Interdiction in the Early Folding of the p53 DNA-Binding Domain Leads to Its Amyloid-Like Misfolding

Abstract

In this article, we investigate two issues: (a) the initial contact formation events along the folding pathway of the DNA-binding domain of the tumor suppressor protein p53 (core p53); and (b) the intermolecular events leading to its conversion into a prion-like form upon incubation with peptide P8(250-257). In the case of (a), the calculations employ the sequential collapse model (SCM) to identify the segments involved in the initial contact formation events that nucleate the folding pathway. The model predicts that there are several possible initial non-local contacts of comparative stability. The most stable of these possible initial contacts involve the protein segments 159AMAIY163 and 251ILTII255, and it is the only native-like contact. Thus, it is predicted to constitute “Nature’s shortcut” to the native structure of the core domain of p53. In the case of issue (b), these findings are then combined with experimental evidence showing that the incubation of the core domain of p53 with peptide P8(250-257), which is equivalent to the native protein segment 250PILTIITL257, leads to an amyloid conformational transition. It is explained how the SCM predicts that P8(250-257) effectively interdicts in the formation of the most stable possible initial contact and, thereby, disrupts the subsequent normal folding. Interdiction by polymeric P8(250-257) seeds is also studied. It is then hypothesized that enhanced folding through one or several of the less stable contacts could play a role in P8(250-257)-promoted core p53 amyloid misfolding. These findings are compared to previous results obtained for the prion protein. Experiments are proposed to test the hypothesis presented regarding core p53 amyloid misfolding.

A Perspective on Interdicting in Protein Misfolding for Therapeutic Drug Design: Modulating the Formation of Nonlocal Contacts in α-Synuclein as a Strategy against Parkinson’s Disease

“…induce the aggregation of native α-synuclein. 115 Finally, experiments have also shown that a capped peptide including the segment 71 VTGVTAVAQKTV 82 tends to form β-sheet rich oligomers under prefibrillar conditions. 83 These results, combined with the lack of pathogenic aggregation of truncated α-synuclein, suggest a hypothesis concerning the relationship between nonlocal contact formation and the α-synuclein aggregation and pathogenicity mechanism.…”

“…If the hypothesis presented above is correct, a possible FITR/FIP strategy to prevent the pathogenic aggregation of α-synuclein becomes available: Design an interdicting molecule that preferentially binds to segment 70 VVTGV 74 , that through interdiction of the formation of contact 3−72, displaces the nonlocal equilibrium toward the other contacts between the NAC and the C-terminal domains. In principle, the FITR could be either of the pair of the contact-defining native segments 1 MDVFM 5 or 70 VVTGV 74 , but the observed tendency of capped peptides including segment 71 VTGVTA-VAQKTV 82 to form oligomers suggests that 70 VVTGV 74 should not be employed as the basis for the FIP. 117 Thus, the FIP can probably be developed more safely from segment 1 MDVFM 5 .…”

“…In previous work, based on the SCM results, we predicted FITRs and initial candidate folding interdiction peptides (FIPs) for several viral proteins, including the SARS COV-2 spike core domain and ribose phosphatase, Influenza A M1 and Ebola VP40 . In related work, we also investigated the misfolding of the DNA-binding domain of p53 upon binding peptide P8(250–257) . In these works, we also reviewed the manifold challenges that empirical in vivo demonstration of the interdiction concept might face. − …”

“…A very important question in this context is whether the segments predicted by the SCM could function as FIPs without chemical modification or a minimal one, for example to ensure solubility. Self-peptides have been shown experimentally to affect the folding mechanism of several globular proteins. − Moreover, incubation with self-peptide p(250–257) predicted by the SCM to be involved in the formation of the dominant early contact of p53, has been shown to seriously disrupt its folding leading to its conversion into an amyloid-like isoform . Also, incubation with self-peptide 105–124 of RNAase A, containing the SCM predicted most stable primary contact segment 116–120, and also segment 106–110 included in the second-best primary contact 106–110, suffices to almost completely shut down the folding process .…”

“… 9 In related work, we also investigated the misfolding of the DNA-binding domain of p53 upon binding peptide P8(250–257). 71 In these works, we also reviewed the manifold challenges that empirical in vivo demonstration of the interdiction concept might face. 7 − 9 …”