Biomolecular Recognition and Binding Mechanisms

生物分子识别和结合机制

• 批准号: 10262088
• 负责人: Ruth Nussinov
• 金额: $ 47.34万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10262088
• 关键词: 3-Dimensional; Adenocarcinoma; Affect; Affinity; Antiviral Agents; Apoptosis; Architecture; Atlas of Cancer Mortality in the United States; Binding; Binding Sites; Biological; Calcium; Calmodulin; Cancer Biology; Cell Cycle Regulation; Cell Differentiation process; Cell Proliferation; Cell physiology; Cells; Chromatin; Chromatin Structure; Code; Colorectal Cancer; Communities; Competitive Binding; Development; Drug Targeting; Drug resistance; Environment; Epigenetic Process; Event; Evolution; Gene Duplication; Genome; Goals; Growth; Guanosine Triphosphate; Helicobacter pylori; Host Defense; Hydrolysis; Immune response; Immune signaling; Incidence; Inflammation; Intervention; KRAS2 gene; Lead; Link; MAP Kinase Gene; MEKs; Malignant Neoplasms; Malignant neoplasm of lung; Membrane; Mission; Molecular; Molecular Conformation; Molecular Mimicry; Mutation; NF-kappa B; Oncogenes; Oncogenic; Oncogenic Viruses; Open Reading Frames; Organism; Outcome; Pancreatic Ductal Adenocarcinoma; Pathogenicity; Pathway Analysis; Pathway interactions; Pattern; Pharmaceutical Preparations; Pharmacology; Physiological; Play; Population; Post-Translational Modification Alteration; Property; Protein Family; Protein Isoforms; Proteins; RALGDS gene; RNA Splicing; Ras Signaling Pathway; Ras/Raf; Reaction; Receptor Protein-Tyrosine Kinases; Regimen; Regulation; Research; Role; S Phase; Second Messenger Systems; Shapes; Signal Pathway; Signal Transduction; Signaling Molecule; Site; Structure; Surface; Therapeutic; Time; Tissues; Toxic effect; Treatment Efficacy; Tumor Necrosis Factor Receptor; Tumor Suppressor Proteins; Ursidae Family; Variant; Viral Proteins; Work; anticancer research; antiviral immunity; base; c-myc Genes; cancer cell; cancer initiation; cell growth; cell type; chronic infection; drug discovery; insight; interest; mimicry; nanomolar; pathogen; precision medicine; prophylactic; protein folding; ras Proteins; response; senescence; stem cells; trait; tumor

In the cell pathways are wired, i.e. interconnected directly or indirectly; in cancer, the pathways are rewired, the consequence of dysregulation. Rewiring can be the outcome of a number of events, including oncogenic mutations in protein coding regions, over/under expression, gene duplication/deletion - i.e. different copy number, altered splicing patterns, altered post-translational modifications, alterations in genome epigenetics or chromatin structures, and more. Enormous effort is invested by the community to elucidate the wiring and this rewiring. Despite this, figuring out the cellular network - beyond cellular diagrams illustrating pathways' connectivity - is still a significant challenge. Tracking the flow of the molecular circuitry of key cellular processes is expected to be immensely useful for selecting and evaluating signaling molecules/pathways as drug targets and for prioritizing research. However, the problem is compounded by the variability across cell types. While all pathways can be expected to take place in all cells types, which are at the basal level and which are elevated - or quenched - vary. Flagging the cellular pathway chart with this information for given cell type and state is essential. Doing this systematically will establish a major advance in cancer biology. Can we then identify pathways that can promote Ras oncogenicity and encode drug resistance? From the standpoint of the cancer cell, these pathways need to be independent - and corresponding - to the major Ras signaling pathways, MAPK and PI3K. These two properties are of cardinal importance: independence confers the ability to signal even when Ras signaling is blocked by drugs; correspondence implies that they can bestow the same functions as the MAPK or PI3K signaling do. Which cellular pathways are endowed with both properties? To identify those pathways, the first step involves determining the ultimate modes of action at the 'bottom' of the MAPK and PI3K pathways; the second step explores which other cellular pathways accomplish similar roles at the same pathway 'bottom' steps. When turned on, these pathways would act to promote cell proliferation independently and correspondingly to MAPK/PI3K. This means that in oncogenic cells these pathways - together with MAPK and PI3K - would aggravate tumor proliferation; and when Ras signaling is blocked they would substitute for the inhibited pathway. Since drug resistance often emerges, targeting these coincidentally with Ras is expected to be highly beneficial. We outlined suspect pathways - those leading to the expression (or activation) of YAP1 and c-Myc. We proposed that these pathways fulfill similar roles in cell cycle regulation from the G1 to the S phase. We also ask whether these - corresponding and independent - signaling pathways are all equally likely. This is a critical question since to minimize cell toxicity only a subset of pathways can be targeted at any given time. We suggest that the selection of the more favored pathway(s) should be cell type-dependent - here stem cell versus differentiated cell. Deciphering Independent and corresponding core pathways is crucial for complete understanding and successful pharmacology. Over the last couple of years we have been increasingly interested in the oncogenic state. We aim to figure out the mechanisms of key proteins and their signaling networks in the cell. Among these, we have particularly focused on the Ras protein, its activation mechanism, how oncogenic mutations can shift the landscape and how it affects its signaling. Among the Ras isoforms, we focus on its most abundant isoform, KRas-4B. We seek to figure out how the membrane attachment affects its activation and signaling; the mechanism through which calmodulin acts to promote cancer through its interaction with K-Ras4B, the detailed activation mechanisms of the oncogenic mutations, and how RASSF5, which links Ras with the Hippo pathway and YAP1 acts as a tumor suppressor. Signaling pathways shape and transmit the cell's reaction to its changing environment; however, pathogens can circumvent this response by manipulating host signaling. To subvert host defense, they beat it at its own game: they hijack host pathways by mimicking the binding surfaces of host-encoded proteins. For this, it is not necessary to achieve global protein homology; imitating merely the interaction surface is sufficient. Different protein folds often interact via similar protein-protein interface architectures. This similarity in binding surfaces permits the pathogenic protein to compete with a host target protein. Thus, rather than binding a host-encoded partner, the host protein hub binds the pathogenic surrogate. The outcome can be dire: rewiring or repurposing the host pathways, shifting the cell signaling landscape and consequently the immune response. They can also cause persistent infections as well as cancer by modulating key signaling pathways, such as those involving Ras. Mapping the rewired host-pathogen 'superorganism' interaction network - along with its structural details - is critical for in-depth understanding of pathogenic mechanisms and developing efficient therapeutics. Currently, we focus on the role of molecular mimicry in pathogen host evasion as well as types of molecular mimicry mechanisms that emerged during evolution. The tumor necrosis factor receptor (TNFR) associated factor3 (TRAF3) is a key node in innate and adaptive immune signaling pathways. TRAF3 negatively regulates the activation of the canonical and non-canonical NF-kappaB pathways and is one of the key proteins in antiviral immunity. Here we provide a structural overview of TRAF3 signaling in terms of its competitive binding and consequences to the cellular network. For completion, we also include molecular mimicry of TRAF3 physiological partners by some viral proteins. By out-competing host partners, these aim to subvert TRAF3 antiviral action. Mechanistically, dynamic, competitive binding by the organism's own proteins and same-site adaptive pathogen mimicry follow the same conformational selection principles. Our premise is that irrespective of the eliciting event - physiological or acquired pathogenic trait - pathway activation (or suppression) may embrace similar conformational principles. However, even though here we largely focus on competitive binding at a shared site, similar to physiological signaling other pathogen subversion mechanisms can also be at play. Altogether, we take a comprehensive look at signaling from the structural standpoint aiming in cancer, inflammation and pathogen intervention. We have also taken up mapping of pathogen protein intervention in host pathways, hijacking its signaling. We have focused on Helicobacter pylori and oncogenic viruses. Additionally, we have been looking at pathways. We asked are the receptor tyrosine kinase (RTK) and JAK-STAT-driven proliferation pathways parallel or redundant? And what about those of K-Ras4B versus N-Ras? 'Parallel' proliferation pathways accomplish a similar drug resistance outcome. Thus, are they 'redundant'? We argued that there is a fundamental distinction between parallel and redundant. Cellular proliferation pathways are influenced by the genome sequence, 3D organization and chromatin accessibility, and determined by protein availability prior to cancer emergence. We suggested that if they operate the same downstream protein families, they are redundant; if evolutionary-independent, they are parallel. Thus, RTK and JAK-STAT-driven proliferation pathways are parallel; those of Ras isoforms are redundant. Our Precision Medicine Call to map cancer proliferation pathways is vastly important since it can expedite effective therapeutics.

在细胞中，通路是连接的，即直接或间接地相互连接；在癌症中，通路被重新连接，这是失调的结果。重接线可能是许多事件的结果，包括蛋白质编码区致癌突变、过度/不足表达、基因复制/缺失（即拷贝数不同、剪接模式改变、翻译后修饰改变、基因组表观遗传学或染色质结构改变等）。社区投入了巨大的努力来阐明布线和这种重新布线。尽管如此，弄清楚蜂窝网络——超越说明通路连接的蜂窝图——仍然是一个重大挑战。跟踪关键细胞过程的分子电路的流动预计将对选择和评估作为药物靶点的信号分子/途径以及优先研究非常有用。然而，这个问题由于细胞类型的可变性而变得更加复杂。虽然所有的途径都可以在所有的细胞类型中发生，但在基础水平和升高或熄灭的细胞类型各不相同。用这些信息标记给定细胞类型和状态的细胞通路图是必要的。系统地进行这一研究将使癌症生物学取得重大进展。那么，我们能否确定可以促进Ras致癌性和编码耐药性的途径？从癌细胞的角度来看，这些通路需要独立于主要的Ras信号通路MAPK和PI3K，并与之相对应。这两个特性至关重要：独立性赋予Ras信号被药物阻断时也能发出信号的能力；对应意味着它们可以赋予与MAPK或PI3K信号相同的功能。哪些细胞通路同时具有这两种特性？为了识别这些通路，第一步包括确定MAPK和PI3K通路“底部”的最终作用模式；第二步探索哪些其他细胞通路在相同的通路“底部”步骤中完成类似的作用。当这些通路开启时，它们会独立地促进细胞增殖，并与MAPK/PI3K相对应。这意味着在致癌细胞中，这些通路与MAPK和PI3K一起会加剧肿瘤的增殖；当Ras信号被阻断时，它们会替代被抑制的途径。由于耐药性经常出现，靶向与Ras巧合的这些位点预计是非常有益的。我们概述了导致YAP1和c-Myc表达（或激活）的可疑途径。我们认为这些通路在细胞周期从G1期到S期的调控中发挥着相似的作用。我们也会问这些相应的和独立的信号通路是否都是同样可能的。这是一个关键的问题，因为在任何给定的时间，只有一个子集的途径可以靶向最小化细胞毒性。我们建议选择更有利的途径应该是细胞类型依赖的-这里是干细胞与分化细胞。破译独立的和相应的核心通路对于完整的理解和成功的药理学至关重要。在过去的几年里我们对致癌状态越来越感兴趣。我们的目标是找出细胞中关键蛋白及其信号网络的机制。其中，我们特别关注Ras蛋白，其激活机制，致癌突变如何改变景观以及它如何影响其信号传导。在Ras异构体中，我们重点研究了其最丰富的异构体KRas-4B。我们试图弄清楚膜附着如何影响其激活和信号传导；钙调素通过与K-Ras4B相互作用促进癌症的机制，致癌突变的详细激活机制，以及连接Ras与Hippo通路和YAP1的RASSF5如何作为肿瘤抑制因子。信号通路塑造并传递细胞对环境变化的反应；然而，病原体可以通过操纵宿主信号来规避这种反应。为了破坏宿主的防御，它们用自己的游戏打败了宿主：它们通过模仿宿主编码蛋白质的结合表面来劫持宿主的途径。为此，不需要实现全局蛋白同源性；仅仅模仿交互表面就足够了。不同的蛋白质折叠通常通过相似的蛋白质-蛋白质界面结构相互作用。这种结合表面的相似性使致病蛋白能够与宿主靶蛋白竞争。因此，宿主蛋白中心不是与宿主编码的伴侣结合，而是与致病替代物结合。结果可能是可怕的：重新布线或重新利用宿主途径，改变细胞信号景观，从而改变免疫反应。它们还可以通过调节关键的信号通路，如涉及Ras的信号通路，引起持续感染和癌症。绘制重新连接的宿主-病原体“超级有机体”相互作用网络及其结构细节，对于深入了解致病机制和开发有效的治疗方法至关重要。目前，我们主要关注分子模仿在病原体宿主逃避中的作用以及在进化过程中出现的分子模仿机制的类型。肿瘤坏死因子受体（TNFR）相关因子3 （TRAF3）是先天和适应性免疫信号通路的关键节点。TRAF3负调控规范和非规范NF-kappaB通路的激活，是抗病毒免疫的关键蛋白之一。在这里，我们就其竞争性结合和对细胞网络的影响提供了TRAF3信号的结构概述。为了完善，我们还包括一些病毒蛋白对TRAF3生理伴侣的分子模仿。通过与宿主伙伴竞争，它们旨在破坏TRAF3抗病毒作用。从机制上讲，生物体自身蛋白质的动态竞争性结合和同位点适应性病原体模仿遵循相同的构象选择原则。我们的前提是，不管诱发事件是生理的还是获得性的致病特性，途径激活（或抑制）可能包含类似的构象原则。然而，尽管我们主要关注的是共享位点上的竞争性结合，但与生理信号类似，其他病原体颠覆机制也可能起作用。总之，我们从结构的角度全面研究信号在癌症、炎症和病原体干预中的作用。我们还研究了病原体蛋白在宿主通路中的干预，劫持其信号传导。我们关注的是幽门螺杆菌和致癌病毒。此外，我们一直在研究途径。我们的问题是受体酪氨酸激酶（RTK）和jak - stat驱动的增殖途径是平行的还是冗余的？那K-Ras4B和N-Ras呢？“平行”增殖途径实现了类似的耐药结果。因此，它们是“多余的”吗？我们认为平行和冗余之间有根本的区别。细胞增殖途径受基因组序列、三维组织和染色质可及性的影响，并由癌症出现前的蛋白质可用性决定。我们认为，如果它们操作相同的下游蛋白家族，它们是冗余的；如果它们是进化独立的，那么它们是平行的。因此，RTK和jak - stat驱动的增殖途径是平行的；Ras同工异构体是多余的。我们的精确医学呼吁绘制癌症增殖途径是非常重要的，因为它可以加快有效的治疗。