Gwangrog Lee

• Doctor of Philosophy
• Professor (Full) at Korea Advanced Institute of Science and Technology

During efferocytosis, phagocytic cells recognize dying cells by receptors binding to ligands specifically exposed on apoptotic cells. Multiple phagocytic receptors and some of their signaling pathways have been identified. However, the downstream pathways of tethering receptors that secure apoptotic cells remain elusive. It is generally assumed tha...

Significance Ler [locus of e nterocyte e ffacement (LEE)-encoded regulator], encoded by the first gene of the LEE1 operon in enteropathogenic Escherichia coli (EPEC), represses its own transcription driven by two promoters separated by 10 bp. We found that Ler does this repression through a DNA loop of 16 helical turns, in which RNA polymerase is t...

Loading a Spring To regulate cellular RNA levels, transcription must be balanced by RNA degradation. An important player is the exosome, which can unwind and degrade structured RNA. Lee et al. (p. 1726 ) used single-molecule fluorescence analysis to investigate how degradation and unwinding are coupled in the catalytic subunit of the yeast exosome...

Single-molecule tracking provides new insights into how an ATP-independent endo-proteolytic machine digests collagen fibrils during their remodeling.

The eukaryotic exosome catalyzes a series of reactions such as RNA processing and decay. Rrp44 is a key catalytic subunit of the yeast exosome complex and enables multi-enzymatic activities, including endoribonuclease, exoribonuclease and duplex unwinding. Its exoribonuclease and unwinding activities are indispensable for the complete degradation o...

λ exonuclease degrades one strand of duplex DNA in the 5'-to-3' direction to generate a 3' overhang required for recombination. Its ability to hydrolyze thousands of nucleotides processively is attributed to its ring structure, and most studies have focused on the processive phase. Here we have used single-molecule fluorescence resonance energy tra...

Molecular motors have inspired many avenues of research for nanotechnology but most molecular motors studied so far allow only unidirectional movement. The archaeal RNA-exosome is a reversible motor that can either polymerize or degrade an RNA strand, depending on the chemical environments. We developed a single molecule fluorescence assay to analy...

Anfinsen's thermodynamic hypothesis implies that proteins can encode for stretching through reversible loss of structure. However, large in vitro extensions of proteins that occur through a progressive unfolding of their domains typically dissipate a significant amount of energy, and therefore are not thermodynamically reversible. Some coiled-coil...

The eukaryotic exosome catalyzes a series of reactions such as RNA processing and decay. Rrp44 is a key catalytic subunit of the yeast exosome complex and enables multi-enzymatic activities, including endoribonuclease, exoribonuclease and duplex unwinding. Its exoribonuclease and unwinding activities are indispensable for the complete degradation o...

Biological systems are constantly under mechanical stress either during movement or when acted upon by external forces. The identification of proteins motifs that behave as biological springs will be important for understanding how cells respond to mechanical stimuli and can also propel the design of non-biological nanomaterials. We report here ide...

The exposure of cancer cells to ionizing radiation results in potentially lethal DNA lesions. For this reason, identification and quantification of various lesions have intensively been investigated. It has also been anticipated that DNA lesions may affect not only the chemical but also the mechanical integrity of the double helix. However, the rel...

RNA biosynthesis involves a certain frequency of errors due to inherent inaccuracies of enzymes involved. Although DNA damage is repaired, RNA errors are rapidly eliminated. In particular, the degradation of 3’ poly A tail is very important in RNA metabolism to maintain the fidelity of mRNA synthesis in the cell. A key enzyme involved in both RNA p...

The nanomechanical fingerprints elasticity of UV-damage to DNA in a dose- and sequence-dependent manner, using Atomic Force Microscopy (AFM)-based single-molecule force spectroscopy, was analyzed. The force spectrograms results indicate a significant differences in the elasticity of UV-treated individual DNA molecules as compared to the untreated D...

A cantilever device based on competitive binding of an immobilized receptor to immobilized and soluble ligand and capable of measuring solution-phase thermodynamic quantities is described. Through multiple binary queries, the device stochastically measures the probability of the formation of a bound complex between immobilized protein and immobiliz...

Ankyrin repeats are an amino-acid motif believed to function in protein recognition; they are present in tandem copies in diverse proteins in nearly all phyla. Ankyrin repeats contain antiparallel alpha-helices that can stack to form a superhelical spiral. Visual inspection of the extrapolated structure of 24 ankyrin-R repeats indicates the possibi...

The elasticity of single amylose chains in solvents that promote or inhibit the formation of inter-residue hydrogen bonds was examined by AFM (see picture). Hydrogen bonds were found to rigidify the amylose chain in solvents of low dielectric constant, and the (Chemical Equation Presented) strength of inter-residue hydrogen bonds in sugars can be m...

In this paper we review the conformational analysis of sugar rings placed under tension during mechanical manipulations of single polysaccharide molecules with the atomic force microscope and during steered molecular dynamics simulations. We examine the role of various chemical bonds and linkages between sugar rings in inhibiting or promoting their...

Recent atomic force microscopy stretching measurements of single polysaccharide molecules suggest that their elasticity is governed by force-induced conformational transitions of the pyranose ring. However, the mechanism of these transitions and the mechanics of the pyranose ring are not fully understood. Here we use steered molecular dynamics simu...

Recent single-molecule atomic force microscopy (AFM) experiments have revealed that some polysaccharides display large deviations from force-extension relationships of other polymers which typically behave as simple entropic springs. However, the mechanism of these deviations has not been fully elucidated. Here we report the use of novel quantum me...

Single molecules of beta-1 --> 6-linked d-glucose polysaccharides, when stretched in an atomic force microscope, display a hookean-like elasticity unusual for polymers. High-level ab initio calculations and microsecond-scale molecular dynamics simulations reveal that this elasticity is governed by force-induced rotations of the exocyclic group on t...

Self-assembled polymers whose main chains are defined by reversible DNA base pairing form bridges between the tip of an atomic force microscope and substrate. The forces associated with the rupture of these assemblies are independent of polymer bridge length, and they resemble those expected for the isolated associations defining the polymer bridge...