matts; West, Gun; Mattjus, Peter; Salminen, Tiina A.

doi:10.1016/j.jmb.2005.10.031

Cited by 50 publications

(95 citation statements)

References 40 publications

(48 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…6 Our x-ray data rectify discrepancies with previous three-dimensional modeling of HET-C2 regarding identification of key residues of the sugar head group recognition center (11). In our threedimensional jigsaw model (data not shown), the HET-C2 core region precisely superimposed with the crystallographic structure, but a different location emerged for C-terminal residues (Trp 208 ), and no structure was obtained for the first 38 amino acids of the N terminus.…”

Section: Discussionmentioning

confidence: 45%

Structural Determination and Tryptophan Fluorescence of Heterokaryon Incompatibility C2 Protein (HET-C2), a Fungal Glycolipid Transfer Protein (GLTP), Provide Novel Insights into Glycolipid Specificity and Membrane Interaction by the GLTP Fold

Kenoth

Simanshu

Kamlekar

et al. 2010

Journal of Biological Chemistry

View full text Add to dashboard Cite

HET-C2 is a fungal protein that transfers glycosphingolipids between membranes and has limited sequence homology with human glycolipid transfer protein (GLTP). The human GLTP fold is unique among lipid binding/transfer proteins, defining the GLTP superfamily. Herein, GLTP fold formation by HET-C2, its glycolipid transfer specificity, and the functional role(s) of its two Trp residues have been investigated. X-ray diffraction (1.9 Å ) revealed a GLTP fold with all key sugar headgroup recognition residues (Asp 66 , Asn 70 , Lys 73 , Trp 109 , and His 147 ) conserved and properly oriented for glycolipid binding. Far-UV CD showed secondary structure dominated by ␣-helices and a cooperative thermal unfolding transition of 49°C, features consistent with a GLTP fold. Environmentally induced optical activity of Trp/Tyr/Phe (2:4:12) detected by near-UV CD was unaffected by membranes containing glycolipid but was slightly altered by membranes lacking glycolipid. Trp fluorescence was maximal at ϳ355 nm and accessible to aqueous quenchers, indicating free exposure to the aqueous milieu and consistent with surface localization of the two Trps. Interaction with membranes lacking glycolipid triggered significant decreases in Trp emission intensity but lesser than decreases induced by membranes containing glycolipid. Binding of glycolipid (confirmed by electrospray injection mass spectrometry) resulted in a blue-shifted emission wavelength maximum (ϳ6 nm) permitting determination of binding affinities. The unique positioning of Trp 208 at the HET-C2 C terminus revealed membrane-induced conformational changes that precede glycolipid uptake, whereas key differences in residues of the sugar headgroup recognition center accounted for altered glycolipid specificity and suggested evolutionary adaptation for the simpler glycosphingolipid compositions of filamentous fungi.Self/nonself recognition is a universally important process, encompassing intercellular interactions ranging from vertebrate immune responses to somatic chimera formation in protists, filamentous fungi, sponges, ascidians, and tunicates. Self/ nonself discrimination becomes critical for filamentous fungi during hyphal fusion, which enables the exchange of cytoplasm and nuclei during the assimilative growth phase (1-4). Nonself recognition triggers a postfusion, programmed cell death process known as vegetative incompatibility, which leads to heterokaryon death. The benefits of vegetative incompatibility include prevention of transmission of deleterious cytoplasmic elements (i.e. viruses) as well as restriction of plundering by parasitic genotypes.het genes are known to play a major role in vegetative incompatibility processes that occur in Neurospora crassa and Podospora anserina. het genes exhibit extensive polymorphism and generally encode proteins carrying a HET domain (1-4). Originally, this domain was linked to the het-c2 gene of P. anserina, where it was shown to encode a protein similar in size and with limited sequence homology to mammalian glycolipid transfer...

show abstract

Section: Discussionmentioning

confidence: 45%

Structural Determination and Tryptophan Fluorescence of Heterokaryon Incompatibility C2 Protein (HET-C2), a Fungal Glycolipid Transfer Protein (GLTP), Provide Novel Insights into Glycolipid Specificity and Membrane Interaction by the GLTP Fold

Kenoth

Simanshu

Kamlekar

et al. 2010

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…We analyzed the hydration properties of the unliganded binding pockets for several holoproteins, including the mouse major urinary protein (MUP, PDB ID 1znk) (12), the bovine apo-glycolipid transfer protein (GLTP, PDB ID 1wbe) (13), and the secretin pilot protein (PDB ID 1y9l) (14), and identified both the high occupancy hydration sites using the WaterMap program (4,5) and the low occupancy cavity regions using the protocol described in the methods section. Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The starting structures for the mouse major urinary protein (MUP), the bovine apo-GLTP and the secretin pilot protein are taken from PDB with PDB IDs 1znk, 1wbe, 1y9l respectively (12)(13)(14). All the nonprotein molecules were then removed and protein preparation wizard (23) was used to modify the structures of the proteins for simulation.…”

Section: Systems and Simulationsmentioning

confidence: 99%

Ligand binding to protein-binding pockets with wet and dry regions

Wang

Berne

Friesner

2011

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

191

190

View full text Add to dashboard Cite

Biological processes often depend on protein–ligand binding events, yet accurate calculation of the associated energetics remains as a significant challenge of central importance to structure-based drug design. Recently, we have proposed that the displacement of unfavorable waters by the ligand, replacing them with groups complementary to the protein surface, is the principal driving force for protein–ligand binding, and we have introduced the WaterMap method to account this effect. However, in spite of the adage “nature abhors vacuum,” one can occasionally observe situations in which a portion of the receptor active site is so unfavorable for water molecules that a void is formed there. In this paper, we demonstrate that the presence of dry regions in the receptor has a nontrivial effect on ligand binding affinity, and suggest that such regions may represent a general motif for molecular recognition between the dry region in the receptor and the hydrophobic groups in the ligands. With the introduction of a term attributable to the occupation of the dry regions by ligand atoms, combined with the WaterMap calculation, we obtain excellent agreement with experiment for the prediction of relative binding affinities for a number of congeneric ligand series binding to the major urinary protein receptor. In addition, WaterMap when combined with the cavity contribution is more predictive than at least one specific implementation [Abel R, Young T, Farid R, Berne BJ, Friesner RA (2008) J Am Chem Soc 130:2817–2831] of the popular MM-GBSA approach to binding affinity calculation.

show abstract

“…The polar sugars and lipid head groups are hydrogen-bonded at the protein surface for presentation to T-cell receptors. Similarly, the structures of human and bovine glycolipid transfer proteins (60,61) reveal analogous modes of substrate binding; the polar glycone moieties are positioned at the protein surface, whereas the lipid tails are bound within a single hydrophobic tunnel completely enclosed within the protein environment. Structural studies of the membrane-lipid activator proteins saposin B (62) and human G M2 activator protein (G M2 AP) (63,64) further exemplify lipid substrate binding by encapsulation within hydrophobic protein cores.…”

Section: Discussionmentioning

confidence: 99%

Structural and Mechanistic Analyses of endo-Glycoceramidase II, a Membrane-associated Family 5 Glycosidase in the Apo and GM3 Ganglioside-bound Forms

Caines

Vaughan

Tarling

et al. 2007

Journal of Biological Chemistry

View full text Add to dashboard Cite

endo-Glycoceramidase, a membrane-associated family 5 glycosidase, deviates from the typical polysaccharide substrate specificity of other soluble members of the family, preferentially hydrolyzing glycosidic linkages between the oligosaccharide and ceramide moieties of gangliosides. Here we report the first x-ray crystal structures of an endo-glycoceramidase from Rhodococcus sp., in the apo form, in complex with the ganglioside G M3 (Svennerholm ganglioside nomenclature (Svennerholm, L. (1964) J. Lipid Res. 5, 145-155)), and trapped as a glycosyl-enzyme intermediate. These snapshots provide the first molecular insight into enzyme recognition and association with gangliosides, revealing the structural adaptations necessary for glycosidase-catalyzed hydrolysis and detailing a novel ganglioside binding topology. Consistent with the chemical duality of the substrate, the active site of endo-glycoceramidase is split into a wide, polar cavity to bind the polyhydroxylated oligosaccharide moiety and a narrow, hydrophobic tunnel to bind the ceramide lipid chains. The specific interactions with the ceramide polar head group manifest a surprising aglycone specificity, an observation substantiated by our kinetic analyses. Collectively, the reported structural and kinetic data provide insight toward rational redesign of the synthetic glycosynthase mutant of endo-glycoceramidase to enable facile synthesis of nonnatural, therapeutically useful gangliosides.

show abstract

Structural Evidence for Adaptive Ligand Binding of Glycolipid Transfer Protein

Cited by 50 publications

References 40 publications

Structural Determination and Tryptophan Fluorescence of Heterokaryon Incompatibility C2 Protein (HET-C2), a Fungal Glycolipid Transfer Protein (GLTP), Provide Novel Insights into Glycolipid Specificity and Membrane Interaction by the GLTP Fold

Structural Determination and Tryptophan Fluorescence of Heterokaryon Incompatibility C2 Protein (HET-C2), a Fungal Glycolipid Transfer Protein (GLTP), Provide Novel Insights into Glycolipid Specificity and Membrane Interaction by the GLTP Fold

Ligand binding to protein-binding pockets with wet and dry regions

Structural and Mechanistic Analyses of endo-Glycoceramidase II, a Membrane-associated Family 5 Glycosidase in the Apo and GM3 Ganglioside-bound Forms

Contact Info

Product

Resources

About