[{"data":1,"prerenderedAt":1739},["ShallowReactive",2],{"mdc--ko6m75-key":3},{"data":4,"body":5},{},{"type":6,"children":7},"root",[8,17,24,99,103,109,122,157,160,166,183,188,259,264,300,303,309,350,353,359,410,422,427,435,438,444,470,475,507,510,516,521,556,561,595,598,604,609,631,634,640,645,663,666,672,677,706,724,732,737,765,770,788,791,797,802,816,821,842,847,883,886,892,904,940,945,996,999,1005,1010,1019,1037,1046,1064,1069,1077,1080,1086,1143,1148,1174,1177,1183,1188,1226,1231,1239,1242,1248,1258,1289,1294,1321,1331,1344,1347,1353,1358,1385,1390,1398,1403,1429,1447,1450,1456,1461,1479,1484,1530,1535,1538,1544,1594,1597,1603,1608,1631,1634,1640,1645,1658,1669,1687,1690,1696],{"type":9,"tag":10,"props":11,"children":13},"element","h2",{"id":12},"molecular-forces-and-protein-folding-fun-detailed-walkthrough-skipping-the-boxed-special-topic-sections",[14],{"type":15,"value":16},"text","Molecular Forces and Protein Folding — fun, detailed walkthrough (skipping the boxed “Special topic” sections)",{"type":9,"tag":18,"props":19,"children":21},"h3",{"id":20},"_1-big-picture-what-proteins-are-and-why-folding-matters",[22],{"type":15,"value":23},"1) Big picture: what proteins are and why folding matters 🧬",{"type":9,"tag":25,"props":26,"children":27},"ul",{},[28,61,73],{"type":9,"tag":29,"props":30,"children":31},"li",{},[32,38,40,45,47,52,54,59],{"type":9,"tag":33,"props":34,"children":35},"strong",{},[36],{"type":15,"value":37},"Proteins",{"type":15,"value":39}," are unbranched polymers of ",{"type":9,"tag":33,"props":41,"children":42},{},[43],{"type":15,"value":44},"L-amino acids",{"type":15,"value":46}," whose sequence is encoded by genes. Each amino acid contributes a repeating ",{"type":9,"tag":33,"props":48,"children":49},{},[50],{"type":15,"value":51},"backbone",{"type":15,"value":53}," (–NH–CαH–CO–) plus a ",{"type":9,"tag":33,"props":55,"children":56},{},[57],{"type":15,"value":58},"side chain",{"type":15,"value":60}," (size/shape/charge varies).",{"type":9,"tag":29,"props":62,"children":63},{},[64,66,71],{"type":15,"value":65},"Despite being “just a chain,” proteins often adopt a ",{"type":9,"tag":33,"props":67,"children":68},{},[69],{"type":15,"value":70},"unique, stable 3D structure",{"type":15,"value":72}," because internal interactions (within the chain, plus with water) strongly bias certain conformations.",{"type":9,"tag":29,"props":74,"children":75},{},[76,78,83,85,90,92,97],{"type":15,"value":77},"Many proteins contain ",{"type":9,"tag":33,"props":79,"children":80},{},[81],{"type":15,"value":82},"secondary structure",{"type":15,"value":84}," (α-helices, β-sheets). Some proteins ",{"type":9,"tag":33,"props":86,"children":87},{},[88],{"type":15,"value":89},"do not have a single stable fold",{"type":15,"value":91},", ranging from equilibria between conformations to fully ",{"type":9,"tag":33,"props":93,"children":94},{},[95],{"type":15,"value":96},"unstructured",{"type":15,"value":98}," states.",{"type":9,"tag":100,"props":101,"children":102},"hr",{},[],{"type":9,"tag":18,"props":104,"children":106},{"id":105},"_2-covalent-modifications-permanent-ish-structural-changes",[107],{"type":15,"value":108},"2) Covalent modifications: permanent-ish structural changes 🔗",{"type":9,"tag":110,"props":111,"children":112},"p",{},[113,115,120],{"type":15,"value":114},"Beyond the normal amino acids + peptide bonds, proteins often include extra ",{"type":9,"tag":33,"props":116,"children":117},{},[118],{"type":15,"value":119},"covalent features",{"type":15,"value":121},":",{"type":9,"tag":25,"props":123,"children":124},{},[125,135,145],{"type":9,"tag":29,"props":126,"children":127},{},[128,133],{"type":9,"tag":33,"props":129,"children":130},{},[131],{"type":15,"value":132},"Disulfide bonds (Cys–Cys)",{"type":15,"value":134},": common within a chain or connecting chains (insulin, immunoglobulins). They can strongly constrain folding and stability.",{"type":9,"tag":29,"props":136,"children":137},{},[138,143],{"type":9,"tag":33,"props":139,"children":140},{},[141],{"type":15,"value":142},"Phosphorylation",{"type":15,"value":144}," (Ser/Thr/Tyr): reversible covalent addition that changes electronic structure and supports signaling cascades.",{"type":9,"tag":29,"props":146,"children":147},{},[148,150,155],{"type":15,"value":149},"There are ",{"type":9,"tag":33,"props":151,"children":152},{},[153],{"type":15,"value":154},"hundreds",{"type":15,"value":156}," of known covalent modifications; each can create new functional properties.",{"type":9,"tag":100,"props":158,"children":159},{},[],{"type":9,"tag":18,"props":161,"children":163},{"id":162},"_3-electrostatic-forces-charges-dipoles-and-screening",[164],{"type":15,"value":165},"3) Electrostatic forces: charges, dipoles, and “screening” ⚡",{"type":9,"tag":110,"props":167,"children":168},{},[169,174,176,181],{"type":9,"tag":33,"props":170,"children":171},{},[172],{"type":15,"value":173},"Core rule:",{"type":15,"value":175}," electrostatic interaction energy depends on charges, distance, and the ",{"type":9,"tag":33,"props":177,"children":178},{},[179],{"type":15,"value":180},"dielectric constant",{"type":15,"value":182}," of the medium (water screens strongly).",{"type":9,"tag":110,"props":184,"children":185},{},[186],{"type":15,"value":187},"Key ideas:",{"type":9,"tag":25,"props":189,"children":190},{},[191,201,242],{"type":9,"tag":29,"props":192,"children":193},{},[194,199],{"type":9,"tag":33,"props":195,"children":196},{},[197],{"type":15,"value":198},"Ion–ion",{"type":15,"value":200}," interactions are long-range compared to other noncovalent forces.",{"type":9,"tag":29,"props":202,"children":203},{},[204,206],{"type":15,"value":205},"Even without net charge, molecules can interact via:",{"type":9,"tag":25,"props":207,"children":208},{},[209,217,225],{"type":9,"tag":29,"props":210,"children":211},{},[212],{"type":9,"tag":33,"props":213,"children":214},{},[215],{"type":15,"value":216},"Ion–dipole",{"type":9,"tag":29,"props":218,"children":219},{},[220],{"type":9,"tag":33,"props":221,"children":222},{},[223],{"type":15,"value":224},"Dipole–dipole",{"type":9,"tag":29,"props":226,"children":227},{},[228,233,235,240],{"type":9,"tag":33,"props":229,"children":230},{},[231],{"type":15,"value":232},"Induced dipole / dispersion",{"type":15,"value":234}," interactions (requires ",{"type":9,"tag":33,"props":236,"children":237},{},[238],{"type":15,"value":239},"polarizability",{"type":15,"value":241},")",{"type":9,"tag":29,"props":243,"children":244},{},[245,250,252,257],{"type":9,"tag":33,"props":246,"children":247},{},[248],{"type":15,"value":249},"Water’s dielectric constant (~80)",{"type":15,"value":251}," strongly reduces charge–charge interactions compared to vacuum, but ",{"type":9,"tag":33,"props":253,"children":254},{},[255],{"type":15,"value":256},"fixed ion pairs",{"type":15,"value":258}," (e.g., Lys–Asp) can still stabilize proteins—even on the surface.",{"type":9,"tag":110,"props":260,"children":261},{},[262],{"type":15,"value":263},"How electrostatics can unfold proteins:",{"type":9,"tag":25,"props":265,"children":266},{},[267,277],{"type":9,"tag":29,"props":268,"children":269},{},[270,275],{"type":9,"tag":33,"props":271,"children":272},{},[273],{"type":15,"value":274},"Low ionic strength",{"type":15,"value":276}," → less shielding by counter-ions → charge interactions become stronger → repulsion can destabilize folding and promote denaturation/aggregation.",{"type":9,"tag":29,"props":278,"children":279},{},[280,285,287],{"type":9,"tag":33,"props":281,"children":282},{},[283],{"type":15,"value":284},"Extreme pH",{"type":15,"value":286}," changes protonation states:",{"type":9,"tag":25,"props":288,"children":289},{},[290,295],{"type":9,"tag":29,"props":291,"children":292},{},[293],{"type":15,"value":294},"Low pH protonates carboxylates → breaks salt bridges and can increase net positive charge → repulsion → unfolding.",{"type":9,"tag":29,"props":296,"children":297},{},[298],{"type":15,"value":299},"High pH deprotonates amino groups → net negative charge rises → repulsion → unfolding.",{"type":9,"tag":100,"props":301,"children":302},{},[],{"type":9,"tag":18,"props":304,"children":306},{"id":305},"_4-van-der-waals-interactions-weak-but-everywhere",[307],{"type":15,"value":308},"4) Van der Waals interactions: “weak but everywhere” 🤝",{"type":9,"tag":25,"props":310,"children":311},{},[312,331],{"type":9,"tag":29,"props":313,"children":314},{},[315,317,322,324,329],{"type":15,"value":316},"These are collected non-ionic electrostatic interactions often described by a ",{"type":9,"tag":33,"props":318,"children":319},{},[320],{"type":15,"value":321},"Lennard–Jones potential",{"type":15,"value":323},": attractive at moderate distances, ",{"type":9,"tag":33,"props":325,"children":326},{},[327],{"type":15,"value":328},"strongly repulsive",{"type":15,"value":330}," when atoms get too close (orbital overlap).",{"type":9,"tag":29,"props":332,"children":333},{},[334,336,341,343,348],{"type":15,"value":335},"Important point: vdW forces are ",{"type":9,"tag":33,"props":337,"children":338},{},[339],{"type":15,"value":340},"short-range",{"type":15,"value":342}," but become powerful in a ",{"type":9,"tag":33,"props":344,"children":345},{},[346],{"type":15,"value":347},"well-packed protein core",{"type":15,"value":349}," because there are so many contacts.",{"type":9,"tag":100,"props":351,"children":352},{},[],{"type":9,"tag":18,"props":354,"children":356},{"id":355},"_5-hydrogen-bonding-directional-glue-but-context-matters",[357],{"type":15,"value":358},"5) Hydrogen bonding: directional glue (but context matters) 🧷",{"type":9,"tag":25,"props":360,"children":361},{},[362,374,384],{"type":9,"tag":29,"props":363,"children":364},{},[365,367,372],{"type":15,"value":366},"A ",{"type":9,"tag":33,"props":368,"children":369},{},[370],{"type":15,"value":371},"hydrogen bond",{"type":15,"value":373}," forms when an electronegative atom approaches a hydrogen that’s already covalently bound to an electronegative atom. It’s shorter than a simple electrostatic interaction.",{"type":9,"tag":29,"props":375,"children":376},{},[377,382],{"type":9,"tag":33,"props":378,"children":379},{},[380],{"type":15,"value":381},"Peptide bonds have strong dipoles",{"type":15,"value":383}," (O partially negative, N partially positive), supporting hydrogen bonding patterns and secondary structure.",{"type":9,"tag":29,"props":385,"children":386},{},[387,389],{"type":15,"value":388},"Two key experimental facts:",{"type":9,"tag":390,"props":391,"children":392},"ol",{},[393,398],{"type":9,"tag":29,"props":394,"children":395},{},[396],{"type":15,"value":397},"Hydrogen bonds are abundant in native proteins (networks; most peptide bonds are hydrogen bonded).",{"type":9,"tag":29,"props":399,"children":400},{},[401,403,408],{"type":15,"value":402},"Breaking internal H-bonds ",{"type":9,"tag":33,"props":404,"children":405},{},[406],{"type":15,"value":407},"without water",{"type":15,"value":409}," is very unfavorable (large stability in dry environments like seeds/spores).",{"type":9,"tag":110,"props":411,"children":412},{},[413,415,420],{"type":15,"value":414},"Important nuance: In water, the “benefit” of an internal H-bond competes with ",{"type":9,"tag":33,"props":416,"children":417},{},[418],{"type":15,"value":419},"H-bonding to water",{"type":15,"value":421},", so isolating its net contribution is difficult.",{"type":9,"tag":110,"props":423,"children":424},{},[425],{"type":15,"value":426},"Water as a “denaturant-ish” solvent:",{"type":9,"tag":25,"props":428,"children":429},{},[430],{"type":9,"tag":29,"props":431,"children":432},{},[433],{"type":15,"value":434},"Water is unusual: open hydrogen-bonded structure and easily perturbed by solutes (Hofmeister effects are mentioned as relevant elsewhere in the course).",{"type":9,"tag":100,"props":436,"children":437},{},[],{"type":9,"tag":18,"props":439,"children":441},{"id":440},"_6-the-hydrophobic-effect-foldings-main-driver-️",[442],{"type":15,"value":443},"6) The hydrophobic effect: folding’s main driver 🌊➡️🫧",{"type":9,"tag":25,"props":445,"children":446},{},[447,459],{"type":9,"tag":29,"props":448,"children":449},{},[450,452,457],{"type":15,"value":451},"Nonpolar groups (hydrocarbon side chains) interact poorly with water, so they tend to be ",{"type":9,"tag":33,"props":453,"children":454},{},[455],{"type":15,"value":456},"buried",{"type":15,"value":458}," in the protein interior—like oil separating from water.",{"type":9,"tag":29,"props":460,"children":461},{},[462,463,468],{"type":15,"value":366},{"type":9,"tag":33,"props":464,"children":465},{},[466],{"type":15,"value":467},"hydrophobicity scale",{"type":15,"value":469}," ranks residues by their tendency to prefer nonpolar environments (e.g., Trp/Ile/Phe/Leu high; Lys/Arg very low).",{"type":9,"tag":110,"props":471,"children":472},{},[473],{"type":15,"value":474},"Origin (in this chapter’s framing):",{"type":9,"tag":25,"props":476,"children":477},{},[478,483,502],{"type":9,"tag":29,"props":479,"children":480},{},[481],{"type":15,"value":482},"Water forms dynamic H-bond networks that are favorable while remaining disordered.",{"type":9,"tag":29,"props":484,"children":485},{},[486,488,493,495,500],{"type":15,"value":487},"Near hydrophobic surfaces, water molecules become more ",{"type":9,"tag":33,"props":489,"children":490},{},[491],{"type":15,"value":492},"ordered",{"type":15,"value":494}," to maintain H-bonds, which is ",{"type":9,"tag":33,"props":496,"children":497},{},[498],{"type":15,"value":499},"entropically unfavorable",{"type":15,"value":501},".",{"type":9,"tag":29,"props":503,"children":504},{},[505],{"type":15,"value":506},"Folding reduces exposed hydrophobic area → fewer ordered water molecules → entropy increases → favorable free energy change.",{"type":9,"tag":100,"props":508,"children":509},{},[],{"type":9,"tag":18,"props":511,"children":513},{"id":512},"_7-thermodynamics-of-nonpolar-interactions-δg-δh-δs-in-water",[514],{"type":15,"value":515},"7) Thermodynamics of nonpolar interactions: ΔG, ΔH, ΔS in water 📉",{"type":9,"tag":110,"props":517,"children":518},{},[519],{"type":15,"value":520},"When putting a hydrophobe into water:",{"type":9,"tag":25,"props":522,"children":523},{},[524,534,544],{"type":9,"tag":29,"props":525,"children":526},{},[527,532],{"type":9,"tag":33,"props":528,"children":529},{},[530],{"type":15,"value":531},"Entropy decreases",{"type":15,"value":533}," (water ordering) → unfavorable",{"type":9,"tag":29,"props":535,"children":536},{},[537,542],{"type":9,"tag":33,"props":538,"children":539},{},[540],{"type":15,"value":541},"Enthalpy decreases",{"type":15,"value":543}," somewhat (favorable water–solute interactions) → partially compensatory",{"type":9,"tag":29,"props":545,"children":546},{},[547,549,554],{"type":15,"value":548},"Net ",{"type":9,"tag":33,"props":550,"children":551},{},[552],{"type":15,"value":553},"ΔG > 0",{"type":15,"value":555},", so solubility is low (though not zero).",{"type":9,"tag":110,"props":557,"children":558},{},[559],{"type":15,"value":560},"When two hydrophobes associate:",{"type":9,"tag":25,"props":562,"children":563},{},[564,574,584],{"type":9,"tag":29,"props":565,"children":566},{},[567,569],{"type":15,"value":568},"Exposed hydrophobic surface area decreases → fewer ordered waters → ",{"type":9,"tag":33,"props":570,"children":571},{},[572],{"type":15,"value":573},"ΔS increases",{"type":9,"tag":29,"props":575,"children":576},{},[577,579],{"type":15,"value":578},"Fewer water–surface favorable contacts → ",{"type":9,"tag":33,"props":580,"children":581},{},[582],{"type":15,"value":583},"ΔH increases",{"type":9,"tag":29,"props":585,"children":586},{},[587,588,593],{"type":15,"value":548},{"type":9,"tag":33,"props":589,"children":590},{},[591],{"type":15,"value":592},"ΔG decreases",{"type":15,"value":594},", so association is favored.",{"type":9,"tag":100,"props":596,"children":597},{},[],{"type":9,"tag":18,"props":599,"children":601},{"id":600},"_8-motions-in-proteins-dynamics-contribute-stability",[602],{"type":15,"value":603},"8) Motions in proteins: dynamics contribute stability 🕺",{"type":9,"tag":110,"props":605,"children":606},{},[607],{"type":15,"value":608},"Proteins move across huge timescales (ps to years): vibrations, side-chain rotations, domain motions, allosteric transitions, folding/unfolding, complex dissociation, etc.\nThermodynamic punchline in this text:",{"type":9,"tag":25,"props":610,"children":611},{},[612],{"type":9,"tag":29,"props":613,"children":614},{},[615,617,622,624,629],{"type":15,"value":616},"More dynamics → higher ",{"type":9,"tag":33,"props":618,"children":619},{},[620],{"type":15,"value":621},"entropy",{"type":15,"value":623}," → lower ",{"type":9,"tag":33,"props":625,"children":626},{},[627],{"type":15,"value":628},"free energy",{"type":15,"value":630}," → can stabilize (flexible loops can contribute noticeably).",{"type":9,"tag":100,"props":632,"children":633},{},[],{"type":9,"tag":18,"props":635,"children":637},{"id":636},"_9-the-protein-folding-problem-levinthal-paradox",[638],{"type":15,"value":639},"9) The protein folding problem: Levinthal paradox 🧩",{"type":9,"tag":110,"props":641,"children":642},{},[643],{"type":15,"value":644},"Levinthal’s argument: random search across conformations is impossibly slow.",{"type":9,"tag":25,"props":646,"children":647},{},[648,653,658],{"type":9,"tag":29,"props":649,"children":650},{},[651],{"type":15,"value":652},"Even with only 2 conformations per residue, a 100-residue chain has 2^100 possibilities (~10^30).",{"type":9,"tag":29,"props":654,"children":655},{},[656],{"type":15,"value":657},"At ~10^-13 s per conformational change, exploring everything would take ~10^9 years.",{"type":9,"tag":29,"props":659,"children":660},{},[661],{"type":15,"value":662},"Yet many proteins fold in seconds/minutes → folding is not a blind search; it uses efficient routes.",{"type":9,"tag":100,"props":664,"children":665},{},[],{"type":9,"tag":18,"props":667,"children":669},{"id":668},"_10-folded-unfolded-transitions-two-state-unfolding-curves",[670],{"type":15,"value":671},"10) Folded ⇌ unfolded transitions: two-state unfolding curves 📈",{"type":9,"tag":110,"props":673,"children":674},{},[675],{"type":15,"value":676},"Experimentally, unfolding can be driven by:",{"type":9,"tag":25,"props":678,"children":679},{},[680,690,698],{"type":9,"tag":29,"props":681,"children":682},{},[683,688],{"type":9,"tag":33,"props":684,"children":685},{},[686],{"type":15,"value":687},"Chemical denaturants",{"type":15,"value":689}," (urea, guanidinium chloride)",{"type":9,"tag":29,"props":691,"children":692},{},[693],{"type":9,"tag":33,"props":694,"children":695},{},[696],{"type":15,"value":697},"Temperature",{"type":9,"tag":29,"props":699,"children":700},{},[701],{"type":9,"tag":33,"props":702,"children":703},{},[704],{"type":15,"value":705},"pH changes",{"type":9,"tag":110,"props":707,"children":708},{},[709,711,716,718,723],{"type":15,"value":710},"Many proteins show ",{"type":9,"tag":33,"props":712,"children":713},{},[714],{"type":15,"value":715},"sigmoidal",{"type":15,"value":717}," “melting/unfolding curves,” often interpreted as a ",{"type":9,"tag":33,"props":719,"children":720},{},[721],{"type":15,"value":722},"two-state equilibrium",{"type":15,"value":121},{"type":9,"tag":25,"props":725,"children":726},{},[727],{"type":9,"tag":29,"props":728,"children":729},{},[730],{"type":15,"value":731},"unfolded ⇌ folded\nWithin the transition region, you can estimate fractions of folded/unfolded from spectroscopic signals (CD, fluorescence, etc.).",{"type":9,"tag":110,"props":733,"children":734},{},[735],{"type":15,"value":736},"Kinetics connection (two-state case):",{"type":9,"tag":25,"props":738,"children":739},{},[740,745],{"type":9,"tag":29,"props":741,"children":742},{},[743],{"type":15,"value":744},"Folding/unfolding rates: kf and ku",{"type":9,"tag":29,"props":746,"children":747},{},[748,750,756,758,763],{"type":15,"value":749},"Equilibrium constant: K = ",{"type":9,"tag":751,"props":752,"children":753},"span",{},[754],{"type":15,"value":755},"folded",{"type":15,"value":757},"/",{"type":9,"tag":751,"props":759,"children":760},{},[761],{"type":15,"value":762},"unfolded",{"type":15,"value":764}," = kf/ku (often observed; supports two-state).",{"type":9,"tag":110,"props":766,"children":767},{},[768],{"type":15,"value":769},"Complications to two-state behavior mentioned:",{"type":9,"tag":25,"props":771,"children":772},{},[773,778,783],{"type":9,"tag":29,"props":774,"children":775},{},[776],{"type":15,"value":777},"Disulfide bond formation (especially wrong pairings)",{"type":9,"tag":29,"props":779,"children":780},{},[781],{"type":15,"value":782},"Proline cis/trans isomerization",{"type":9,"tag":29,"props":784,"children":785},{},[786],{"type":15,"value":787},"Proteolytic processing producing multiple disulfide-linked chains (often not reversible).",{"type":9,"tag":100,"props":789,"children":790},{},[],{"type":9,"tag":18,"props":792,"children":794},{"id":793},"_11-thermodynamics-of-folding-δg-δh-tδs-️",[795],{"type":15,"value":796},"11) Thermodynamics of folding: ΔG = ΔH − TΔS ⚖️",{"type":9,"tag":110,"props":798,"children":799},{},[800],{"type":15,"value":801},"Define folding free energy:",{"type":9,"tag":25,"props":803,"children":804},{},[805],{"type":9,"tag":29,"props":806,"children":807},{},[808,810,815],{"type":15,"value":809},"ΔG°folding = G°folded − G°unfolded\nStable folding means ΔG°folding is ",{"type":9,"tag":33,"props":811,"children":812},{},[813],{"type":15,"value":814},"negative",{"type":15,"value":501},{"type":9,"tag":110,"props":817,"children":818},{},[819],{"type":15,"value":820},"Magnitude reality-check:",{"type":9,"tag":25,"props":822,"children":823},{},[824],{"type":9,"tag":29,"props":825,"children":826},{},[827,829,834,836,841],{"type":15,"value":828},"Typical ΔG°folding is only about ",{"type":9,"tag":33,"props":830,"children":831},{},[832],{"type":15,"value":833},"–20 to –60 kJ/mol",{"type":15,"value":835},", comparable to “only a few hydrogen bonds,” meaning stability is a ",{"type":9,"tag":33,"props":837,"children":838},{},[839],{"type":15,"value":840},"small difference between large opposing terms",{"type":15,"value":501},{"type":9,"tag":110,"props":843,"children":844},{},[845],{"type":15,"value":846},"Thermodynamic message:",{"type":9,"tag":25,"props":848,"children":849},{},[850],{"type":9,"tag":29,"props":851,"children":852},{},[853,855],{"type":15,"value":854},"Folding stability is a delicate balance:",{"type":9,"tag":25,"props":856,"children":857},{},[858,868,878],{"type":9,"tag":29,"props":859,"children":860},{},[861,866],{"type":9,"tag":33,"props":862,"children":863},{},[864],{"type":15,"value":865},"Favorable enthalpy",{"type":15,"value":867}," (many interactions in the folded state)",{"type":9,"tag":29,"props":869,"children":870},{},[871,876],{"type":9,"tag":33,"props":872,"children":873},{},[874],{"type":15,"value":875},"Unfavorable entropy",{"type":15,"value":877}," (loss of chain conformational freedom)",{"type":9,"tag":29,"props":879,"children":880},{},[881],{"type":15,"value":882},"Plus big solvent contributions (especially hydrophobic effect).",{"type":9,"tag":100,"props":884,"children":885},{},[],{"type":9,"tag":18,"props":887,"children":889},{"id":888},"_12-calorimetry-and-dsc-watching-unfolding-via-heat-capacity",[890],{"type":15,"value":891},"12) Calorimetry and DSC: watching unfolding via heat capacity 🔥",{"type":9,"tag":110,"props":893,"children":894},{},[895,897,902],{"type":15,"value":896},"Differential scanning calorimetry (DSC) measures ",{"type":9,"tag":33,"props":898,"children":899},{},[900],{"type":15,"value":901},"heat capacity CP",{"type":15,"value":903}," as temperature changes.",{"type":9,"tag":25,"props":905,"children":906},{},[907,919,929],{"type":9,"tag":29,"props":908,"children":909},{},[910,912,917],{"type":15,"value":911},"Unfolding shows up as a ",{"type":9,"tag":33,"props":913,"children":914},{},[915],{"type":15,"value":916},"peak",{"type":15,"value":918}," (large heat absorption).",{"type":9,"tag":29,"props":920,"children":921},{},[922,927],{"type":9,"tag":33,"props":923,"children":924},{},[925],{"type":15,"value":926},"Tm",{"type":15,"value":928}," is where CP is maximal (midpoint of unfolding).",{"type":9,"tag":29,"props":930,"children":931},{},[932,934,939],{"type":15,"value":933},"The baseline difference between folded and unfolded CP gives ",{"type":9,"tag":33,"props":935,"children":936},{},[937],{"type":15,"value":938},"ΔCP",{"type":15,"value":501},{"type":9,"tag":110,"props":941,"children":942},{},[943],{"type":15,"value":944},"Interpretations emphasized:",{"type":9,"tag":25,"props":946,"children":947},{},[948,953,965],{"type":9,"tag":29,"props":949,"children":950},{},[951],{"type":15,"value":952},"Unfolded proteins have larger CP partly because exposing hydrophobics increases water ordering effects.",{"type":9,"tag":29,"props":954,"children":955},{},[956,958,963],{"type":15,"value":957},"Integrating the peak area gives ",{"type":9,"tag":33,"props":959,"children":960},{},[961],{"type":15,"value":962},"ΔHcal",{"type":15,"value":964}," (calorimetric enthalpy).",{"type":9,"tag":29,"props":966,"children":967},{},[968,970,974,976,981,983],{"type":15,"value":969},"Comparing ",{"type":9,"tag":33,"props":971,"children":972},{},[973],{"type":15,"value":962},{"type":15,"value":975}," with ",{"type":9,"tag":33,"props":977,"children":978},{},[979],{"type":15,"value":980},"ΔHvH",{"type":15,"value":982}," (van’t Hoff enthalpy from equilibrium analysis) helps assess:",{"type":9,"tag":25,"props":984,"children":985},{},[986,991],{"type":9,"tag":29,"props":987,"children":988},{},[989],{"type":15,"value":990},"Two-state cooperativity (often ΔHcal ≈ ΔHvH for small single-domain proteins)",{"type":9,"tag":29,"props":992,"children":993},{},[994],{"type":15,"value":995},"Multi-domain behavior (domains unfolding independently can change ratios).",{"type":9,"tag":100,"props":997,"children":998},{},[],{"type":9,"tag":18,"props":1000,"children":1002},{"id":1001},"_13-energetics-breakdown-where-enthalpyentropy-come-from",[1003],{"type":15,"value":1004},"13) Energetics breakdown: where enthalpy/entropy come from 🧠",{"type":9,"tag":110,"props":1006,"children":1007},{},[1008],{"type":15,"value":1009},"This chapter lays out qualitative contributors:",{"type":9,"tag":110,"props":1011,"children":1012},{},[1013,1018],{"type":9,"tag":33,"props":1014,"children":1015},{},[1016],{"type":15,"value":1017},"Unfolded state (in water)",{"type":15,"value":121},{"type":9,"tag":25,"props":1020,"children":1021},{},[1022,1027,1032],{"type":9,"tag":29,"props":1023,"children":1024},{},[1025],{"type":15,"value":1026},"Many favorable interactions of polar/ionized groups with water (enthalpically favorable)",{"type":9,"tag":29,"props":1028,"children":1029},{},[1030],{"type":15,"value":1031},"High chain conformational freedom (entropy favorable)",{"type":9,"tag":29,"props":1033,"children":1034},{},[1035],{"type":15,"value":1036},"But water around hydrophobics is restricted (entropy unfavorable).",{"type":9,"tag":110,"props":1038,"children":1039},{},[1040,1045],{"type":9,"tag":33,"props":1041,"children":1042},{},[1043],{"type":15,"value":1044},"Folded state",{"type":15,"value":121},{"type":9,"tag":25,"props":1047,"children":1048},{},[1049,1054,1059],{"type":9,"tag":29,"props":1050,"children":1051},{},[1052],{"type":15,"value":1053},"Many intramolecular favorable interactions (H-bonds, packing, salt bridges)",{"type":9,"tag":29,"props":1055,"children":1056},{},[1057],{"type":15,"value":1058},"Chain entropy decreases (unfavorable)",{"type":9,"tag":29,"props":1060,"children":1061},{},[1062],{"type":15,"value":1063},"Hydrophobic burial releases ordered waters → water entropy increases (favorable).",{"type":9,"tag":110,"props":1065,"children":1066},{},[1067],{"type":15,"value":1068},"A key table-like message:",{"type":9,"tag":25,"props":1070,"children":1071},{},[1072],{"type":9,"tag":29,"props":1073,"children":1074},{},[1075],{"type":15,"value":1076},"No single term dominates; folding free energy is a net of many contributions.",{"type":9,"tag":100,"props":1078,"children":1079},{},[],{"type":9,"tag":18,"props":1081,"children":1083},{"id":1082},"_16-what-dsc-instruments-actually-do-practical-view",[1084],{"type":15,"value":1085},"16) What DSC instruments actually do (practical view) 🧪",{"type":9,"tag":25,"props":1087,"children":1088},{},[1089,1108,1120],{"type":9,"tag":29,"props":1090,"children":1091},{},[1092,1094,1099,1101,1106],{"type":15,"value":1093},"Two cells: ",{"type":9,"tag":33,"props":1095,"children":1096},{},[1097],{"type":15,"value":1098},"sample",{"type":15,"value":1100}," (protein solution) and ",{"type":9,"tag":33,"props":1102,"children":1103},{},[1104],{"type":15,"value":1105},"reference",{"type":15,"value":1107}," (buffer). Heat both at the same rate.",{"type":9,"tag":29,"props":1109,"children":1110},{},[1111,1113,1118],{"type":15,"value":1112},"The instrument measures extra power needed to keep temperatures equal → gives ",{"type":9,"tag":33,"props":1114,"children":1115},{},[1116],{"type":15,"value":1117},"excess heat capacity",{"type":15,"value":1119}," vs temperature (thermogram).",{"type":9,"tag":29,"props":1121,"children":1122},{},[1123,1125],{"type":15,"value":1124},"Thermogram regions:",{"type":9,"tag":390,"props":1126,"children":1127},{},[1128,1133,1138],{"type":9,"tag":29,"props":1129,"children":1130},{},[1131],{"type":15,"value":1132},"pre-transition baseline",{"type":9,"tag":29,"props":1134,"children":1135},{},[1136],{"type":15,"value":1137},"unfolding peak",{"type":9,"tag":29,"props":1139,"children":1140},{},[1141],{"type":15,"value":1142},"post-transition baseline",{"type":9,"tag":110,"props":1144,"children":1145},{},[1146],{"type":15,"value":1147},"Model-free vs model-based:",{"type":9,"tag":25,"props":1149,"children":1150},{},[1151,1160,1169],{"type":9,"tag":29,"props":1152,"children":1153},{},[1154,1158],{"type":9,"tag":33,"props":1155,"children":1156},{},[1157],{"type":15,"value":962},{"type":15,"value":1159},": model-free (area under peak, baseline-corrected).",{"type":9,"tag":29,"props":1161,"children":1162},{},[1163,1167],{"type":9,"tag":33,"props":1164,"children":1165},{},[1166],{"type":15,"value":980},{"type":15,"value":1168},": model-dependent (assumes a model, often two-state), derived from the temperature dependence of K extracted from the thermogram.",{"type":9,"tag":29,"props":1170,"children":1171},{},[1172],{"type":15,"value":1173},"Pitfalls: aggregation and irreversibility can distort peaks and mislead ΔH estimates.",{"type":9,"tag":100,"props":1175,"children":1176},{},[],{"type":9,"tag":18,"props":1178,"children":1180},{"id":1179},"_17-ligands-and-stability-tm-shifts-with-binding",[1181],{"type":15,"value":1182},"17) Ligands and stability: Tm shifts with binding 🎯",{"type":9,"tag":110,"props":1184,"children":1185},{},[1186],{"type":15,"value":1187},"Core principle (Le Chatelier applied to folding):",{"type":9,"tag":25,"props":1189,"children":1190},{},[1191,1209],{"type":9,"tag":29,"props":1192,"children":1193},{},[1194,1196,1201,1203,1208],{"type":15,"value":1195},"If ligand binds ",{"type":9,"tag":33,"props":1197,"children":1198},{},[1199],{"type":15,"value":1200},"preferentially to the folded/native state",{"type":15,"value":1202},", it stabilizes folding → ",{"type":9,"tag":33,"props":1204,"children":1205},{},[1206],{"type":15,"value":1207},"Tm increases",{"type":15,"value":501},{"type":9,"tag":29,"props":1210,"children":1211},{},[1212,1213,1218,1220,1225],{"type":15,"value":1195},{"type":9,"tag":33,"props":1214,"children":1215},{},[1216],{"type":15,"value":1217},"preferentially to the unfolded state",{"type":15,"value":1219},", it destabilizes folding → ",{"type":9,"tag":33,"props":1221,"children":1222},{},[1223],{"type":15,"value":1224},"Tm decreases",{"type":15,"value":501},{"type":9,"tag":110,"props":1227,"children":1228},{},[1229],{"type":15,"value":1230},"The chapter writes this with equilibria like:",{"type":9,"tag":25,"props":1232,"children":1233},{},[1234],{"type":9,"tag":29,"props":1235,"children":1236},{},[1237],{"type":15,"value":1238},"N + L ⇌ NL and N ⇌ U, showing ligand binding changes the effective unfolding equilibrium constant and thereby shifts Tm.",{"type":9,"tag":100,"props":1240,"children":1241},{},[],{"type":9,"tag":18,"props":1243,"children":1245},{"id":1244},"_18-denaturants-vs-osmolytes-opposite-effects-️",[1246],{"type":15,"value":1247},"18) Denaturants vs osmolytes: opposite effects 🧴🛡️",{"type":9,"tag":110,"props":1249,"children":1250},{},[1251,1256],{"type":9,"tag":33,"props":1252,"children":1253},{},[1254],{"type":15,"value":1255},"Denaturants (chaotropes)",{"type":15,"value":1257},": urea, guanidinium chloride",{"type":9,"tag":25,"props":1259,"children":1260},{},[1261,1266,1271],{"type":9,"tag":29,"props":1262,"children":1263},{},[1264],{"type":15,"value":1265},"At high concentrations (6–10 M) they unfold proteins to random-coil-like states.",{"type":9,"tag":29,"props":1267,"children":1268},{},[1269],{"type":15,"value":1270},"They work differently than SDS (explicitly emphasized).",{"type":9,"tag":29,"props":1272,"children":1273},{},[1274,1276],{"type":15,"value":1275},"Mechanistic idea emphasized here:",{"type":9,"tag":25,"props":1277,"children":1278},{},[1279,1284],{"type":9,"tag":29,"props":1280,"children":1281},{},[1282],{"type":15,"value":1283},"Denaturants increase solubility of both polar and nonpolar side chains, correlating with accessible surface area.",{"type":9,"tag":29,"props":1285,"children":1286},{},[1287],{"type":15,"value":1288},"They effectively make it more favorable for protein surfaces—especially the huge buried interior surface—to be solvated → unfolding.",{"type":9,"tag":110,"props":1290,"children":1291},{},[1292],{"type":15,"value":1293},"Free-energy picture:",{"type":9,"tag":25,"props":1295,"children":1296},{},[1297,1309],{"type":9,"tag":29,"props":1298,"children":1299},{},[1300,1302,1307],{"type":15,"value":1301},"Denaturant stabilizes both folded and unfolded states, but stabilizes ",{"type":9,"tag":33,"props":1303,"children":1304},{},[1305],{"type":15,"value":1306},"unfolded more",{"type":15,"value":1308}," (more surface exposed → stronger effect), so ΔG°folding becomes less negative and can cross 0 at a midpoint concentration.",{"type":9,"tag":29,"props":1310,"children":1311},{},[1312,1314,1319],{"type":15,"value":1313},"Often observed: ",{"type":9,"tag":33,"props":1315,"children":1316},{},[1317],{"type":15,"value":1318},"linear dependence",{"type":15,"value":1320}," of ΔG°folding on denaturant concentration with slope m.",{"type":9,"tag":110,"props":1322,"children":1323},{},[1324,1329],{"type":9,"tag":33,"props":1325,"children":1326},{},[1327],{"type":15,"value":1328},"Osmolytes",{"type":15,"value":1330},": TMAO, sarcosine, sucrose, proline",{"type":9,"tag":25,"props":1332,"children":1333},{},[1334,1339],{"type":9,"tag":29,"props":1335,"children":1336},{},[1337],{"type":15,"value":1338},"Protect proteins against stress by stabilizing the folded state.",{"type":9,"tag":29,"props":1340,"children":1341},{},[1342],{"type":15,"value":1343},"Mechanistic picture here: osmolytes make peptide–osmolyte interactions less favorable; the unfolded state is penalized more (more exposure), increasing folded stability.",{"type":9,"tag":100,"props":1345,"children":1346},{},[],{"type":9,"tag":18,"props":1348,"children":1350},{"id":1349},"_20-foldingunfolding-kinetics-and-chevron-plots-️",[1351],{"type":15,"value":1352},"20) Folding/unfolding kinetics and chevron plots ⛰️",{"type":9,"tag":110,"props":1354,"children":1355},{},[1356],{"type":15,"value":1357},"Typical experiment design:",{"type":9,"tag":25,"props":1359,"children":1360},{},[1361,1373],{"type":9,"tag":29,"props":1362,"children":1363},{},[1364,1366,1371],{"type":15,"value":1365},"Start unfolded at high denaturant → rapidly dilute to low denaturant → watch ",{"type":9,"tag":33,"props":1367,"children":1368},{},[1369],{"type":15,"value":1370},"refolding",{"type":15,"value":1372}," (often first-order kinetics).",{"type":9,"tag":29,"props":1374,"children":1375},{},[1376,1378,1383],{"type":15,"value":1377},"For unfolding: mix folded protein into strong denaturant → watch ",{"type":9,"tag":33,"props":1379,"children":1380},{},[1381],{"type":15,"value":1382},"unfolding",{"type":15,"value":1384}," (also first-order).",{"type":9,"tag":110,"props":1386,"children":1387},{},[1388],{"type":15,"value":1389},"For a two-state system:",{"type":9,"tag":25,"props":1391,"children":1392},{},[1393],{"type":9,"tag":29,"props":1394,"children":1395},{},[1396],{"type":15,"value":1397},"Observed rate: kobs = kf + ku\nIn refolding conditions usually ku ≪ kf, so kobs ≈ kf; in unfolding conditions often kf ≪ ku, so kobs ≈ ku.",{"type":9,"tag":110,"props":1399,"children":1400},{},[1401],{"type":15,"value":1402},"Empirical linear relationships used:",{"type":9,"tag":25,"props":1404,"children":1405},{},[1406,1418],{"type":9,"tag":29,"props":1407,"children":1408},{},[1409,1411,1416],{"type":15,"value":1410},"log kf = log kf(water) + mf",{"type":9,"tag":751,"props":1412,"children":1413},{},[1414],{"type":15,"value":1415},"den",{"type":15,"value":1417}," (mf negative)",{"type":9,"tag":29,"props":1419,"children":1420},{},[1421,1423,1427],{"type":15,"value":1422},"log ku = log ku(water) + mu",{"type":9,"tag":751,"props":1424,"children":1425},{},[1426],{"type":15,"value":1415},{"type":15,"value":1428}," (mu positive)",{"type":9,"tag":110,"props":1430,"children":1431},{},[1432,1434,1438,1440,1445],{"type":15,"value":1433},"Plotting log(rate) vs ",{"type":9,"tag":751,"props":1435,"children":1436},{},[1437],{"type":15,"value":1415},{"type":15,"value":1439}," gives a ",{"type":9,"tag":33,"props":1441,"children":1442},{},[1443],{"type":15,"value":1444},"V-shape",{"type":15,"value":1446}," (the “chevron plot”), with intersection at Cm where kf = ku.",{"type":9,"tag":100,"props":1448,"children":1449},{},[],{"type":9,"tag":18,"props":1451,"children":1453},{"id":1452},"_21-mutational-studies-and-the-transition-state-φ-values",[1454],{"type":15,"value":1455},"21) Mutational studies and the transition state: Φ-values 🧷",{"type":9,"tag":110,"props":1457,"children":1458},{},[1459],{"type":15,"value":1460},"Protein engineering (point mutations, insertions/deletions) is used to probe:",{"type":9,"tag":25,"props":1462,"children":1463},{},[1464,1469,1474],{"type":9,"tag":29,"props":1465,"children":1466},{},[1467],{"type":15,"value":1468},"stability changes",{"type":9,"tag":29,"props":1470,"children":1471},{},[1472],{"type":15,"value":1473},"folding/unfolding rate changes",{"type":9,"tag":29,"props":1475,"children":1476},{},[1477],{"type":15,"value":1478},"which residues are essential vs merely stabilizing",{"type":9,"tag":110,"props":1480,"children":1481},{},[1482],{"type":15,"value":1483},"Key quantities:",{"type":9,"tag":25,"props":1485,"children":1486},{},[1487,1492],{"type":9,"tag":29,"props":1488,"children":1489},{},[1490],{"type":15,"value":1491},"Transition state free energies for folding/unfolding (relative to unfolded or native).",{"type":9,"tag":29,"props":1493,"children":1494},{},[1495,1497,1502,1504,1509,1511,1516,1517],{"type":15,"value":1496},"The ",{"type":9,"tag":33,"props":1498,"children":1499},{},[1500],{"type":15,"value":1501},"Φ-value",{"type":15,"value":1503}," measures how much a mutation destabilizes the ",{"type":9,"tag":33,"props":1505,"children":1506},{},[1507],{"type":15,"value":1508},"transition state",{"type":15,"value":1510}," relative to how much it destabilizes the ",{"type":9,"tag":33,"props":1512,"children":1513},{},[1514],{"type":15,"value":1515},"folded state",{"type":15,"value":121},{"type":9,"tag":25,"props":1518,"children":1519},{},[1520,1525],{"type":9,"tag":29,"props":1521,"children":1522},{},[1523],{"type":15,"value":1524},"Φ ≈ 0: residue not “native-like” in transition state",{"type":9,"tag":29,"props":1526,"children":1527},{},[1528],{"type":15,"value":1529},"Φ ≈ 1: residue interactions in transition state similar to folded state",{"type":9,"tag":110,"props":1531,"children":1532},{},[1533],{"type":15,"value":1534},"This enables mapping of what parts of the structure are already formed at the transition state.",{"type":9,"tag":100,"props":1536,"children":1537},{},[],{"type":9,"tag":18,"props":1539,"children":1541},{"id":1540},"_23-what-the-transition-state-is-like-conceptually",[1542],{"type":15,"value":1543},"23) What the transition state is like (conceptually) 🧠",{"type":9,"tag":25,"props":1545,"children":1546},{},[1547,1559,1571],{"type":9,"tag":29,"props":1548,"children":1549},{},[1550,1552,1557],{"type":15,"value":1551},"The transition state typically contains ",{"type":9,"tag":33,"props":1553,"children":1554},{},[1555],{"type":15,"value":1556},"native hydrophobic long-range interactions",{"type":15,"value":1558}," that stabilize weak secondary structure.",{"type":9,"tag":29,"props":1560,"children":1561},{},[1562,1564,1569],{"type":15,"value":1563},"It often resembles a ",{"type":9,"tag":33,"props":1565,"children":1566},{},[1567],{"type":15,"value":1568},"distorted folded structure",{"type":15,"value":1570},", with a more “folded-like” nucleus and increasing distortion away from it.",{"type":9,"tag":29,"props":1572,"children":1573},{},[1574,1576],{"type":15,"value":1575},"The chapter stresses ensembles:",{"type":9,"tag":25,"props":1577,"children":1578},{},[1579,1584,1589],{"type":9,"tag":29,"props":1580,"children":1581},{},[1582],{"type":15,"value":1583},"unfolded: very diverse ensemble",{"type":9,"tag":29,"props":1585,"children":1586},{},[1587],{"type":15,"value":1588},"folded: tight ensemble",{"type":9,"tag":29,"props":1590,"children":1591},{},[1592],{"type":15,"value":1593},"transition state: intermediate ensemble, often closer to folded than unfolded",{"type":9,"tag":100,"props":1595,"children":1596},{},[],{"type":9,"tag":18,"props":1598,"children":1600},{"id":1599},"_24-molten-globule-compact-secondary-structure-but-loose-core",[1601],{"type":15,"value":1602},"24) Molten globule: compact + secondary structure, but loose core 🫠",{"type":9,"tag":110,"props":1604,"children":1605},{},[1606],{"type":15,"value":1607},"A “molten globule” is a partially structured intermediate often seen under mildly denaturing conditions.\nCore characteristics listed:",{"type":9,"tag":390,"props":1609,"children":1610},{},[1611,1616,1621,1626],{"type":9,"tag":29,"props":1612,"children":1613},{},[1614],{"type":15,"value":1615},"relatively compact (only ~10–30% larger than native)",{"type":9,"tag":29,"props":1617,"children":1618},{},[1619],{"type":15,"value":1620},"substantial secondary structure (far-UV CD remains)",{"type":9,"tag":29,"props":1622,"children":1623},{},[1624],{"type":15,"value":1625},"weak/absent tight tertiary packing (near-UV CD largely disappears)",{"type":9,"tag":29,"props":1627,"children":1628},{},[1629],{"type":15,"value":1630},"increased flexibility (rapidly interconverting conformations)",{"type":9,"tag":100,"props":1632,"children":1633},{},[],{"type":9,"tag":18,"props":1635,"children":1637},{"id":1636},"_25-folding-funnels-many-routes-down-the-landscape",[1638],{"type":15,"value":1639},"25) Folding funnels: many routes down the landscape 🌀",{"type":9,"tag":110,"props":1641,"children":1642},{},[1643],{"type":15,"value":1644},"The chapter explains why 1D reaction-coordinate diagrams are misleading for protein folding:",{"type":9,"tag":25,"props":1646,"children":1647},{},[1648,1653],{"type":9,"tag":29,"props":1649,"children":1650},{},[1651],{"type":15,"value":1652},"unfolded state has many conformations; there isn’t a single path",{"type":9,"tag":29,"props":1654,"children":1655},{},[1656],{"type":15,"value":1657},"real energy landscapes have “blind alleys” and nonproductive intermediates",{"type":9,"tag":110,"props":1659,"children":1660},{},[1661,1663,1668],{"type":15,"value":1662},"So the modern cartoon is a ",{"type":9,"tag":33,"props":1664,"children":1665},{},[1666],{"type":15,"value":1667},"folding funnel",{"type":15,"value":121},{"type":9,"tag":25,"props":1670,"children":1671},{},[1672,1677,1682],{"type":9,"tag":29,"props":1673,"children":1674},{},[1675],{"type":15,"value":1676},"wide at top (many unfolded conformations)",{"type":9,"tag":29,"props":1678,"children":1679},{},[1680],{"type":15,"value":1681},"narrowing as trajectories converge",{"type":9,"tag":29,"props":1683,"children":1684},{},[1685],{"type":15,"value":1686},"key barrier region corresponds to the transition state (“saddle point”)",{"type":9,"tag":100,"props":1688,"children":1689},{},[],{"type":9,"tag":18,"props":1691,"children":1693},{"id":1692},"quick-memory-hooks",[1694],{"type":15,"value":1695},"Quick memory hooks ✅",{"type":9,"tag":25,"props":1697,"children":1698},{},[1699,1709,1719,1729],{"type":9,"tag":29,"props":1700,"children":1701},{},[1702,1707],{"type":9,"tag":33,"props":1703,"children":1704},{},[1705],{"type":15,"value":1706},"ΔG = ΔH − TΔS",{"type":15,"value":1708},": folding is a small net difference between big competing terms.",{"type":9,"tag":29,"props":1710,"children":1711},{},[1712,1717],{"type":9,"tag":33,"props":1713,"children":1714},{},[1715],{"type":15,"value":1716},"Hydrophobic effect = water entropy story",{"type":15,"value":1718},": bury nonpolar surface → release ordered waters → folding becomes favorable.",{"type":9,"tag":29,"props":1720,"children":1721},{},[1722,1727],{"type":9,"tag":33,"props":1723,"children":1724},{},[1725],{"type":15,"value":1726},"Two-state unfolding",{"type":15,"value":1728},": sigmoidal curves; Tm is midpoint; DSC peak area → ΔHcal.",{"type":9,"tag":29,"props":1730,"children":1731},{},[1732,1737],{"type":9,"tag":33,"props":1733,"children":1734},{},[1735],{"type":15,"value":1736},"Denaturants vs osmolytes",{"type":15,"value":1738},": denaturants favor solvation/exposure; osmolytes favor burial/folding.",1775084292148]