Chunli Yan

University of Texas at Austin | UT · Department of Biomedical Engineering

Transcription-coupled repair is essential for the removal of DNA lesions from the transcribed genome. The pathway is initiated by CSB protein binding to stalled RNA polymerase II. Mutations impairing CSB function cause severe genetic disease. Yet, the ATP-dependent mechanism by which CSB powers RNA polymerase to bypass certain lesions while trigger...

Protein arginine methyltransferases (PRMTs) are essential epigenetic and post-translational regulators in eukaryotic organisms. Dysregulation of PRMTs is intimately related to multiple types of human diseases, particularly cancer. Based on the previously reported PRMT1 inhibitors bearing the diamidine pharmacophore, we performed virtual screening t...

Critical for transcription initiation and bulky lesion DNA repair, TFIIH provides an exemplary system to connect molecular mechanisms to biological outcomes due to its strong genetic links to different specific human diseases. Recent advances in structural and computational biology provide a unique opportunity to re-examine biologically relevant mo...

DNA replication origins serve as sites of replicative helicase loading. In all eukaryotes, the six-subunit origin recognition complex (Orc1-6; ORC) recognizes the replication origin. During late M-phase of the cell-cycle, Cdc6 binds to ORC and the ORC–Cdc6 complex loads in a multistep reaction and, with the help of Cdt1, the core Mcm2-7 helicase on...

Advances in cryo-electron microscopy (cryo-EM) have revolutionized the structural investigation of large macromolecular assemblies. In this review, we first provide a broad overview of modeling methods used for flexible fitting of molecular models into cryo-EM density maps. We give special attention to approaches rooted in molecular simulations – a...

Constitutive activation of STAT3 can play a vital role in the development of melanoma. STAT3-targeted therapeutics are reported to show efficacy in melanomas harboring the BRAFV600E mutant and also in vemurafenib-resistant melanomas. We designed and synthesized a series of substituted nitric oxide (NO)-releasing quinolone-1,2,4-triazole/oxime hybri...

Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically...

RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre-initiation complexes (PICs) using single particle cryo-electron microscopy (cryo-EM). We observe stable Pol III–TFIIIB complexes using nucleic acid scaffolds mi...

Thymine DNA glycosylase (TDG) is a pivotal enzyme with dual roles in both genome maintenance and epigenetic regulation. TDG is involved in cytosine demethylation at CpG sites in DNA. Here we have used molecular modeling to delineate the lesion search and DNA base interrogation mechanisms of TDG. First, we examined the capacity of TDG to interrogate...

Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite arc...

Human flap endonuclease 1 (FEN1) and related structure-specific 5’nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5’nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recogni...

Integrin αν β3 expression is altered in various diseases and has been proposed as a drug target. Here we use a rational design approach to develop a therapeutic protein, which we call ProAgio, that binds to integrin αν β3 outside the classical ligand-binding site. We show ProAgio induces apoptosis of integrin αν β3 -expressing cells by recruiting a...

Supplementary Figures 1-11 and Supplementary Tables 1-2

Tyrosyl-DNA phosphodiesterase 2 (TDP2) processes protein/DNA adducts resulting from abortive DNA topoisomerase II (Top2) activity. TDP2 inhibition could provide synergism with the Top2 poison class of chemotherapeutics. By virtual screening of the NCI diversity small molecule database, we identified selective TDP2 inhibitors and experimentally veri...

In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of th...

Densities are shown as a semi-transparent surface following a similar colour scheme to that in the main section. A region corresponding to the double-psi beta-barrel domain composing the conserved core of Pol II within Rpb1 and Rpb2 is shown as an example of near-atomic resolution features. Colour scheme for the promoter DNA is shown at the bottom.

By aligning the three models of holo-PICs (CC, OC, and ITC) using the rigid part of Pol II, sequential states are morphed with a special focus on the nucleic acids regions.

Densities are shown as a semi-transparent surface following a similar colour scheme to that in the main section. A region corresponding to the active site of Pol II is shown as an example of near-atomic resolution features. Color scheme for the promoter DNA is shown at the bottom.

Replicative DNA polymerases (Pols) frequently possess two distinct DNA processing activities - DNA synthesis (polymerization) and proofreading (3'-5' exonuclease activity). The polymerase and exonuclease reactions are performed alternately and are spatially separated in different protein domains. Thus, the growing DNA primer terminus has to undergo...

PolB domains are colored as follows: N-terminal domain in light blue; exonuclease domain in green; palm domain in cyan; fingers domain in gold and thumb domain in red. PCNA and DNA are shown in grey and black.

PolB domains are colored as follows: N-terminal domain in light blue; exonuclease domain in green; palm domain in cyan; fingers domain in gold and thumb domain in red. PCNA and DNA are shown in grey and black. The hinge region is highlighted in yellow.

Contact residues are explicitly shown in ball and stick representation. Contact types are colored as follows: Salt-bridges in light blue and red; persistent hydrogen bonds (other than salt bridges) in cyan and dark blue; hydrophobic interaction in green and purple.

Contact residues are explicitly shown in ball and stick representation. Contact types are colored as follows: Salt-bridges in light blue and red; persistent hydrogen bonds (other than salt bridges) in cyan and dark blue; hydrophobic interaction in green and purple.

Only the palm and thumb domains of PolB are shown for clarity.

Small angle X-ray scattering (SAXS) Electron microscopy (EM) DNA replication and repair While conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM) and small angle X-ray scattering...

Replication Protein A (RPA) is an essential scaffold for many DNA processing machines; its function relies on its modular architecture. Here, we report (15)N-nuclear magnetic resonance heteronuclear relaxation analysis to characterize the movements of single-stranded (ss) DNA binding and protein interaction modules in the RPA70 subunit. Our results...

Proliferating cell nuclear antigen (PCNA) is a pivotal replication protein, which also controls cellular responses to DNA damage. Posttranslational modification of PCNA by SUMO and ubiquitin modulate these responses. How the modifiers alter PCNA-dependent DNA repair and damage tolerance pathways is largely unknown. We used hybrid methods to identif...

Protein kinases are mutated or otherwise rendered constitutively active in numerous cancers where they are attractive therapeutic targets with well over a dozen kinase inhibitors now being used in therapy. While fluorescent sensors have capacity to measure changes in kinase activity, surprisingly they have not been utilized for biomarker studies. A...

eEF-2K is a potential target for treating cancer. However, potent specific inhibitors for this enzyme are lacking. Previously, we identified 2,6-diamino-4-(2-fluorophenyl)-4H-thiopyran-3,5-dicarbonitrile (DFTD) as an inhibitor of eEF-2K. Here we describe its mechanism of action against eEF-2K, on the basis of kinetic, mutational, and docking studie...

Protein arginine methylation is a posttranslational modification critical for a variety of biological processes. Misregulation of protein arginine methyltransferases (PRMTs) have been linked to many pathological conditions. Most current PRMT inhibitors display limited specificity and selectivity, indiscriminately targeting many methyltransferase en...

The bacterial recombinase RecA mediates homologous recombination and recombinational DNA repair through homology search and strand exchange. During homologous recombination, RecA binds an incoming single-stranded DNA (ssDNA) in its primary binding site, site I, to form a nucleoprotein filament whose crystal structure is known. The structure of the...

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Proliferating cell nuclear antigen and the checkpoint clamp Rad9-Rad1-Hus1 topologically encircle DNA and act as mobile platforms in the recruitment of proteins involved in DNA damage response and cell cycle regulation. To fulfill these vital cellular functions, both clamps need to be opened and loaded onto DNA by a clamp loader complex—a process,...

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural...

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Recently, in a virtual screening strategy to identify new compounds targeting the D-recruitment site (DRS) of the c-Jun N-terminal kinases (JNKs), we identified the natural product (-)-zuonin A. Here we report the asymmetric synthesis of (-)-zuonin A and its enantiomer (+)-zuonin A. A kinetic analysis for the inhibition of c-Jun phosphorylation by...

The JNK–JIP1 interaction represents an attractive target for the selective inhibition of JNK-mediated signaling. We report a virtual screening (VS) workflow, based on a combination of three-dimensional shape and electrostatic similarity, to discover novel scaffolds for the development of non-ATP competitive inhibitors of JNK targeting the JNK–JIP i...

Processivity clamps such as proliferating cell nuclear antigen (PCNA) and the checkpoint sliding clamp Rad9/Rad1/Hus1 (9-1-1) act as versatile scaffolds in the coordinated recruitment of proteins involved in DNA replication, cell-cycle control, and DNA repair. Association and handoff of DNA-editing enzymes, such as flap endonuclease 1 (FEN1), with...

Due to their role in cellular signaling mitogen activated protein (MAP) kinases represent targets of pharmaceutical interest. However, the majority of known MAP kinase inhibitors compete with cellular ATP and target an ATP binding pocket that is highly conserved in the 500 plus representatives of the human protein kinase family. Here we review prog...

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ERK2 primarily recognizes substrates through two recruitment sites, which lie outside the active site cleft of the kinase. These recruitment sites bind modular-docking sequences called docking sites and are potentially attractive sites for the development of non-ATP competitive inhibitors. The D-recruitment site (DRS) and the F-recruitment site (FR...

Effective virtual screening relies on our ability to make accurate prediction of protein-ligand binding, which remains a great challenge. In this work, utilizing the molecular-mechanics Poisson-Boltzmann (or Generalized Born) surface area approach, we have evaluated the binding affinity of a set of 156 ligands to seven families of proteins, trypsin...

Distance constraints between Lig-D and ERK2 were set based on the known interactions of the two motifs (RR and ΦA-X-ΦB) with phosphatase (PDB ID: 2GPH). Distance constraints between Lig-F and ERK2 were set to make the Phe-Xaa-Phe motif (DEF motif) binding a hydrophobic pocket formed between the P+1 site, the αF helix and the MAP kinase insert. The...

The mechanisms by which MAP kinases recognize and phosphorylate substrates are not completely understood. Efforts to understand the mechanisms have been compromised by the lack of MAPK-substrate structures. While MAPK-substrate docking is well established as a viable mechanism for bringing MAPKs and substrates into close proximity the molecular det...

The up-regulation of JNK activity is associated with a number of disease states. The JNK-JIP1 interaction represents an attractive target for the inhibition of JNK-mediated signaling. In this study, molecular dynamics simulations have been performed on the apo-JNK1 and the JNK1•L-pepJIP1 and JNK1•D-pepJIP1 complexes to investigate the interaction b...

Thermal disruption of protein structure and function is a potentially powerful therapeutic vehicle. With the emerging nanoparticle-targeting and femtosecond laser technology, it is possible to deliver heating locally to specific molecules. It is therefore important to understand how fast a protein can unfold or lose its function at high temperature...

Histone deacetylases (HDACs) play an important role in gene transcription, and inhibitors of HDACs can induce cell differentiation and suppress cell proliferation in tumor cells. Histone deacetylase1 (HDAC1) binds suberanilohydroxamic acid (SAHA) and 7-phenyl-2, 4, 6-hepta-trienoyl hydroxamic acid (CG-1521) with moderately low affinity (DeltaG = -8...

The quantitative structure-activity relationship (QSAR) was performed on the phloroglucinol derivatives, a kind of anti-tumor agents, to predict their biological activities through their molecular features and properties. Using genetic algorithm (GA) as the statistical method, a robust model with R² = 0.9504, q² = 0.9096, was...

Dichotomin B shows cell growth inhibitory activities against p-388 lymphocytic leukemia cells. However, its spatial conformation and the primary factors affecting its activity are not very clear. Here we optimize the primary structure of dichotomin B at the DFT (density functional theory) with B3LYP parameterization, HF (Hartree-Fock) and ONIOM (ou...

The geometry of dichotomin A, cyclo(-Gly-Thr-Phe-Leu-Tyr-Val-) is optimized at the density functional theory (DFT) with B3LYP parameterization, Hartree–Fock (HF) and our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) levels of theory. The gauge-including atomic orbital (GIAO) methods at both the HF and DFT levels of theo...

The structural aspects for the complexation of (+)-catechin (CA) and (−)-epicatechin (EC) (an enantiomer) to β-cyclodextrins (CDs) were explored by using a semi-empirical PM3 method. In the β-CD/CA inclusion complex, the orientation in which the aromatic A-ring of CA projects onto the 2-OH/3-OH face of β-CD, and the B-ring projects from the 6-OH fa...

The inclusion interaction between quercetin and β-cyclodextrin (β-CD) binding site has been investigated, based on PM3 and ONIOM2 methods. The obtained results clearly indicate that the orientation in which the B ring of the guest molecule located near the secondary hydroxyls of the β-CD cavity is preferred in the binding energy. Moreover, Analyses...

The inclusion process involving β-cyclodextrin (β-CD) and quercetin has been investigated by using the PM3 quantum-mechanical semi-empirical method. In the β-CD quercetin inclusion complex, a large portion of the flavonoid skeleton is included in the β-CD cavity and the bond connected ring B with ring C is inclined to the molecular axis of β-CD. Th...

Polyparameter linear free energy relationships (LFERs) on rate constants (kOH) for gas-phase reactions of hydroxyl radicals with polycyclic aromatic hydrocarbons (PAHs) and polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) were developed. Quantum chemical descriptors and partial least squares (PLS) regression were used for model develop...