Convergent evolution of kidney sizes and supraorbital salt glands for birds living in saline habitats.

Only a small number of avian species inhabit salty environments. To understand how they adapted, we examined the evolution of kidney sizes, supraorbital salt glands (SSGs), and the utilization of salty habitats across 230 species spanning 25 avian orders. Phylogenetic analysis indicates that SSGs, large kidneys, and thriving in salty habitats emerged convergently in birds. Transition rate analysis reveals that species possessing SSGs and large kidneys tended to move from low-to high-salinity environments, while others moved in the opposite direction. However, habitat salinity also influenced kidney evolution; lineages residing in high-salinity environments tended to develop larger kidneys than those in low-salinity environments. Our findings suggest that SSGs and large kidneys may have evolved through adaptation to high salinity. Overall, habitat conditions and physiological traits influenced avian adaptation to salty environments in a reciprocal manner. These results shed the new light on the evolutionary mechanisms underlying functional diversity in birds.

Molecular Effects of Li+-Coordinating Binders and Negatively Charged Binders on the Li+ Local Mobility near the Electrolyte/LiFePO4 Cathode Interface within Lithium-Ion Batteries.

The development of lithium-ion batteries (LIBs) is important in the realm of energy storage. Understanding the intricate effects of binders on the Li+ transport at the cathode/electrolyte interface in LIBs remains a challenge. This study utilized molecular dynamics simulations to compare the molecular effects of conventional polyvinylidene difluoride (PVDF), Li+-coordinating polyethylene oxide (PEO), and negatively charged polystyrene sulfonate (PSS) binders on local Li+ mobility at the electrolyte/LiFePO4 (LFP) cathode interface. By examining concentration profiles of Li+, three different polymer binders, and anions near Li+-rich LFP and Li+-depleted FePO4 (FP) surfaces, we found a superior performance of the negatively charged PSS on enhancing Li+ distribution near the Li+-depleted FP surface. The radial distribution function and coordination number analyses revealed the potent interactions of PEO and PSS with Li+ disrupting Li+ coordination with electrolyte solvents. Our simulations also revealed the effects of non-uniform binder dispersions on the Li+ local mobility near the cathode surface. The combined results provide a comparative insight into Li+ transport at the electrolyte/cathode interface influenced by distinct binder chemistries, offering a profound understanding of the binder designs for high-performance LIBs.

Low but highly geographically structured genomic diversity of East Asian Eurasian otters and its conservation implications.

Populations of Eurasian otters Lutra lutra, one of the most widely distributed apex predators in Eurasia, have been depleted mainly since the 1950s. However, a lack of information about their genomic diversity and how they are organized geographically in East Asia severely impedes our ability to monitor and conserve them in particular management units. Here, we re-sequenced and analyzed 20 otter genomes spanning continental East Asia, including a population at Kinmen, a small island off the Fujian coast, China. The otters form three genetic clusters (one of L. l. lutra in the north and two of L. l. chinensis in the south), which have diverged in the Holocene. These three clusters should be recognized as three conservation management units to monitor and manage independently. The heterozygosity of the East Asian otters is as low as that of the threatened carnivores sequenced. Historical effective population size trajectories inferred from genomic variations suggest that their low genomic diversity could be partially attributed to changes in the climate since the mid-Pleistocene and anthropogenic intervention since the Holocene. However, no evidence of genetic erosion, mutation load, or high level of inbreeding was detected in the presumably isolated Kinmen Island population. Any future in situ conservation efforts should consider this information for the conservation management units.

Real-Time Observation for Dynamic Oscillation during Self-Assembly and Clearance of Aß42.

The dynamic oscillation implicated in structural heterogeneity during the self-assembly of amyloid peptide 1-42 (Aß42) may play a crucial role in eliciting cellular responses. We developed a real-time monitoring platform to observe an oscillatory non-equilibrium interaction that dominated the Aß42 clearance by neuronal cells during interplay with an oscillator (lipopolysaccharide, LPS). Molecular dynamics studies indicated that the electrostatic and hydrophobic segments of LPS involved in the temporary heteromolecular association and slightly decelerated the intrinsic thermally-induced protein dynamics of Aß42. A bait-specific intervention strategy could temporarily slow down the self-propagation of Aß42 to extend the lifetime of autonomous oscillation and augment Aß42 clearance of neuronal cells. The lifetime increment of oscillation shows a bait concentration-dependent manner to reflect the non-equilibrium binding strength. This relationship may serve as a predictor for Alzheimer's disease drug discovery.

Molecular effects of site-specific phosphate-methylated primer on the structure and motions of Taq DNA polymerase.

Polymerase chain reaction (PCR) is a powerful molecular biology assay for gene detection and quantification. Conventional DNA primers for PCR often suffer from poor sensitivity in specific gene detection. Recently, oligonucleotides containing methyl phosphotriester (MPTE-DNA) have been developed with enhanced DNA hybridization and improved gene detection sensitivity. Yet, site-specific MPTE-modifications on DNA primers have been reported to affect PCR amplification efficiencies while the detailed mechanism remains elusive. Here, we utilized molecular dynamics (MD) simulation to examine the effects of site-specific MPTE-modified primers on the structure and motions of DNA/Taq polymerase complexes. All tested MPTE-DNA/Taq complexes exhibited RMSD values below 2 Å, indicating insignificant effects of all methylation sites on the complex stability. The energetic and hydrogen-bonding analyses suggest minor effects of methylation at t-3, t-4, t-6, and t-7 positions on the DNA-Taq interaction. Principal component analyses further reveal that only t-3, and t-7 methylations preserve the motions of the Taq thumb domain. The site-specific methylation affects the interaction between DNA and the surrounding protein residues, resulting in allosteric-like effects on the DNA/Taq complex. The MD data complement the best experimentally observed PCR efficacies for the t-3 and t-7 positions among all tested MPTE-primers. The unveiled molecular insights can benefit the design of novel PCR primers for improving genetic testing platforms.

Divergent effects of cholesterol on the structure and fluidity of liposome and catanionic vesicle membranes.

Lipid-like ion-pair amphiphile vesicles, or catanionic vesicles, have emerged as potential drug carriers. The effects of cholesterol on the properties of catanionic vesicles have yet been systematically studied. Here, we compared the effects of cholesterol on the structures and fluidities of dipalmitoylphosphatidylcholine liposomes and catanionic vesicles with similar main transition temperatures (Tm ). For liposomes, fluorescence anisotropy (FA) thermograms reveal typical condensing and disordering effects of cholesterol above and below Tm respectively. In contrast, FA and molecular simulation data reveal that catanionic bilayers below Tm are more fluidic due to shorter alkyl chains. This leads to only condensing effects of cholesterol for catanionic vesicles at all temperatures. Our results provide important insights into the fabrication of catanionic vesicles as novel drug carriers.

Solute Diffusivity and Local Free Volume in Cross-Linked Polymer Network: Implication of Optimizing the Conductivity of Polymer Electrolyte.

The diffusion of small molecules or ions within polymeric materials is critical for their applications, such as polymer electrolytes. Cross-linking has been one of the common strategies to modulate solute diffusivity and a polymer's mechanical properties. However, various studies have shown different effects of cross-linking on altering the solute transports. Here, we utilized coarse-grained molecular dynamics simulation to systematically analyze the effects of cross-linking and polymer rigidity of solute diffusive behaviors. Above the glass transition temperature Tg, the solute diffusion followed the Vogel-Tammann-Fulcher (VTF) equation, D = D0 e-Ea/R(T-T0). Other than the conventional compensation relation between the activation energy Ea and the pre-exponential factor D0, we also identified a correlation between Ea and Vogel temperature T0. We further characterized an empirical relation between T0 and cross-linking density. Integrating the newly identified correlations among the VTF parameters, we formulated a relation between solute diffusion and the cross-linking density. The combined results proposed the criteria for the optimal solute diffusivity in cross-linked polymers, providing generic guidance for novel polymer electrolyte design.

Not out of the woods yet: Signatures of the prolonged negative genetic consequences of a population bottleneck in a rapidly re-expanding wader, the black-faced spoonbill Platalea minor.

The long-term persistence of a population which has suffered a bottleneck partly depends on how historical demographic dynamics impacted its genetic diversity and the accumulation of deleterious mutations. Here we provide genomic evidence for the genetic effect of a recent population bottleneck in the endangered black-faced spoonbill (Platalea minor) after its rapid population recovery. Our data suggest that the bird's effective population size, Ne , had been relatively stable (7500-9000) since 22,000 years ago; however, a recent brief yet severe bottleneck (Ne  = 20) which we here estimated to occur around the 1940s wiped out >99% of its historical Ne in roughly three generations. Despite a >15-fold population recovery since 1988, we found that black-faced spoonbill population has higher levels of inbreeding (7.4 times more runs of homozygosity) than its sister species, the royal spoonbill (P. regia), which is not thought to have undergone a marked population contraction. Although the two spoonbills have similar levels of genome-wide genetic diversity, our results suggest that selection on more genes was relaxed in the black-faced spoonbill; moreover individual black-faced spoonbills carry more putatively deleterious mutations (Grantham's score > 50), and may therefore express more deleterious phenotypic effects than royal spoonbills. Here we demonstrate the value of using genomic indices to monitor levels of genetic erosion, inbreeding and mutation load in species with conservation concerns. To mitigate the prolonged negative genetic effect of a population bottleneck, we recommend that all possible measures should be employed to maintain population growth of a threatened species.

Revised Atomic Charges for OPLS Force Field Model of Poly(Ethylene Oxide): Benchmarks and Applications in Polymer Electrolyte.

Poly(ethylene oxide) (PEO)-based polymers are common hosts in solid polymer electrolytes (SPEs) for high-power energy devices. Molecular simulations have provided valuable molecular insights into structures and ion transport mechanisms of PEO-based SPEs. The calculation of thermodynamic and kinetic properties rely crucially on the dependability of the molecular force fields describing inter- and intra-molecular interactions with the target system. In this work, we reparametrized atomic partial charges for the widely applied optimized potentials for liquid simulations (OPLS) force field of PEO. The revised OPLS force field, OPLSR, improves the calculations of density, thermal expansion coefficient, and the phase transition of the PEO system. In particular, OPLSR greatly enhances the accuracy of the calculated dielectric constant of PEO, which is critical for simulating polymer electrolytes. The reparameterization method was further applied to SPE system of PEO/LiTFSI with O:Li ratio of 16:1. Based on the reparametrized partial charges, we applied separate charge-scaling factors for PEO and Li salts. The charge-rescaled OPLSR model significantly improves the resulting kinetics of Li+ transport while maintaining the accurate description of coordination structures within PEO-based SPE. The proposed OPLSR force field can benefit the future simulation studies of SPE systems.

Comparing the Ion-Conducting Polymers with Sulfonate and Ether Moieties as Cathode Binders for High-Power Lithium-Ion Batteries.

Two types of ion-conducting polyimides with sulfonate or ether functional groups were synthesized as ion-type or coordination-type cathode binders for lithium-ion batteries (LIBs), respectively. Although superior ion transport abilities have been reported for both types of ion-conducting polymers, their electrochemical performances are significantly different and the corresponding transport mechanisms at the electrolyte/electrode interface remain elusive. Here, we combine experimental and computational techniques to investigate the cathode interface in the presence of both functional polymer binders in comparison with the poly(vinylidene fluoride) (PVDF) binder as reference. A broad shoulder in the cyclic voltammogram accompanied by a poor rate performance of battery tests was observed for a LiFePO4 cathode with coordination-type ether-based polyimide (EPI) binder. In contrast, a LiFePO4 cathode with ion-type sulfonated polyimide (SPI) binder exhibits smaller concentration polarization, achieving satisfactory capacity at high current density. Simulations show that the ether-based binder strongly coordinates Li ions and thus slows the diffusion of Li ions. This leads to the reduction of the LIB electrochemical performance at a high C-rate. In contrast, the negative moiety of the SPI binder leads to less localization of Li ions, allowing a slightly higher Li-ion mobility. Conventional PVDF shows no affinity to Li ions, leading to less Li-ion accumulation at the electrode/electrolyte interface. Yet, the cathode surface covered with PVDF shows the lowest Li-ion diffusivity compared to those with the two types of Li-ion-conducting binders. Therefore, cathodes with SPI and PVDF binders show less polarization at the electrode interface and allow higher C-rate performance of LIBs. The combined results provide a comprehensive understanding of the mechanism of ion conduction in ion- and coordination-type Li-ion-conducting polymer binders. This gives valuable insight into the design of next-generation polymer materials for high-power LIBs.

Strict allopatric speciation of sky island Pyrrhula erythaca species complex.

Increasing evidence of post-divergence gene flow between taxa is shifting our understanding on the mode of speciation. A fundamental question arises concerning the circumstances under which strict allopatric speciation still holds true. Sky island populations might undergo reduced gene flow by niche conservatism to highland habitats and follow divergence in an allopatric manner. In this study, we tested this hypothesis in the sky island Grey-headed Bullfinch (Pyrrhula erythaca) species complex via statistical analyses of both genetic and ecological data. Results of coalescent-based analysis of multiple nuclear loci suggested that P. e. owstoni likely colonized Taiwan island during the severe mid-Pleistocene glacial climate followed by strictly allopatric divergence from P. e. erythaca distributed in Himalayas-Hengduan mountains and central North China. Results of ecological niche modeling suggested that their speciation may be attributed to the niche conservatism of these birds and the lack of a suitable ecological corridor during subsequent milder glacial episodes. In addition, we delimited the traditionally defined P. erythaca into two full species, P. erythaca in the Asian mainland and P. owstoni on the island of Taiwan, based on both genetic and behavioural evidences. These results suggest that ecology can have a dynamic role in allowing highland populations to expand their ranges and isolated by habitat barriers to diversify in a strictly allopatric manner.

Effects of Cholesterol on Water Permittivity of Biomimetic Ion Pair Amphiphile Bilayers: Interplay between Membrane Bending and Molecular Packing.

Ion pair amphiphile (IPA), a molecular complex composed of a pair of cationic and anionic amphiphiles, is an inexpensive phospholipid substitute to fabricate vesicles with various pharmaceutical applications. Modulating the physicochemical and permeation properties of IPA vesicles are important for carrier designs. Here, we applied molecular dynamics simulations to examine the cholesterol effects on the structures, mechanics, and water permittivity of hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dodecyltrimethylammonium- hexadecylsulfate (DTMA-HS) IPA bilayers. Structural and mechanical analyses indicate that both IPA systems are in gel phase at 298 K. Adding cholesterol induces alkyl chain ordering around the rigid sterol ring and increases the cavity density within the hydrophilic region of both IPA bilayers. Furthermore, the enhanced alkyl chain ordering and the membrane deformation energy induced by cholesterol increase the permeation free energy penalty. In contrast, cholesterol has minor effects on the water local diffusivities within IPA membranes. Overall, the cholesterol reduces the water permittivity of rigid IPA membranes due to the synergistic effects of increased alkyl chain ordering and enhanced membrane mechanical modulus. The results provide molecular insights into the effects of molecular packing and mechanical deformations on the water permittivity of biomimetic IPA membranes, which is critical for designing IPA vesicular carriers.

Importance of Hydrophilic Groups on Modulating the Structural, Mechanical, and Interfacial Properties of Bilayers: A Comparative Molecular Dynamics Study of Phosphatidylcholine and Ion Pair Amphiphile Membranes.

An ion pair amphiphile (IPA), a molecular complex composed of two oppositely charged amphiphiles, is a phospholipid mimic which differs from a phospholipid only in the hydrophilic compositions. Here, we utilized molecular dynamics (MD) simulations to compare the bilayer systems composed of phosphatidylcholines (PC) and alkyltrimethylammonium-alkylsulfate IPAs with various alkyl chain lengths. The membrane properties for both liquid-disordered (Ld) and gel (S) phase bilayers were examined via running simulations above and below the main transition temperatures. The electrostatic attraction between the IPA hydrophilic groups leads to a more ordered molecular packing within both S and Ld phase IPA membranes, as revealed by the molecular area, deuterium order parameter, and gauche conformation analyses. Furthermore, IPA bilayers possess a higher area compressibility modulus, molecular tilt modulus, and effective bending rigidity than PC systems. The variation of hydrophilic groups of IPA also leads to fewer hydrogen bonds on the membrane surface and smaller electrostatic potentials for the biomimetic bilayer. The non-covalently linked head groups of IPA further decouple alkyl tilting and surface water retention. The combined results reveal the importance of hydrophilic groups of amphiphiles on modulating the membrane properties, which also provides insights for designs of biomimetic membranes.

The Effects of Alkyl Chain Combinations on the Structural and Mechanical Properties of Biomimetic Ion Pair Amphiphile Bilayers.

Ion pair amphiphile (IPA), a lipid-like complex composed of a pair of cationic and anionic surfactants, has great potentials in various pharmaceutical applications. In this work, we utilized molecular dynamics (MD) simulation to systematically examine the structural and mechanical properties of the biomimetic bilayers consist of alkyltrimethyl-ammonium-alkylsulfate (CmTMA⁺-CnS-) IPAs with various alkyl chain combinations. Our simulations show an intrinsic one-atom offset for the CmTMA⁺ and CnS- alignment, leading to the asymmetric index definition of ΔC = m - (n + 1). Larger |ΔC| gives rise to higher conformational fluctuations of the alkyl chains with the reduced packing order and mechanical strength. In contrast, increasing the IPA chain length enhances the van der Waals interactions within the bilayer and thus improves the bilayer packing order and mechanical properties. Further elongating the CmTMA⁺-CnS- alkyl chains to m and n ≥ 12 causes the liquid disorder to gel phase transition of the bilayer at 298 K, with the threshold membrane properties of 0.45 nm² molecular area, deuterium order parameter value of 0.31, and effective bending rigidity of 20 kBT, etc. The combined results provide molecular insights into the design of biomimetic IPA bilayers with wide structural and mechanical characteristics for various applications.

Interplay between alkyl chain asymmetry and cholesterol addition in the rigid ion pair amphiphile bilayer systems.

Ion pair amphiphile (IPA), a molecular complex composed of a pair of cationic and anionic surfactants, has been proposed as a novel phospholipid substitute. Controlling the physical stability of IPA vesicles is important for its application developments such as cosmetic and drug deliveries. To investigate the effects of IPA alkyl chain combinations and the cholesterol additive on the structural and mechanical properties of IPA vesicular bilayers, we conducted a series of molecular dynamics studies on the hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dodecyltrimethylammonium-hexadecylsulfate (DTMA-HS) IPA bilayers with cholesterol. We found that both IPA bilayers are in the gel phase at 298 K, consistent with experimental observations. Compared with the HTMA-DS system, the DTMA-HS bilayer has more disordered alkyl chains in the hydrophobic region. When adding cholesterol, it induces alkyl chain ordering around its rigid sterol ring. Yet, cholesterol increases the molecular areas for all species and disturbs the molecular packing near the hydrophilic region and the bilayer core. Cholesterol also promotes the alkyl chain mismatch between the IPA moieties, especially for the DTMA-HS bilayer. The combined effects lead to non-monotonically enhancement of the membrane mechanical moduli for both IPA-cholesterol systems. Furthermore, cholesterol can form H-bonds with the alkylsulfate and thus enhance the contribution of alkylsulfate to the overall mechanical moduli. Combined results provide valuable molecular insights into the roles of each IPA component and the cholesterol on modulating the IPA bilayer properties.

Secondary Structure of Rat and Human Amylin across Force Fields.

The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and ß-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and ß-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards ß-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils.

Basis function sampling: a new paradigm for material property computation.

Wang-Landau sampling, and the associated class of flat histogram simulation methods have been remarkably helpful for calculations of the free energy in a wide variety of physical systems. Practically, convergence of these calculations to a target free energy surface is hampered by reliance on parameters which are unknown a priori. Here, we derive and implement a method built upon orthogonal functions which is fast, parameter-free, and (importantly) geometrically robust. The method is shown to be highly effective in achieving convergence. An important feature of this method is its ability to attain arbitrary levels of description for the free energy. It is thus ideally suited to in silico measurement of elastic moduli and other material properties related to free energy perturbations. We demonstrate the utility of such applications by applying our method to calculate the Frank elastic constants of the Lebwohl-Lasher model of liquid crystals.

Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient ß-sheet.

Amyloid formation is implicated in more than 20 human diseases, yet the mechanism by which fibrils form is not well understood. We use 2D infrared spectroscopy and isotope labeling to monitor the kinetics of fibril formation by human islet amyloid polypeptide (hIAPP or amylin) that is associated with type 2 diabetes. We find that an oligomeric intermediate forms during the lag phase with parallel ß-sheet structure in a region that is ultimately a partially disordered loop in the fibril. We confirm the presence of this intermediate, using a set of homologous macrocyclic peptides designed to recognize ß-sheets. Mutations and molecular dynamics simulations indicate that the intermediate is on pathway. Disrupting the oligomeric ß-sheet to form the partially disordered loop of the fibrils creates a free energy barrier that is the origin of the lag phase during aggregation. These results help rationalize a wide range of previous fragment and mutation studies including mutations in other species that prevent the formation of amyloid plaques.

Effect of proline mutations on the monomer conformations of amylin.

The formation of human islet amyloid polypeptide (hIAPP) is implicated in the loss of pancreatic ß-cells in type II diabetes. Rat amylin, which differs from human amylin at six residues, does not lead to formation of amyloid fibrils. Pramlintide is a synthetic analog of human amylin that shares three proline substitutions with rat amylin. Pramlintide has a much smaller propensity to form amyloid aggregates and has been widely prescribed in amylin replacement treatment. It is known that the three prolines attenuate ß-sheet formation. However, the detailed effects of these proline substitutions on full-length hIAPP remain poorly understood. In this work, we use molecular simulations and bias-exchange metadynamics to investigate the effect of proline substitutions on the conformation of the hIAPP monomer. Our results demonstrate that hIAPP can adopt various ß-sheet conformations, some of which have been reported in experiments. The proline substitutions perturb the formation of long ß-sheets and reduce their stability. More importantly, we find that all three proline substitutions of pramlintide are required to inhibit ß conformations and stabilize the α-helical conformation. Fewer substitutions do not have a significant inhibiting effect.

α-helix to ß-hairpin transition of human amylin monomer.

The human islet amylin polypeptide is produced along with insulin by pancreatic islets. Under some circumstances, amylin can aggregate to form amyloid fibrils, whose presence in pancreatic cells is a common pathological feature of Type II diabetes. A growing body of evidence indicates that small, early stage aggregates of amylin are cytotoxic. A better understanding of the early stages of the amylin aggregation process and, in particular, of the nucleation events leading to fibril growth could help identify therapeutic strategies. Recent studies have shown that, in dilute solution, human amylin can adopt an α-helical conformation, a ß-hairpin conformation, or an unstructured coil conformation. While such states have comparable free energies, the ß-hairpin state exhibits a large propensity towards aggregation. In this work, we present a detailed computational analysis of the folding pathways that arise between the various conformational states of human amylin in water. A free energy surface for amylin in explicit water is first constructed by resorting to advanced sampling techniques. Extensive transition path sampling simulations are then employed to identify the preferred folding mechanisms between distinct minima on that surface. Our results reveal that the α-helical conformer of amylin undergoes a transformation into the ß-hairpin monomer through one of two mechanisms. In the first, misfolding begins through formation of specific contacts near the turn region, and proceeds via a zipping mechanism. In the second, misfolding occurs through an unstructured coil intermediate. The transition states for these processes are identified. Taken together, the findings presented in this work suggest that the inter-conversion of amylin between an α-helix and a ß-hairpin is an activated process and could constitute the nucleation event for fibril growth.