Prof. Huan-Xiang Zhou (Department of Chemistry and Department of Physics, University of Illinois at Chicago)
Proteins are made up of 20 types of amino acids with varying physical properties. Amino acids with ionizable and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on these amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have profound effects such as protein denaturation and switch-like response of signal transduction networks. This talk will present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, I will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins will be highlighted.
Prof. Yuko Okamoto (Nagoya University)
Prof. Charles L. Brooks III (University of Michigan, USA)
Prof. John Straub (Boston University, USA)
Dr. Karissa Sanbonmatsu (Los Alamos National Laboratory, USA)
Using an integrated approach, we combine data from X-ray crystallography, cryo-EM and biochemical data. Over the past decade, we have developed a pipeline that begins with X-ray crystallographic structures and uses molecular simulation to produce all-atom models consistent with cryo-EM reconstructions. Theses models are then used as beginning and end points for simulations of large-scale conformational changes. Our strategy has been highly successful in the case of the accommodation conformational change during tRNA selection in bacteria. Here, we predicted the universally conserved accommodation corridor, the importance of which has been verified in several independent experimental studies. We have also recently identified the hybrid corridor, responsible for tRNA hybrid state formation during translocation. Our latest addition to our pipeline is the incorporation of chemical probing data describing the mobility of the RNA backbone in solution. We have developed a novel algorithm to generate molecular dynamics simulations highly consistent with chemical probing data. We have applied these techniques to ribosomes to investigate their dynamics and conformational changes.
Dr. Yasushi Okada (RIKEN QBiC)
Prof. Akihiro Kusumi (Institute for Frontier Medical Sciences, Kyoto University)
Dr. Takeshi Sato (Institute for Protein Research, Osaka University)
Dr. Kohsuke Inomata (RIKEN Quantitative Biology Center)
In-cell NMRとは細胞内蛋白質に対する選択的な高分解能異種核多次元NMR測定のことで、蛋白質の構造・動的挙動を原子レベルで解析することが可能である。我々は、HIV-1ウイルスのTat1蛋白質由来のCell Penetrating Peptide(CPP)を利用して、高効率に安定同位体標識された蛋白質を細胞質に導入することで、ヒト等高等哺乳動物体細胞におけるin-cell NMR測定に成功した。またその過程で、pyrenebutyrateによる細胞処理、細胞質におけるCPPの切断が、目的蛋白質の細胞質・核質への均一な導入に必須であることを見出した。更に、上記手法を用いて、細胞内における蛋白質の、細胞内在性の蛋白質との相互作用と、外部投与した低分子薬剤との相互作用を検出する試みを行い、一定の成果を得た。また、細胞内での蛋白質の構造安定性を重水素/軽水素交換実験によって解析したところ、in vitroに比べて不安定であることを示唆する結果を得た。上記に示すように、in-cell NMRという手法を用いることによって、高等哺乳動物体細胞内のような複雑な環境下において、特定の蛋白質の構造・動態を原子レベルで解析することが可能となった。本発表では、これまでの成果を概観するとともに、現在進行中のプロジェクト、特に細胞内蛋白質の構造安定性解析に関する進捗と今後の展望について述べる。
Dr. Yasuhito Karino (Institute for Chemical Research, Kyoto University)
Solvation free energy is one of the most important physical quantities to elucidate the hydration effect on protein in solution phase. In this study, the solvation free energy of horse heart cytochrome c immersed in water was calculated using the molecular dynamics simulation coupled with the energy-representation method. The protein intramolecular energy and the solvation free energy are found to compensate each other in the course of equilibrium structural fluctuation, and the roles of the attractive and repulsive components in the protein-water interaction are examined for the solvation free energy.
Prof. Sandeep Patel (Department of Chemistry and Biochemistry, University of Delaware, USA)
Molecular simulations today are applied across many scientific disciplines. Complementing experiment, these tools afford a molecular-level understanding and interpretation of physico-chemical processes at spatial and temporal resolutions inaccessible to experiment. At the heart of such methods is the description of interactions between atoms and molecules, the force field. Traditionally, non-reactive force fields have treated electrostatic interactions using an additive, Coulomb model between fixed partial charges on atomic sites. Though quite successful, there has been conjecture as to the effects of incorporating non-additivity in classical force fields, particularly in biological systems. Over the last several decades, attempts to incorporate electrostatic non-additivity in the form of inducible dipole interactions or dynamically varying partial charges have provided a vast body of knowledge that has aided in the development of a new class of force fields attempting to explicitly account for non-additive effects. We will present our recent work in developing one such class of models, charge equilibration force fields, and select applications of such models to aqueous solution interfaces, ion solvation and specific ion effects, hydrophobocity, model membrane bilayers and simple integral membrane peptides such as the gramicidin A bacterial channel, and protein-ligand binding. Finally, we will discuss recent development and application of graphical processing units (GPU's) for molecular dynamics simulations.
Dr. Morten O. Jensen (D.E.Shaw Research, New York, USA)
Long molecular dynamics (MD) simulations, which recently reached the millisecond timescale for the first time, may prove a powerful tool in advancing the understanding of protein function. Here I will discuss our MD studies of the conformational changes associated with ion channel voltage gating. Our results reveal an atomic-level structural mechanism applicable to the entire Na+/K+/Ca2+ voltage-gated ion channel superfamily, reconciling much apparently conflicting experimental data.
Dr. Kiyoshi Yagi (University of Illinois at Urbana-Champaign, USA)
エネルギー・環境問題の解決は新触媒の発見が鍵である．現在，工業的に実用化されている触媒は，有機金属錯体などの均一系触媒と担体に金属等を固定した不均一系触媒とに大別される．前者は高活性・高選択性を有することが特徴で，要求の厳しい創薬や有機合成で用いられる．しかし，均一系触媒は溶液に溶かして用いられるため，回収が困難なのが欠点である．従って，多くの工業的な化学反応には，頑丈かつ回収が容易な不均一系触媒が好まれる．一方，第３の触媒として，酵素のような生体触媒がある．天然の生体触媒は工業触媒に匹敵するTOFを有し，大変有望である．しかし，人工的な修正を加えると多くの場合失活する．この原因は，反応物（基質）を巧妙に認識する機能が人口修飾の際に失われてしまうため，と考えられている．酵素と基質の関係は鍵と鍵穴によく例えられるが，高活性な触媒として機能するためには，形の一致だけでなく，反応物を捕まえ，生成物をリリースするというサイクルが効率良く働かなければならない．このような動的機構に対する基礎的な理解は未だ不十分であり，そのため設計指針が立たないのが現状である．酵素の高い分子認識能力はエネルギー移動過程と密接な関係にあるように思う．分子を認識したという信号（エネルギー）が伝わり，次のアクションの引き金を引く，という仕組みがアミノ酸配列の中に隠されているはずである．これを理論的に解き明かすことが我々の大きな目標である．我々は分子振動理論の開発に携わってきた．従来の振動理論は孤立小分子（~10原子）が対象であったが，我々はその適用範囲を拡大し，数百自由度を扱える方法論を提案した．さらに，現在，タンパク（数千自由度）を対象とした理論開発を進めている．ただし，ここでの開発方針は単純なスケールアップではない．大自由度系にありながら，特異的なエネルギーの流れを作ることは可能なのか，それはどのような因子で制御されるのか，という疑問に答えるには現実的なモデルが必要である．具体的には，振動モード間のエネルギー交換における量子効果，調和・非調和カップリングの影響について議論する．
Dr. Zenmei Ohkubo (Department of Biochemistry and Beckman Institute, University of Illinois at Urbana-Champaign, USA)
Characterizing atomic details of membrane binding of peripheral membrane proteins by molecular dynamics (MD) has been seriously hindered by the slow dynamics of membrane reorganization associated with the phenomena. Consequently, the resulting structures are largely biased by the initial configuration of the lipids and proteins in the simulation system. To expedite lateral diffusion of lipid molecules and to accelerate formation of the optimal interaction between peripheral proteins and lipid headgroups during MD simulations, we have developed a highly mobile membrane mimetic (HMMM) model. The HMMM model is composed of an organic solvent layer as the hydrophobic core sandwiched by water and with short-tailed phospholipids at the interface whose acyl tails are immersed in the organic phase. This configuration is formed spontaneously and rapidly, regardless of the initial position or orientation of the short-tailed lipids. The short-tailed lipids in the HMMM model exhibit about two orders of magnitude larger lateral diffusion than full lipids in conventional membrane models, whereas the membrane profile of the HMMM model is essentially the same as those of the full-membrane models. As a challenging test of membrane binding of a peripheral protein without any guide, the GLA domain of human coagulation factor FVII was initially placed in bulk water in the HMMM model to simulate. During the MD simulation, the GLA domain inserted itself into the membrane spontaneously and reproducibly, with interactions closely matching those obtained previously using full membranes. The HMMM model is extremely efficient in capturing the mechanism of membrane binding of a wide spectrum of peripheral proteins, as well as other membrane-associated phenomena.
Prof. Jinahan Chen (Department of Biochemistry, Kansas State University, USA)
Intrinsically disordered proteins (IDPs) are a class of newly recognized functional proteins that rely on a lack of stable structure for function. They are highly prevalent in biology, play key roles in crucial cellular functions, and are extensively involved human diseases. For signaling and regulation, IDPs frequently fold into stable structures upon recognition of specific targets. Understanding the mechanisms of these binding-folding interactions is of significant importance because they underlie the organization of important regulatory networks that control various aspects of cellular decision-making. I will discuss some of the key lessons that we have learned from our recent atomistic and coarse-grained simulations several small regulatory IDPs. In particular, I will discuss how an intriguing interplay of nascent structures, intrinsic flexibility, and charges might facilitate efficient and versatile regulation of IDP function.
