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Donghan Lee

Publications and source records attributed to Donghan Lee.

9 recordsLinked to original sources
PubMed2006

RAP uses a histidine switch to regulate its interaction with LRP in the ER and Golgi.

The receptor associated protein (RAP) is an antagonist and molecular chaperone that binds tightly to low-density lipoprotein receptor family members in the endoplasmic reticulum (ER). After escorting these receptors to the Golgi, RAP dissociates from the receptors. The molecular mechanism of the dissociation has been unknown until now. The solution structure of RAP-D3 domain presented here reveals a striking increase in positively charged residues on the surface of this RAP domain due to protonation of solvent-exposed histidine sidechains as the pH is reduced from a near neutral pH of the ER to the acidic pH of the Golgi. Structure-based mutagenesis studies in vitro and in cells confirm that the protonation of histidine residues as a consequence of the pH changes modulate the binding/release of RAP from LRP. This histidine switch may serve as a general mechanism for regulating cell trafficking events.

Alanine↗
PubMed2005

Effective rotational correlation times of proteins from NMR relaxation interference.

Knowledge of the effective rotational correlation times, tauc, for the modulation of anisotropic spin-spin interactions in macromolecules subject to Brownian motion in solution is of key interest for the practice of NMR spectroscopy in structural biology. The value of tauc enables an estimate of the NMR spin relaxation rates, and indicates possible aggregation of the macromolecular species. This paper reports a novel NMR pulse scheme, [15N,1H]-TRACT, which is based on transverse relaxation-optimized spectroscopy and permits to determine tauc for 15N-1H bonds without interference from dipole-dipole coupling of the amide proton with remote protons. [15N,1H]-TRACT is highly efficient since only a series of one-dimensional NMR spectra need to be recorded. Its use is suggested for a quick estimate of the rotational correlation time, to monitor sample quality and to determine optimal parameters for complex multidimensional NMR experiments. Practical applications are illustrated with the 110 kDa 7,8-dihydroneopterin aldolase from Staphylococcus aureus, the uniformly 15N-labeled Escherichia coli outer membrane protein X (OmpX) in 60 kDa mixed OmpX/DHPC micelles with approximately 90 molecules of unlabeled 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), and the 16 kDa pheromone-binding protein from Bombyx mori, which cover a wide range of correlation times.

Aldehyde-Lyases↗
PubMed2005

Unusual heme-histidine bond in the active site of a chaperone.

The heme chaperone CcmE is essential for the delivery of heme to c-type cytochromes. It forms an unusual transient, yet covalent, bond between an essential histidine, H130, and heme. We report on the discovery of the chemical structure of this bond solved by NMR, where the heme vinyl is cross-linked at the beta carbon to the Ndelta1 of H130. As this type of heme linkage has not been described previously in any cytochrome or hemoprotein, it represents a novel type of heme-histidine complex.

Amino Acid Sequence↗
PubMed2005

Polychromatic selective population inversion for TROSY experiments with large proteins.

This paper presents polychromatic selective polarization inversion (PC-SPI) as an alternative to the polarization transfer methods recently developed for the application of NMR to large biological molecules. Theoretical and numerical considerations indicate that PC-SPI has the potential for more efficient polarization transfer under conditions of rapid transverse relaxation compared to J coupling- and cross-correlated relaxation-based transfers. The main advantage offered by the method presented here is the maintenance of near-optimal trajectories of inversion of the individual components of the spin magnetization while using broadband optimized pulses. A 2D experiment was implemented combining PC-SPI with TROSY-based chemical shift correlation. The experiment was applied to detect (15)N-(1)H chemical shift correlation spectra of a 200 kDa complex consisting of an 80% (2)H- and uniformly (15)N,(13)C-labeled 22 kDa portion of complement receptor type 1 and unlabeled C3b of complement (180 kDa).

Binding Sites↗
PubMed2005

Detection of C',Calpha correlations in proteins using a new time- and sensitivity-optimal experiment.

Sensitivity- and time-optimal experiment, called COCAINE (CO-CA In- and aNtiphase spectra with sensitivity Enhancement), is proposed to correlate chemical shifts of (13)C' and (13)C(alpha) spins in proteins. A comparison of the sensitivity and duration of the experiment with the corresponding theoretical unitary bounds shows that the COCAINE experiment achieves maximum possible transfer efficiency in the shortest possible time, and in this sense the sequence is optimal. Compared to the standard HSQC, the COCAINE experiment delivers a 2.7-fold gain in sensitivity. This newly proposed experiment can be used for assignment of backbone resonances in large deuterated proteins effectively bridging (13)C' and (13)C(alpha) resonances in adjacent amino acids. Due to the spin-state selection employed, the COCAINE experiment can also be used for efficient measurements of one-bond couplings (e.g. scalar and residual dipolar couplings) in any two-spin system (e.g. the N/H in the backbone of protein).

Calcium↗
PubMed2002

NMR structure of the unliganded Bombyx mori pheromone-binding protein at physiological pH.

The nuclear magnetic resonance structure of the unliganded pheromone-binding protein (PBP) from Bombyx mori at pH above 6.5, BmPBP(B), consists of seven helices with residues 3-8, 16-22, 29-32, 46-59, 70-79, 84-100, and 107-124, and contains the three disulfide bridges 19-54, 50-108, and 97-117. This polypeptide fold encloses a large hydrophobic cavity, with a sufficient volume to accommodate the natural ligand bombykol. The polypeptide folds in free BmPBP(B) and in crystals of a BmPBP-bombykol complex are nearly identical, indicating that the B-form of BmPBP in solution represents the active conformation for ligand binding.

Carrier Proteins↗