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.

细胞内的通路是有线的，即直接或间接互连；在癌症中，通路被重新连接，这是失调的结果。重连可能是许多事件的结果，包括蛋白质编码区的致癌突变、过度/表达不足、基因重复/缺失——即不同的拷贝数、改变的剪接模式、改变的翻译后修饰、基因组表观遗传学或染色质结构的改变等等。社区投入了巨大的努力来阐明接线和重新接线。尽管如此，弄清楚蜂窝网络（除了说明路径连接的蜂窝图之外）仍然是一个重大挑战。跟踪关键细胞过程的分子回路的流动预计对于选择和评估作为药物靶点的信号分子/通路以及确定研究的优先顺序非常有用。然而，细胞类型之间的差异使问题变得更加复杂。虽然所有途径都可以发生在所有细胞类型中，但基础水平和升高（或猝灭）的细胞类型有所不同。对于给定的细胞类型和状态，使用此信息标记细胞通路图至关重要。系统地进行这项工作将在癌症生物学方面取得重大进展。那么我们能否确定促进 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，并且与之相对应。这两个特性至关重要：即使 Ras 信号传导被药物阻断，独立性也赋予其发出信号的能力；对应关系意味着它们可以赋予与 MAPK 或 PI3K 信号传导相同的功能。哪些细胞通路具有这两种特性？为了识别这些途径，第一步涉及确定 MAPK 和 PI3K 途径“底部”的最终作用模式；第二步探索哪些其他细胞途径在同一途径“底部”步骤中发挥相似的作用。当打开时，这些通路将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，这些途径与 MAPK 和 PI3K 一起会加剧肿瘤增殖；当 Ras 信号传导被阻断时，它们会替代被抑制的途径。由于耐药性经常出现，因此与 Ras 同时靶向这些耐药性预计将非常有益。我们概述了可疑的途径 - 那些导致 YAP1 和 c-Myc 表达（或激活）的途径。我们提出这些途径在从 G1 到 S 期的细胞周期调节中发挥相似的作用。我们还询问这些对应和独立的信号传导途径是否都具有相同的可能性。这是一个关键问题，因为为了最大限度地减少细胞毒性，在任何给定时间只能针对一部分途径。我们建议，更有利的途径的选择应该取决于细胞类型 - 这里是干细胞与分化细胞。破译独立和相应的核心途径对于完全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。我们的目标是弄清楚细胞中关键蛋白质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、致癌突变如何改变格局以及它如何影响其信号传导。在 Ras 同工型中，我们重点关注其最丰富的同工型 KRas-4B。我们试图弄清楚膜附着如何影响其激活和信号传导；钙调蛋白通过与 K-Ras4B 相互作用促进癌症的机制、致癌突变的详细激活机制，以及将 Ras 与 Hippo 通路和 YAP1 连接起来的 RASSF5 ​​如何充当肿瘤抑制因子。信号通路塑造并传递细胞对其不断变化的环境的反应；然而，病原体可以通过操纵宿主信号传导来规避这种反应。为了破坏宿主的防御，他们用自己的方式击败了宿主：他们通过模仿宿主编码蛋白质的结合表面来劫持宿主途径。为此，没有必要实现全局蛋白质同源性；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允许致病蛋白与宿主靶蛋白竞争。因此，宿主蛋白中心不是结合宿主编码的配偶体，而是结合致病性替代物。结果可能是可怕的：重新布线或重新调整宿主途径，改变细胞信号传导格局，从而改变免疫反应。它们还可以通过调节关键信号通路（例如涉及 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，我们关注分子拟态在病原体宿主逃避中的作用以及进化过程中出现的分子拟态机制的类型。肿瘤坏死因子受体 (TNFR) 相关因子 3 (TRAF3) 是先天性和适应性免疫信号通路的关键节​​点。 TRAF3 负向调节经典和非经典 NF-kappaB 通路的激活，是抗病毒免疫的关键蛋白之一。在这里，我们从竞争性结合和对细胞网络的影响方面提供了 TRAF3 信号传导的结构概述。为了完整起见，我们还包括一些病毒蛋白对 TRAF3 生理伙伴的分子模拟。通过与宿主合作伙伴竞争，它们的目的是破坏 TRAF3 的抗病毒作用。从机制上讲，生物体自身蛋白质和同位点适应性病原体拟态的动态、竞争性结合遵循相同的构象选择原则。我们的前提是，无论引发事件 - 生理或获得的致病性状 - 途径激活（或抑制）都可能包含类似的构象原理。然而，尽管在这里我们主要关注共享位点的竞争性结合，但与生理信号传导类似，其他病原体颠覆机制也可能发挥作用。总而言之，我们从结构角度全面审视信号传导，旨在癌症、炎症和病原体干预。我们还绘制了病原体蛋白对宿主途径的干预图谱，劫持了其信号传导。我们重点关注幽门螺杆菌和致癌病毒。此外，我们一直在寻找途径。我们问受体酪氨酸激酶 (RTK) 和 JAK-STAT 驱动的增殖途径是平行的还是冗余的？ K-Ras4B 与 N-Ras 的对比又如何呢？ “平行”增殖途径实现了类似的耐药结果。那么，它们是“多余的”吗？我们认为并行和冗余之间存在根本区别。细胞增殖途径受到基因组序列、3D 组织和染色质可及性的影响，并由癌症出现之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质家族，那么它们就是多余的；如果进化无关，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 亚型的那些是多余的。我们的精准医学呼吁绘制癌症增殖途径非常重要，因为它可以加快有效的治疗。