# Quantitative Biology 2017: Computational and Single-Molecule Biophysics

23-26 June 2017
Peking University, China
Asia/Shanghai timezone
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## Contribution List

Displaying 73 contributions out of 73
Type: Poster Session: Poster
Plant-specific insert (PSI), an extra region of approximately 100 amino acid residues present in most plant aspartic proteases, is involved in host defense and vacuolar targeting. PSI functions via interacting with membranes of microbes. However, the detailed mechanism of PSI-induced membrane disruption is not clear. Recently, the high-resolution crystal structure of PSI of *Solanum tuberosum* asp ... More
Presented by Hua YU
Type: Invited Talk Session: Talk
Development of useful approaches to classify large-scale data sets and to extract biological insights is of considerable importance in the post-genomic era. Here we propose an approach to classify proteomes and protein sets based on protein distributions in terms of two basic attributes, protein lengths (L) and protein intrinsic disorder contents (ID). We systematically construct the two-dimension ... More
Presented by Prof. Hong GUO on 25 Jun 2017 at 16:40
Type: Oral Presentation Session: Talk
Antimicrobial peptides (AMPs) are innately secreted or generated peptides by animals and plants, which have broad-spectrum antimicrobial activities against various microbes such as bacteria, virus and fungi. It is believed that AMPs carry great potential to be developed into a new generation of antibiotics and may help us to survive in the war against ‘super bugs’. Even more interestingly, rec ... More
Presented by Dr. Chen SONG on 24 Jun 2017 at 14:50
Type: Poster
Cas9 is a RNA guided, multi-domain DNA endonuclease which that has been engineered as a wildly-used tool for genomic editing and manipulation. The complementarity between RNA guide sequence and DNA drives Cas9 to recognize its target and to subsequently induce double-strand DNA breaks. However, the off-target binding and cleavage by Cas9 pose as one of the major challenges in its applications. Pre ... More
Presented by Ms. Mengyi YANG
Type: Invited Talk Session: Talk
Alzheimer’s disease is characterized by the coexistence of the intracellular neurofirillary tangles of tau proteins and the extracellular senile plaques of amyloid-β (Aβ) proteins. Tau is an intrinsically disordered protein and it is experimentally challenging to characterize its conformational ensembles. Many factors, such as fibril seeds and polyanions (e.g., heparin), affect tau’s folding ... More
Presented by Prof. Guanghong WEI on 24 Jun 2017 at 13:30
Type: Poster Session: Poster
The construction of metal binding sites into designed protein scaffolds is an ultimate test of our understanding of structure-function relationships and it will allow us to construct new proteins for biochemistry and biotechnology applications and biological pathways. The negative effects of toxicity of cadmium exposure on human health have has been recognized for many years. Thus, new technologie ... More
Presented by Ms. Hengyi LI
Type: Invited Talk Session: Talk
The central step in eukaryotic homologous recombination (HR) is ATP-dependent DNA-strand exchange mediated by the Rad5 recombinase. In this process, Rad5 assembles on single-stranded DNA (ssDNA) and generates a helical filament that is able to search for and invade homologous double-stranded DNA (dsDNA), thus leading to strand separation and formation of new base pairs between the initiating ssDNA ... More
Presented by Prof. Hongwei WANG on 25 Jun 2017 at 08:30
Type: Invited Talk Session: Talk
Gene activity is the prime mover in the living cell, driving a cell’s function at any given time. I will report on recent advances in our ability to describe the stochastic kinetics of gene regulation, achieved through the combination of single-molecule fluorescence microscopy in individual cells, novel image analysis algorithms, and theoretical modeling. We apply our approach to explore gene re ... More
Presented by Prof. Ido GOLDING on 25 Jun 2017 at 09:00
Type: Oral Presentation Session: Talk
The stochastic kinetics of gene activity has been well characterized, but how this kinetics is modulated by the transcription factors that regulate expression remains largely unknown. We address this question using the Bicoid (Bcd) transcription factor and *hunchback* (*hb*) gene in early Drosophila embryos. We measure, simultaneously, the number of nascent *hb* mRNAs, nuclear Bcd concentration, a ... More
Presented by Dr. Heng XU on 26 Jun 2017 at 10:00
Type: Poster
Rotary sequential hydrolysis of metabolic machine F1-ATPase is a prominent manifestation of high coordination among multiple chemical sites in ring-shaped molecular machines, and is also functionally essential in F1 to tightly couple chemical reactions and central gamma-shaft rotation. High-speed AFM experiments had identified that the sequential hydrolysis was maintained in the F1 stator ring eve ... More
Presented by Mr. Liqiang DAI
Type: Invited Talk Session: Talk
Protein allosteric regulation refers to perturbation at a distance that makes remarkable influence on function. Allosteric effects can be produced through ligand binding, posttranslational modification, or changes in other proteins in the biological network that the target protein is involved. Allosteric drugs have attracted much attention, as they do not compete with endogenous ligands and may be ... More
Presented by Prof. Luhua LAI on 24 Jun 2017 at 08:15
Type: Poster Session: Poster
Cancer cells reprogram its metabolic pathways to support its fast growth and proliferation. Human phosphoglycerate dehydrogenase (PHGDH) catalyzes the first, rate-limiting step in serine biosynthesis. Recent work demonstrating that PHGDH-overexpressing cancer cell lines are uniquely sensitive to PHGDH knockdown even in the presence of exogenous serine whereas lines express little PHGDH are insensi ... More
Presented by Mr. Pei LIU
Type: Poster
Circadian clocks are intrinsic, time-tracking systems that enable organisms to anticipate environmental changes and allow them to adapt their behavior and physiology to the appropriate time of day. Daily behavior that are asynchronous with the natural light/dark cycle, such as shift work, jet lag and sleep deprivation, which are called chronobiology disorders, have been strongly and consistently a ... More
Presented by Ms. Xiaowen XIE
Type: Poster
Several fatal neurodegenerative conditions are caused by mis-folded prion protein. In recent years, great number of experimental and computational efforts have been made to understand the mechanics of the transformation from wild type prion (PrP<sup>C</sup>) to its pathogenic mis-folded form (PrP<sup>SC</sup>). Most of the computational works study the monomer of wild type prion protein and its va ... More
Presented by Mr. Yiming TANG
Type: Invited Talk Session: Talk
Total internal reflection fluorescence (TIRF) microscopy based single molecule fluorescence resonance energy transfer (sm-FRET) has become a widely used tool to examine internal conformational dynamics of surface-attached molecules or interactions between attached and freely-diffusing molecules. In our group, we mainly focus on elucidating molecular mechanisms of the translation machineries and CR ... More
Presented by Prof. Chunlai CHEN on 25 Jun 2017 at 14:30
Type: Invited Talk Session: Talk
The RAD51 DNA strand exchange protein (recombinase) is critical for genome stability, as it participates in accurate DNA repair by homologous recombination, and stabilizes distressed DNA replication forks. The active form of RAD51 is a nucleoprotein filament assembled on ssDNA. The assembly, stability and interactions of the RAD51 filament are tightly regulated by posttranslational modifications, ... More
Presented by Prof. Maria SPIES on 24 Jun 2017 at 11:05
Type: Poster
The neurofibrillary tangles formed by Tau inside neurons are responsible for the damage of neutral tissues in human brain and give rise to a series of neurodegenerative diseases called taupathies. R3, the third repeat fragment of Tau in the microtubule-binding domain, containing the fibril nucleating motif VQIVYK, is critical to the formation of β-sheet-rich fibrillar aggregates of Tau. Interesti ... More
Presented by Ms. Xuewei DONG
Type: Poster
Type II diabetes are associated with the amyloid deposits of the human islet amyloid polypeptide (hIAPP) and the inhibition of β-sheet formation is considered the primary therapeutic strategy for treating Type II diabetes. Increasing experimental and computational studies show that carbon nanoparticles retard peptide fibrillation by slowing down the nucleation process. However, the effect of carb ... More
Presented by Mrs. cuiqin BAI
Type: Oral Presentation Session: Talk
Spermine is a tetravalent polyamine present at millimolar concentrations in all eukaryotic cells. The adsorption of cationic spermine on the surface of anionic microtubules (MTs) may have a potential regulatory role on the complex dynamics of MTs. Experiments have shown that polyamines such as spermines at physiological concentrations can facilitate the nucleation and polymerization of tubulin int ... More
Presented by Prof. Shengfeng CHENG on 26 Jun 2017 at 09:00
Type: Invited Talk Session: Talk
Electronic polarization effects are of critical importance for an accurate representation of ion permeation, ion-mediate ligand binding or any process that involves significant fluctuations in charge density in the confinement. Although the widely used atomic models based on non-polarizable additive force fields are able to shed some light into ion-protein interactions and subsequent transport, of ... More
Presented by Prof. Sergei NOSKOV on 26 Jun 2017 at 08:30
Type: Invited Talk Session: Talk
Collective oscillations are ubiquitous in the biological world. In 1975, Kuramoto proposed a model of globally coupled oscillators with distributed frequencies that exhibits entrainment transition at a critical coupling strength. Yet in many well-studied cell populations, such as yeast cell suspension, dictyostelium and neuronal cell culture, pulsation emerges only when the local cell density exce ... More
Presented by Prof. Leihan TANG on 25 Jun 2017 at 16:10
Type: Oral Presentation Session: Talk
In biological and medical related areas, enormous attention has also been paid to 2D materials due to their active surface that favors various practical applications, such as drug delivery and therapeutic platforms. When incorporating nanomaterials into biological system, the primary concern is the potential toxicity of the foreign materials to living cells (cytotoxicity). In this talk, we will in ... More
Presented by Prof. Weifeng LI on 26 Jun 2017 at 09:20
Type: Poster
Abstract: The fidelity control via substrate (NTP) selection is essential in gene transcription. During transcription elongation, of T7 RNA polymerase (RNAP), a simplest model system, how the substrate selection is achieved is still not clear yet. In this work, we employed all-atom molecular dynamics (MD) simulations and focused on calculating the free energy barrier between the pre-insertion and ... More
Presented by Ms. chunhong LONG
Type: Invited Talk Session: Talk
Transcription, the synthesis of RNA from a complementary DNA template, plays a crucial role in cellular regulation, including differentiation, development, and other fundamental processes. In this talk, I will discuss our results on modeling the RNA polymerase II (Pol II, a system with ~400K atoms) Translocation and other functional conformational changes of this enzyme at sub-millisecond timesca ... More
Presented by Prof. Xuhui HUANG on 25 Jun 2017 at 11:10
Type: Invited Talk Session: Talk
All CRISPR systems require complementary base pairing between an RNA-guided nucleoprotein complex and the target DNA. Off-target activities have also been reported, but we currently lack a comprehensive and quantitative description of sequence-dependent DNA binding and nuclease activation. To address this gap, we developed an experimental platform that directly measures the interactions between fl ... More
Presented by Prof. Ilya FINKELSTEIN on 24 Jun 2017 at 11:35
Type: Poster
Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm ... More
Presented by Dr. Yumeng YAN
Type: Invited Talk Session: Talk
Fluorescent energy transfer has become an indispensable technique for studying dynamics of molecular motors and membrane proteins. The lack of angstrom resolution made it difficult to correlate the results with computer modeling and electron microscopy. Here, we report on our recent efforts in taking advantage of bending elasticity of double-stranded DNA to exert force on the molecules of interest ... More
Presented by Prof. Ming LI on 24 Jun 2017 at 15:30
Type: Poster
Transcription process plays an important role in gene expression. The transcription bursting in bacteria was found to be regulated by supercoiling accumulation and gyrase binding on DNA to release the supercoiling. In this work, we built a multi-state model of the supercoiling accumulation and release in transcription by a RNA polymerase (RNAP), so that to quantitatively describe the experimentall ... More
Presented by Mr. Xiaobo JING
Type: Poster
The bioluminescent bacteria are widely distributed in marine, freshwater and terrestrial environments. They are able to emit visible light mostly with the wavelength in the range of 487-505 nm, whereas accompanied by antenna proteins, the emitted light is found blue or red shifted. The lumazine protein (LumP) and yellow-fluorescent protein (YFP) are two important antenna proteins, which contain hi ... More
Presented by Dr. Yanling LUO
Type: Oral Presentation Session: Talk
Robustness is a critical ability of biological oscillators to function in environmental perturbations. Although central architectures that support robust oscillations have been extensively studied, networks containing the same core vary drastically in their potential to oscillate, and it remains elusive what peripheral modifications to the core contribute to the large variation. We computationally ... More
Presented by Prof. Qiong YANG on 26 Jun 2017 at 10:30
Type: Oral Presentation Session: Talk
Dengue and Zika viruses belong to the Flavivirus family of mosquito-borne infections prevalent in tropical and subtropical regions. They are enveloped, single-stranded positive-sense RNA viruses with a genome of approximately 11kb and form virions of ~45 nm in diameter. In recent years, near-atomistic cryo-EM structures have become available. While these structures reveal the precise organization ... More
Presented by Dr. Roland G HUBER on 24 Jun 2017 at 14:30
Type: Oral Presentation Session: Talk
Homologous recombination is a highly conserved pathway for the repair of double-stranded breaks, and is important for maintaining genomic integrity. Recombination mediators play a vital role to ensure this process occurs successfully. Human RAD52 has been shown to mediate RPA-ssDNA annealing and is synthetic lethal with mutations in other recombination proteins in humans. Here, we use single-molec ... More
Presented by Frank MA on 24 Jun 2017 at 16:30
Type: Oral Presentation Session: Talk
In eukaryotic cells, the Nuclear Pore Complex (NPC) is the sole conduit of cargo transport between the nucleus and cytoplasm. The central channel of NPC lined with intrinsically disordered proteins called Phe-Gly-rich nucleoporins (FG-nups). However, the detailed mechanisms underlying the NPC’s barrier formation and selective permeability have remained elusive. This is partially because conventi ... More
Presented by Dr. Qi SHEN on 26 Jun 2017 at 11:00
Type: Invited Talk Session: Talk
The ubiquitin-proteasome system(UPS) plays a key role in most cellular functions, such as the cell cycle and protein homeostasis, by promoting regulated protein degradation. The supreme regulatory potency of the protein degradation machinery depends on its specificity for substrates. While specificity of the UPS most likely originates from the ubiquitin configurations on substrates, we still do no ... More
Presented by Prof. Ying LV on 24 Jun 2017 at 16:00
Type: Invited Talk Session: Talk
Nanoscale particles have become promising materials in various biomedical applications, however, in order to stimulate and facilitate these applications, there is an urgent need for a better understanding of their biological effects and related molecular mechanism/physics as well. In this talk, I will discuss some of our recent works, mostly molecular modelling, on nanotoxicity and their implicati ... More
Presented by Prof. Ruhong ZHOU on 25 Jun 2017 at 10:40
Type: Poster Session: Poster
NF-$\kappa$B control hundreds of genes associated with multiple physiological and pathological process and its misregulation will result in numbers of diseases, including chronic inflammation and cancers. As the gateway and signaling hub to activate NF-$\kappa$B, IKK has always been the primary target to regulate NF-$\kappa$B activity. Although a number of IKK small molecule inhibitors have been d ... More
Presented by Ms. Hongbo LIU
Type: Oral Presentation Session: Talk
Studies suggest that a large number of genomic ribonucloetides is present in cells. In addition to the ribonucleotides that prime DNA replication, significant amount of ribonucleotides are mis-incorporated into the genome per cell cycle by replicating DNA polymerases and are removed by RNase H2-initiated error-free ribonucloetide excision repair. In the absence of RNase H2 activity, a topoisomeras ... More
Presented by Dr. HENGYAO NIU on 25 Jun 2017 at 15:00
Type: Poster Session: Poster
Firefly bioluminescence is produced by luciferase catalyzing the oxidation of luciferin in the presence of ATP, Mg$^{2+}$ and O$_{2}$. The light emitter is the excited-state oxyluciferin. The light emitter and its formation mechanism have been extensively studied. However, the biosynthesis pathway of luciferin is still unclear. Referring to the tricarboxylic acid cycle, it’s most likely to regen ... More
Presented by Dr. Yuan-Yuan CHENG
Type: Poster
The StPSI has been shown to possess potent antimicrobial activity against human pathogens and is capable of fusing phospholipid vesicles, provided a net anionic vesicle charge and acidic pH are met. To further understand the StPSI’s activity, several in silico investigations were undertaken. Continuous constant pH molecular dynamics were conducted using the crystallographic dimer. The majority o ... More
Presented by Mr. John H. DUPUIS
Type: Poster
Knowledge of the chemistry in an enzyme active site is essential for understanding the biology of that protein. We employ first-principles electronic structure calculations to investigate the oxidoreductive chemistry of the Xanthine Dehydrogenase, XDH, class of enzymes. We have shown that modeling the enzyme : substrate reductive half-reaction as a synchronous metathetic exchange between the subst ... More
Presented by Dr. Predrag-Peter ILICH
Type: Invited Talk Session: Talk
Gram-negative bacteria such as E.coli are typically regarded as "simple" model organisms, yet their cell envelopes are surprisingly complex. Recent studies have revealed that contrary to the traditional view of the cell membrane as a passive bystander in membrane protein function, it plays a key role in protein folding, assembly, and function. To study the dynamics of native membrane proteins and ... More
Presented by Prof. Syma KHALID on 24 Jun 2017 at 14:00
Type: Invited Talk Session: Talk
Proteins work in dynamic and highly specific association with other proteins and biomolecules under tight regulatory control. Elucidation of the structural basis of such associations has been one of the most important contributions of experimental structural biology, especially X-ray crystallography. With the recent rapid progress in molecular dynamics, we venture to make a departure from simula ... More
Presented by Prof. Yibing SHAN on 25 Jun 2017 at 10:10
Type: Poster
Allostery is a biological phenomenon of great importance in regulation and signaling, for example, in kinases, transcription factor, GPCR and heamoglobin. Allosteric drug design has great advantages over previous drug design methods. As a consequence, prediction of allosteric sites has become a hot topic in the field of protein allostery. Many theoretical methods (e.g. normal mode analysis, NMA) c ... More
Presented by Mr. Miao YU
Type: Invited Talk Session: Talk
Chromosome structure is essential in many biological studies. Recent Hi-C experimental studies have been dramatically deepening our understanding of the 3D chromatin. In this talk, we describe the modelling of the chromatin structure utilizing experimental Hi-C data, which provides the spatial details of chromatin. By mapping a plethora of genome features onto the chromatin model, we quantitativel ... More
Presented by Prof. Yiqin GAO on 24 Jun 2017 at 09:15
Type: Poster
G protein-coupled receptors (GPCRs) represent a superfamily of proteins that play indispensible roles in cellular signal transduction, and thus have been extensively studied as therapeutic targets. Embedded in the biological membrane, however, GPCR oligomers are challenging to simulate at attainable computational cost using all-atom models. Toward a practical solution to this challenge, we have in ... More
Presented by Mr. Xiaochuan ZHAO
Type: Oral Presentation Session: Talk
Self-Assembly of proteins/peptides is ubiquitous in chemistry and biology. Knowledge about the dynamic process from a highly-disordered system to the well-assembled structure is critical, not only to understand the structure-function relationships of many proteins, but also to design effective strategies to modulate them. However, it is still a daunting task to model protein self-assembly in diffe ... More
Presented by Prof. Jianing LI on 24 Jun 2017 at 09:45
Type: Poster
Tumor necrosis factor (TNF) is a pluripotent inflammatory cytokine that can induce both the pro-survival nuclear factor kappa B (NF-$\kappa$B) pathway and the pro-apoptotic caspase pathway. Selectively activating only one of the two pathways remains challenging.We used TNF mutants with different receptor binding kinetics to study their effects on NF-$\kappa$B signaling dynamics and cell apoptosis. ... More
Presented by Xiaoling ZHANG
Type: Poster Session: Poster
The proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase unfoldase in the regulatory particle (RP) control the gating of substrate-translocation channel to the proteolytic chamber of the core particle (CP).  Here we report three alternative states of the ATP-gS-bou ... More
Presented by Mr. Yanan ZHU
Type: Invited Talk Session: Talk
Membrane proteins are one of important species in the cell and most of them are targets of drug discovery. The accurate and efficient mechanism studies of these membrane proteins are not only crucial for the understanding of their functions but also critical for drug design. Molecular dynamics (MD) simulation is one of the most powerful tools to do these researches. However, the classical force fi ... More
Presented by Prof. Guohui LI on 26 Jun 2017 at 08:00
Type: Oral Presentation Session: Talk
Unfolded protein, a disordered structure found before folding of newly synthesized protein or after protein denaturation, is a substrate for binding by many cellular factors such as heat-shock proteins, receptors on cell membrane, and biochemical molecules. Well known for their existence, it has been challenging to directly probe interactions between unfolded protein and its binding partners, beca ... More
Presented by Mr. Qingnan TANG on 25 Jun 2017 at 15:30
Type: Invited Talk Session: Talk
Single-molecule techniques have emerged as powerful tools in molecular biology, biochemistry and biophysics. Advances in optical traps or "tweezers", which utilize focused light to trap and manipulate microscopic objects, have made it possible to monitor protein motion on DNA with a resolution of only a few angstroms. Despite these advances, the information that can be obtained is often limited. I ... More
Presented by Prof. Yann CHEMLA on 24 Jun 2017 at 10:35
Type: Poster Session: Poster
Based on our understanding of protein structures, scientists are now able to design proteins with new structures and functions. However, the current protein design studies are focused on proteins in different aqueous solutions. Designing proteins in organic solvents is a new field of protein design, which can help expand protein design to other solvent systems and improve our understanding of prot ... More
Presented by Mr. Xiangyu SUN
Type: Poster
In recent years, covalent drug design has received much attention, as targeting covalent compounds can be applied with low dose for a long residence time by binding to a specific target. At present, the main design method of covalent ligand is to find the reactive amino acid residues in the vicinity of the binding sites with existing non-covalent ligand. With reference to the interaction pattern o ... More
Presented by Mr. Weilin ZHANG
Type: Poster Session: Poster
We investigate the potential ability to attenuate noise in adaptive systems, especially in three-node networks and four-node networks. By enumeration of 393 three-node network topologies that can achieve adaptation robustly, we found that three-node networks are not able to buffer noise while implementing a good adaptation because of the trade-off between sensitivity and noise amplification rate. ... More
Presented by Mr. WEI ZHAO
Type: Poster
Signal-mediated collective oscillation is widespread in nature, where isolated cells change from quiescence state to synchronized oscillation. This could not be captured by the conventional Kuramoto model. Sensory adaptation to the shared signal is also generic, where the cells have reduced response to sufficiently slow signals. Here, we show that sensory adaptation is a generic mechanism to achie ... More
Presented by Mr. Wang SHOUWEN
Type: Oral Presentation Session: Talk
Large-scale conformational change is frequently essential for the proper functioning of macromolecules, especially for membrane transporters and channels, which open and close in response to external signals. Unfortunately, the time scale of such slow conformational changes typically exceeds the technical limit of conventional molecular dynamics (MD) simulations, which can only observe sub-millise ... More
Presented by Dr. Haipeng GONG on 25 Jun 2017 at 11:40
Type: Poster
Single molecule fluorescence resonance energy transfer (sm-FRET) has become widely used tool to reveal dynamic processes and molecule mechanisms hidden under ensemble measurements. However, the upper limit of fluorescent species used in sm-FRET is still orders of magnitude lower than association affinity of many biological processes under physiological conditions. Here, we introduce single molecul ... More
Presented by Ms. Sijia PENG
Type: Invited Talk Session: Talk
Single-molecule magnetic resonance spectroscopy and imaging is one of the ultimate goals in magnetic resonance and will has great applications in a broad range of scientific areas, from life science to physics and chemistry. We and co-workers have successfully obtained the first single-protein spin resonance spectroscopy under ambient conditions [1], realized atomic-scale structure analysis of sin ... More
Presented by Prof. Jiangfeng DU on 25 Jun 2017 at 08:00
Type: Oral Presentation Session: Talk
Intrinsically disordered proteins (IDPs) lack ordered three-dimensional structures. How to get accurate structure ensemble of IDPs is a great challenge. Experimental data, especially the NMR results as the restraints in the molecular dynamics simulations can improve the precision of the computations. In this study, by combing with the bias-exchanged metadynamics and chemical shifts data, we studie ... More
Presented by Dr. Mojie DUAN on 25 Jun 2017 at 17:10
Type: Poster
The lifetime of protein domains and ligand-receptor complexes under force is crucial for the mechanosensing of cellular functions. However, how force affects the lifetime remains poorly understood. Currently, most of the models are derived based on a presumed shape of the energy surface, which restricts the scope of their applications to explain experimental data. Here we report a novel analytical ... More
Presented by Ms. Shiwen GUO
Type: Poster
Here, we studied the complete process of a viral T7 RNA polymerase (RNAP) translocation on DNA during transcription elongation by implementing extensive all-atom molecular dynamics (MD) simulations to construct a Markov state model (MSM). Our studies show that translocation proceeds in a Brownian motion, and the RNAP thermally transits among multiple metastable states. We observed non-synchronized ... More
Presented by Mr. Chao E
Type: Poster
Intrinsically disordered proteins (IDPs) are highly prevalent in eukaryotes. They were found to be associated with various diseases and have been proposed as promising drug targets. However, conventional structure-based drug design approaches cannot be applied directly in IDPs because of its conformational heterogeneity. In our previous work, we have successfully found several small molecules targ ... More
Presented by Mr. Hao RUAN
Type: Poster Session: Poster
G-protein-coupled receptors (GPCRs) constitute a large protein family of receptors that play a key role in transmembrane signal transduction and draw wide attention since it was discovered. Arrestins are a small family of proteins which can bind to GPCRs, block G protein interactions and redirect signaling to G-protein-independent pathways. The detailed mechanism of how arrestin interacts with GPC ... More
Presented by Dali WANG
Type: Invited Talk Session: Talk
DNA methylation on CpG sites is the most common epigenetic modification. Recently, methylation in a non-CpG context was found to occur widely on genomic DNA. Moreover, methylation of non-CpG sites is a highly controlled process, and its level may vary during cellular development. To study non-CpG methylation effects on DNA/protein interactions, we have chosen three human transcription factors (TFs ... More
Presented by Prof. Xiaodong SU on 25 Jun 2017 at 14:00
Type: Poster
The unfolding of protein from a folded state (near room temperature) in low temperature (below 273k) or high pressure (around 2000atm to 7000atm) is a commonly observed phenomenon. Previous theoretical studies on cold denaturation of protein include two dimensional Mercedes-Benz model(MB) of water and bead spring model of hydrophobic protein. In this work, we further demonstrate the mechanism of t ... More
Presented by Ms. wengjie CHEN
Type: Oral Presentation Session: Talk
There are many multi-domain allosteric proteins, where an allosteric signal at the allosteric domain modifies the activity of the function domain. Intrinsically disordered regions (linkers) play an important role in this regulation process. Here, we adopted an “entropic-chain” model to analyze the effect of linkers. Coarse-grained molecular dynamics simulation was performed on a simplified sys ... More
Presented by Mr. Maodong LI on 25 Jun 2017 at 17:30
Type: Poster
Amyloid-β fibril formation has been received considerable attention in the past decades, due to its close association with Alzheimer’s disease (AD). The inhibition of β-sheet formation has been considered as the primary therapeutic strategy for AD. In this respect, graphene oxide (GO) gained significant attention because of its high solubility and good biocompatibility. Experimental studies ha ... More
Presented by Ms. Yujie CHEN
Type: Invited Talk Session: Talk
Which are the mechanisms underlying molecular recognition involved in protein complexes? How do K+ ions efficiently, yet selectively pass through potassium channels? How can designed conformational shifts control binding affinity or selectivity? Molecular dynamics simulation results will be presented to address these questions. Ubiquitin data will be presented that suggest a conformational s ... More
Presented by Prof. Bert DE GROOT on 24 Jun 2017 at 08:45
Type: Poster
Mycolic acids (MAs) are unique long chain fatty acids that are the major component of the outer membrane of mycobacteria, including Mycobacterium tuberculosis. The properties and conformations of MAs, however, are poorly understood. Here, we parameterized coarse-grained models for two major MAs (α-MA and keto-MA) following the philosophy of the Martini force field. The parameters were optimized t ... More
Presented by Dr. Beibei WANG
Type: Poster
Microtubules (MTs), tubular structures made of tubulin dimers, play critical roles in cell structures and functions. Since MTs can assemble and disassemble repeatedly, a property termed dynamic instability, they also serve as a model system to simulate the next-generation smart, dynamic materials that can mimic MTs. A deep understanding of the self-assembly process of MTs has thus not only biologi ... More
Presented by Prof. Shengfeng CHENG
Type: Poster Session: Poster
Tremendous progress in our understanding of DNA metabolism in cells has been made through multi-disciplinary research endeavors. Emerging techniques, such as single- molecule approaches, start to reveal mechanistic details underlying DNA metabolic processes, e.g. DNA replication, transcription and DNA damage repair. In contrast to traditional techniques based on ensemble averaging, single molecule ... More
Presented by Ms. Yanzhou JIANG
Type: Poster Session: Poster
The crucial initial step of genome maintenance processes like DNA replication, repair, and recombination, is always separating the double-stranded genome into its component single-stranded DNA (ssDNA). Once the nascent ssDNA appears, single-stranded DNA binding proteins (SSBs) are always the first to bind to it and help in some important functions, such as safeguarding the ssDNA from degradation, ... More
Presented by Ms. Linyu ZUO
Type: Oral Presentation Session: Talk
The crucial initial step of genome maintenance processes like DNA replication, repair, and recombination, is always separating the double-stranded genome into its component single-stranded DNA (ssDNA). Once the nascent ssDNA appears, single-stranded DNA binding proteins (SSBs) are always the first to bind to it and help in some important functions, such as safeguarding the ssDNA from degradation, ... More
Presented by Dr. Zhi QI on 25 Jun 2017 at 09:30