Biology subjects

Jeong, S.

Publications and source records attributed to Jeong, S..

44 records · Page 3Linked to original sources

bioRxiv2020

Separation of coiled-coil structures in lamin A/C is required for elongation of the filament

Intermediate filaments (IFs) commonly have structural elements of a central -helical coiled-coil domain consisting of coil 1a, coil 1b, coil 2, and their flanking linkers. Recently, crystal structure of a long lamin A/C fragment was determined and showed detailed features of a tetrameric unit. The structure further suggested a new binding mode between tetramers, designated eA22, where a parallel overlap of coil 1a and coil 2 is the key interaction. In this study, we investigated the biochemical effects of genetic mutations causing human diseases, focusing on the eA22 interaction. The mutant proteins exhibited either weakened or augmented interactions between coil 1a and coil 2. The ensuing biochemical results indicated that the interaction requires the separation of the coiled-coils in N-terminal of coil 1a and C-terminal of coil 2, coupled with the structural transition in the central -helical rod domain. This study provides insight into the role of coil 1a as a molecular regulator in elongation of the IF proteins.

molecular biology↗

bioRxiv2019

Computer-aided Binding Mode Prediction and Affinity Maturation of LRR Protein Binder without Structural Determination

Precise binding mode identification and subsequent affinity improvement without structure determination remain a challenge in the development of therapeutic proteins. However, relevant experimental techniques are generally quite costly, and purely computational methods have been unreliable. Here, we show that integrated computational and experimental epitope localization followed by full-atom energy minimization can yield an accurate complex model structure which ultimately enables effective affinity improvement and redesign of binding specificity. As proof-of-concept, we used a leucine-rich repeat (LRR) protein binder, called a repebody (Rb), that specifically recognizes human IgG1 (hIgG1). We performed computationally-guided identification of the Rb:hIgG1 binding mode and leveraged the resulting model to reengineer the Rb so as to significantly increase its binding affinity for hIgG1 as well as redesign its specificity toward multiple IgGs from other species. Experimental structure determination verified that our Rb:hIgG1 model closely matched the co-crystal structure. Using a benchmark of other LRR protein complexes, we further demonstrated that the present approach may be broadly applicable to proteins undergoing relatively small conformational changes upon target binding. Author SummaryIt is quite challenging for computational methods to determine how proteins interact and to design mutations to alter their binding affinity and specificity. Despite recent advances in computational methods, however, in silico evaluation of binding energies has proven to be extremely difficult. We show that, in the case of protein-protein interactions where only small structural changes occur upon target binding, an integrated computational and experimental approach can identify a binding mode and drive reengineering efforts to improve binding affinity or specificity. Using as a model system a leucine-rich repeat (LRR) protein binder that recognizes human IgG1, our approach yielded a model of the protein complex that was very similar to the subsequently experimentally determined co-crystal structure, and enabled design of variants with significantly improved IgG1 binding affinity and with the ability to recognize IgG1 from other species.

bioinformatics↗

bioRxiv2019

Positional isomers of a non-nucleoside substrate differentially affect myosin function

Molecular motors have evolved to transduce chemical energy from adenosine triphosphate into mechanical work to drive essential cellular processes, from muscle contraction to vesicular transport. Dysfunction of these motors is a root cause of many pathologies necessitating the need for intrinsic control over molecular motor function. Herein, we demonstrate that positional isomerism can be used as a simple and powerful tool to control the molecular motor of muscle, myosin. Using three isomers of a synthetic non-nucleoside triphosphate we demonstrate that myosins force and motion generating capacity can be dramatically altered at both the ensemble and single molecule levels. By correlating our experimental results with computation, we show that each isomer exerts intrinsic control by affecting distinct steps in myosins mechano-chemical cycle. Our studies demonstrate that subtle variations in the structure of an abiotic energy source can be used to control the force and motility of myosin without altering myosins structure. Statement of SignificanceMolecular motors transduce chemical energy from ATP into the mechanical work inside a cell, powering everything from muscle contraction to vesicular transport. While ATP is the preferred source of energy, there is growing interest in developing alternative sources of energy to gain control over molecular motors. We synthesized a series of synthetic compounds to serve as alternative energy sources for muscle myosin. Myosin was able to use this energy source to generate force and velocity. And by using different isomers of this compound we were able to modulate, and even inhibit, the activity of myosin. This suggests that changing the isomer of the substrate could provide a simple, yet powerful, approach to gain control over molecular motor function.

biophysics↗

bioRxiv2019

Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms

Brutons tyrosine kinase (Btk) is a key component for B-cell maturation and activation. Btk loss-of-function mutations cause human X-linked agammaglobulinemia (XLA). In contrast, constitutive Btk signaling drives several B-cell neoplasms, which may be treated with tyrosine kinase inhibitors (TKIs). Here, we uncovered the molecular mechanism by which a subset of XLA mutations in the SH2 domain strongly perturbs Btk activation. Using a combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), we discovered an allosteric interface between the SH2 and kinase domain to which multiple XLA mutations map and which is required for Btk activation. As allosteric interactions provide unique targeting opportunities, we developed an engineered repebody protein binding to the Btk SH2 domain and able to disrupt the SH2-kinase interaction. The repebody prevented activation of wild-type and TKI-resistant Btk, inhibited Btk-dependent signaling and proliferation of malignant B-cells. Therefore, the SH2-kinase interface is critical for Btk activation and a targetable site for allosteric inhibition.

cancer biology↗

bioRxiv2019

CVRMS: Cross-validated Rank-based Marker Selection for Genome-wide Prediction of Low Heritability

CVRMS is an R package designed to extract marker subsets from repeated rank-based marker datasets generated from genome-wide association studies or marker effects for genome-wide prediction (https://github.com/lovemun/CVRMS). CVRMS provides an optimized genome-wide biomarker set with the best predictability of phenotype by implemented ridge regression using genetic information. Applying our method to human, animal, and plant datasets with wide heritability (zero to one), we selected hundreds to thousands of biomarkers for precise prediction.

bioinformatics↗

bioRxiv2019

Graphene Quantum Dot Oxidation Governs Noncovalent Biopolymer Adsorption

The graphene quantum dot (GQD) is a carbon allotrope with a planar surface amenable for functionalization and nanoscale dimensions that confer photoluminescent properties. Collectively, these properties render GQDs an advantageous platform for nanobiotechnology applications, including as optical biosensors and delivery platforms. In particular, noncovalent functionalization offers a route to reversible modification and preservation of the pristine GQD substrate. However, a clear paradigm for GQD noncovalent functionalization has yet to be realized. Herein, we demonstrate the feasibility of noncovalent polymer adsorption to the GQD surface, with a specific focus on single-stranded DNA (ssDNA). We study how GQD oxidation level affects the propensity for polymer adsorption by synthesizing and characterizing four types of GQD substrates and investigating noncovalent polymer association to these substrates. Distinct adsorption methods are developed for successful ssDNA attachment based upon the GQDs initial level of oxidation. ssDNA adsorption to the GQD is confirmed by atomic force microscopy, by inducing ssDNA desorption, and with molecular dynamics simulations. ssDNA is determined to adsorb strongly to no-oxidation GQDs, weakly to low-oxidation GQDs, and not at all for heavily oxidized GQDs. We hypothesize that high GQD oxygen content disrupts the graphitic carbon domains responsible for stacking with the aromatic ssDNA bases, thus preventing the formation of stable polymer-GQD complexes. Finally, we develop a more generic adsorption platform and assess how the GQD system is tunable by modifying both the polymer sequence and type.

bioengineering↗

bioRxiv2019

High Throughput Evolution of Near Infrared Serotonin Nanosensors

Release and reuptake of neuromodulator serotonin, 5-HT, is central to mood regulation and neuropsychiatric disorders, whereby imaging serotonin is of fundamental importance to study the brains serotonin signaling system. We introduce a reversible near-infrared nanosensor for serotonin (nIRHT), for which synthetic molecular recognition toward serotonin is systematically evolved from ssDNA-carbon nanotube constructs generated from large libraries of 6.9 x 1010 unique ssDNA sequences. nIRHT produces a [~]200% fluorescence enhancement upon exposure to serotonin with a Kd = 6.3 {micro}M affinity. nIRHT shows selective responsivity towards serotonin over serotonin analogs, metabolites, and receptor-targeting drugs, and a 5-fold increased affinity for serotonin over dopamine. Further, nIRHT can be introduced into the brain extracellular space in acute slice, and can be used to image exogenous serotonin reversibly. Our results suggest evolution of nanosensors could be generically implemented to rapidly develop other neuromodulator probes, and that these probes can image neuromodulator dynamics at spatiotemporal scales compatible with endogenous neuromodulation.

neuroscience↗

bioRxiv2018

CHEMOMETRIC APPROACHES FOR DEVELOPING INFRARED NANOSENSORS TO IMAGE ANTHRACYCLINES

Generation, identification, and validation of optical probes to image molecular targets in a biological milieu remains a challenge. Synthetic molecular recognition approaches leveraging the intrinsic near-infrared fluorescence of single-walled carbon nanotubes is a promising approach for chronic biochemical imaging in tissues. However, generation of nanosensors for selective imaging of molecular targets requires a heuristic approach. Here, we present a chemometric platform for rapidly screening libraries of candidate single-walled carbon nanotube nanosensors against biochemical analytes to quantify fluorescence response to small molecules including vitamins, neurotransmitters, and chemotherapeutics. We further show this approach can be leveraged to identify biochemical analytes that selectively modulate the intrinsic near-infrared fluorescence of candidate nanosensors. Chemometric analysis thus enables identification of nanosensor-analyte hits and also nanosensor fluorescence signaling modalities such as wavelength-shifts that are optimal for translation to biological imaging. Through this approach, we identify and characterize a nanosensor for the chemotherapeutic anthracycline doxorubicin, which provides an up to 17 nm fluorescence red-shift and exhibits an 8 {micro}M limit of detection, compatible with peak circulatory concentrations of doxorubicin common in therapeutic administration. We demonstrate selectivity of this nanosensor over dacarbazine, a chemotherapeutic commonly co-injected with DOX. Lastly, we demonstrate nanosensor tissue compatibility for imaging of doxorubicin in muscle tissue by incorporating nanosensors into the mouse hindlimb and measuring nanosensor response to exogenous DOX administration. Our results motivate chemometric approaches to nanosensor discovery for chronic imaging of drug partitioning into tissues and towards real-time monitoring of drug accumulation.

biochemistry↗