High-resolution crystal structure of the non-specific lipid-transfer protein from maize seedlings

Shin, Dongkun; Lee, Jae Young; Hwang, Kwang Yeon; Kim, Kyeong Kyu; Suh, Se Won

doi:10.1016/s0969-2126(01)00149-6

Cited by 208 publications

(215 citation statements)

References 48 publications

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“…The 20 aliphatic amino acids which form this central cavity are marked in the protein sequences in Figure 1. The continuous hydrophobic tunnel of LTPs has been demonstrated to be the site of fatty acyl chain binding (Shin et al, 1995) and is predicted to have a crucial function in lipid transfer by these proteins. The volume of this tunnel in the BLT4 LTPs is somewhat larger than that of the template maize LTP (the loop region Val60-Gly62 at the bottom of the tunnel is missing from the BLT4 proteins) and is continuous throughout the molecule supporting the hypothesis that these proteins are capable of including a fatty acyl chain.…”

Section: Resultsmentioning

confidence: 99%

“…ClustalV multiple amino acid sequence alignment between the deduced sequence of the low-temperature responsive barley BLT4 proteins (White et al, 1994) and three non-specific lipid-transfer proteins (LTPs) with solved tertiary structures. NLTP_MAIZE, LTP from maize seedling (Shin et al, 1995); NLT1_HORVU, barley endosperm LTP (Heinemann et al, 1996); NLTA_WHEAT, LTP isolated from wheat seeds (Gincel et al, 1994). Sequence codes correspond to Swiss-Prot access codes.…”

Section: Resultsmentioning

confidence: 99%

“…and phosphatidylcholines have been shown to be efficiently transferred by LTPs (Kader, 1996a). X-ray crystallographic and 1 H-NMR analysis of several plant LTPs has demonstrated that they can accommodate only one acyl chain into their binding tunnel without major disturbance in the tertiary structure of the proteins (Gincel et al, 1994; Heinemann et al, 1996;Shin et al, 1995). Therefore, the second acyl chain attached to position 2 of glycerol was modelled on the surface of BLT4.9.…”

Section: Molecular Dynamics Simulation Aided Modelling Of Two Membranmentioning

confidence: 99%

“…Molecular docking and conformational energy minimisation calculations were performed for the protein-ligand complexes using the molecular dynamics and graphical package QUANTA 4.1/CHARMm. As an aid in ligand positioning, the X-ray co-ordinates of the maize lipid-transfer protein-palmitic acid complex were used, which was resolved at 1.8 Å (Shin et al, 1995).…”

Section: Molecular Dynamics Simulations and Evaluationmentioning

confidence: 99%

“…These 3 proteins have a similar structure, in which four α-helices (stabilized by four disulphide bridges) enclose an internal hydrophobic cavity. Co-crystallisation of the maize LTP with palmitate (Shin et al, 1995) shows that this cavity can only accommodate a single acyl chain in an extended configuration.…”

Section: Introductionmentioning

confidence: 99%

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Homology modelling and molecular dynamics aided analysis of ligand complexes demonstrates functional properties of lipid‐transfer proteins encoded by the barley low‐temperature‐inducible gene family, blt4

Keresztessy

Hughes

1998

The Plant Journal

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SummaryThe homology modelling technique was used to predict the tertiary structures of three members of the lowtemperature-inducible barley vegetative shoot epidermal lipid-transfer protein (LTP) family, BLT4, on the basis of the X-ray crystallographically determined three-dimensional structure of a maize seedling LTP. Differences between the maize LTP and the BLT4 family include amino acid substitutions around the entrance and inside the predicted hydrophobic binding tunnels of these proteins. Because of the deletion of the loop region corresponding to Val60-Gly62 of the maize LTP from all three BLT4 LTPs, their internal hydrophobic tunnels are longer. Molecular dynamics modelling shows that BLT4.9 can accommodate hexadecanoic acid in its binding tunnel in similar conformation to the maize LTP. However, modelled cis,cis-9,12-octadecandienoic acid had a more favourable interaction with the BLT4.9 LTP than with the maize protein. Di-cis,cis-9,12-octadecandienoyl phosphatidylglycerol and di-cis,cis-9,12-octadecandienoyl phosphatidylcholine were modelled in the BLT4.9 structure with the fatty acyl group at position 1 embedded in the binding tunnel and the group at position 2 located on the solvent accessible surface of the protein. The results of the modelling suggest that the phospholipid headgroup can form hydrogen and salt bridges with polar and charged residues outside the binding tunnel and the exposed hydrocarbon chain interacts with hydrophobic amino acids on the surface. These results are consistent with the proposal that BLT4 LTPs have a lipid-transfer function associated with frost acclimation in barley.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Molecular Dynamics Simulation Aided Modelling Of Two Membranmentioning

confidence: 99%

Section: Molecular Dynamics Simulations and Evaluationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Homology modelling and molecular dynamics aided analysis of ligand complexes demonstrates functional properties of lipid‐transfer proteins encoded by the barley low‐temperature‐inducible gene family, blt4

Keresztessy

Hughes

1998

The Plant Journal

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Structural trees for protein superfamilies

Ефимов

1997

Proteins

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Structural trees for large protein superfamilies, such as beta proteins with the aligned beta sheet packing, beta proteins with the orthogonal packing of alpha helices, two-layer and three-layer alpha/beta proteins, have been constructed. The structural motifs having unique overall folds and a unique handedness are taken as root structures of the trees. The larger protein structures of each superfamily are obtained by a stepwise addition of alpha helices and/or beta strands to the corresponding root motif, taking into account a restricted set of rules inferred from known principles of the protein structure. Among these rules, prohibition of crossing connections, attention to handedness and compactness, and a requirement for alpha helices to be packed in alpha-helical layers and beta strands in beta layers are the most important. Proteins and domains whose structures can be obtained by stepwise addition of alpha helices and/or beta strands to the same root motif can be grouped into one structural class or a superfamily. Proteins and domains found within branches of a structural tree can be grouped into subclasses or subfamilies. Levels of structural similarity between different proteins can easily be observed by visual inspection. Within one branch, protein structures having a higher position in the tree include the structures located lower. Proteins and domains of different branches have the structure located in the branching point as the common fold.

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Comparison of solution and crystal structures of maize nonspecific lipid transfer protein: A model for a potential in vivo lipid carrier protein

Gomar

Sodano

et al. 1998

Proteins

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The three-dimensional solution structure of maize nonspecific lipid transfer protein (nsLTP) obtained by nuclear magnetic resonance (NMR) is compared to the X-ray structure. Although both structures are very similar, some local structural differences are observed in the first and the fourth helices and in several side-chain conformations. These discrepancies arise partly from intermolecular contacts in the crystal lattice. The main characteristic of nsLTP structures is the presence of an internal hydrophobic cavity whose volume was found to vary from 237 to 513 A3 without major variations in the 15 solution structures. Comparison of crystal and NMR structures shows the existence of another small hollow at the periphery of the protein containing a water molecule in the X-ray structure, which could play an important structural role. A model of the complexed form of maize nsLTP by alpha-lysopalmitoylphosphatidylcholine was built by docking the lipid inside the protein cavity of the NMR structure. The main structural feature is a hydrogen bond found also in the X-ray structure of the complex maize nsLTP/palmitate between the hydroxyl of Tyr81 and the carbonyl of the lipid. Comparison of 12 primary sequences of nsLTPs emphasizes that all residues delineating the cavities calculated on solution and X-ray structures are conserved, which suggests that this large cavity is a common feature of all compared plant nsLTPs. Furthermore several conserved basic residues seem to be involved in the stabilization of the protein architecture.

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High-resolution crystal structure of the non-specific lipid-transfer protein from maize seedlings

Cited by 208 publications

References 48 publications

Homology modelling and molecular dynamics aided analysis of ligand complexes demonstrates functional properties of lipid‐transfer proteins encoded by the barley low‐temperature‐inducible gene family, blt4

Homology modelling and molecular dynamics aided analysis of ligand complexes demonstrates functional properties of lipid‐transfer proteins encoded by the barley low‐temperature‐inducible gene family, blt4

Structural trees for protein superfamilies

Comparison of solution and crystal structures of maize nonspecific lipid transfer protein: A model for a potential in vivo lipid carrier protein

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