<link>https://pages.htgaa.org/2026a/beyza-cennet-batir/projects/individual-final-project/beyza_cennet_batir_paleo_proteins/index.html</link><description>PALEO-PROTEINS Synthetic Cryoprotectants for Therapeutic Hypothermia and Tissue Preservation Author: Beyza Cennet Batır Node: Designer Cells Lab Course: How to Grow (Almost) Anything 2026 Date: 07-04-2026 SECTION 1: ABSTRACT Therapeutic hypothermia — the deliberate cooling of patients to 28–33°C — is a standard of care in complex cardiac, neurological, and organ transplant surgeries, yet it carries an inherent paradox: the very temperatures used to protect tissues also trigger ice crystallization, membrane disruption, oxidative stress, and proteotoxic damage at the cellular level. Existing cryoprotectants such as DMSO, glycerol, and trehalose are either cytotoxic at effective concentrations or structurally inappropriate for intravascular human use. This project proposes a computational-to-bench pipeline for the design, expression, and functional screening of Paleo-Proteins — a suite of synthetic cryoprotective peptides inspired by LEA (Late Embryogenesis Abundant) proteins and dehydrins recovered from 30,000-year-old Siberian permafrost plant specimens (Silene spp.). Using RFdiffusion and ESM-IF for de novo scaffold generation followed by ESMFold structural validation and IUPred3 disorder analysis, we identify the top 5–10 synthetic candidates and express them in E. coli BL21(DE3) under a T7 promoter system with N-terminal His₆-tag purification via Ni-NTA affinity chromatography. Candidates are subjected to a high-throughput automated MTT viability assay in HEK293T and SH-SY5Y cells exposed to progressive hypothermic temperature gradients (37°C → 33°C → 28°C → 4°C → −20°C), using the Opentrons OT-2 for cell dispensing and reagent automation, and the PHERAstar FSX (Ginkgo Bioworks) for absorbance readout. Success is defined as a ≥30% viability improvement over untreated hypothermic controls at an EC₅₀ ≤ 10 μM. DNA constructs are ordered as whole plasmids from Twist Bioscience. This project connects ancient molecular solutions to a pressing modern clinical challenge, advancing the frontier of AI-assisted protein design for biomedical cryoprotection.</description><generator>Hugo</generator><language>en</language><atom:link href="https://pages.htgaa.org/2026a/beyza-cennet-batir/projects/individual-final-project/beyza_cennet_batir_paleo_proteins/index.xml" rel="self" type="application/rss+xml"/></channel></rss>