Self-Assembly of Exendin-4-Derived Dual Peptide Agonists is Mediated by Acylation and Correlated to the Length of Conjugated Fatty Acyl Chains.

Dual glucagon-like peptide-1/glucagon receptor agonists have emerged as promising candidates for the treatment of diabetes and obesity. Issues of degradation sensitivity and rapid renal clearance are addressed, for example, by the conjugation of peptides to fatty acid chains, promoting reversible albumin binding. We use combined dynamic and static light scattering to directly measure the self-assembly of a set of dual peptide agonists based on the exendin-4 structure with varying fatty acid chain lengths in terms of apparent molecular mass and hydrodynamic radius (RS). We use NMR spectroscopy to gain an insight into the molecular architecture of the assembly. We investigate conformational changes of the monomeric subunits resulting from peptide self-assembly and assembly stability as a function of the fatty acid chain length using circular dichroism and fluorescence spectroscopy. Our results demonstrate that self-assembly of the exendin-4-derived dual agonist peptides is essentially driven by hydrophobic interactions involving the conjugated acyl chains. The fatty acid chain length affects assembly equilibria and the assembly stability, although the peptide subunits in the assembly retain a dynamic secondary structure. The assembly architecture is characterized by juxtaposition of the fatty acyl side chains and a hydrophobic cluster of the peptide moiety. This cluster experiences local conformational changes in the assembly compared to the monomeric unit leading to a reduction in solvent exposure. The N-terminal half of the peptide and a C-terminal loop are not in contact with neighboring peptide subunits in the assemblies. Altogether, our study contributes to a thorough understanding of the association characteristics and the tendency toward self-assembly in response to lipidation. This is important not only to achieve the desired bioavailability but also with respect to the physical stability of peptide solutions.

Rapid-Acting and Human Insulins: Hexamer Dissociation Kinetics upon Dilution of the Pharmaceutical Formulation.

PURPOSE: Comparison of the dissociation kinetics of rapid-acting insulins lispro, aspart, glulisine and human insulin under physiologically relevant conditions. METHODS: Dissociation kinetics after dilution were monitored directly in terms of the average molecular mass using combined static and dynamic light scattering. Changes in tertiary structure were detected by near-UV circular dichroism. RESULTS: Glulisine forms compact hexamers in formulation even in the absence of Zn2+. Upon severe dilution, these rapidly dissociate into monomers in less than 10 s. In contrast, in formulations of lispro and aspart, the presence of Zn2+ and phenolic compounds is essential for formation of compact R6 hexamers. These slowly dissociate in times ranging from seconds to one hour depending on the concentration of phenolic additives. The disadvantage of the long dissociation times of lispro and aspart can be diminished by a rapid depletion of the concentration of phenolic additives independent of the insulin dilution. This is especially important in conditions similar to those after subcutaneous injection, where only minor dilution of the insulins occurs. CONCLUSION: Knowledge of the diverging dissociation mechanisms of lispro and aspart compared to glulisine will be helpful for optimizing formulation conditions of rapid-acting insulins.

Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.

There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing denaturant concentration, but several studies using small-angle X-ray scattering (SAXS) have reported no such increase of the radius of gyration (Rg). This inconsistency challenges our current understanding of the mechanism of chemical denaturants, which are widely employed to investigate protein folding and stability. Here, we use a combination of single-molecule Förster resonance energy transfer (FRET), SAXS, dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) to characterize the denaturant dependence of the unfolded state of the spectrin domain R17 and the intrinsically disordered protein ACTR in two different denaturants. Standard analysis of the primary data clearly indicates an expansion of the unfolded state with increasing denaturant concentration irrespective of the protein, denaturant, or experimental method used. This is the first case in which SAXS and FRET have yielded even qualitatively consistent results regarding expansion in denaturant when applied to the same proteins. To more directly illustrate this self-consistency, we used both SAXS and FRET data in a Bayesian procedure to refine structural ensembles representative of the observed unfolded state. This analysis demonstrates that both of these experimental probes are compatible with a common ensemble of protein configurations for each denaturant concentration. Furthermore, the resulting ensembles reproduce the trend of increasing hydrodynamic radius with denaturant concentration obtained by 2f-FCS and DLS. We were thus able to reconcile the results from all four experimental techniques quantitatively, to obtain a comprehensive structural picture of denaturant-induced unfolded state expansion, and to identify the most likely sources of earlier discrepancies.

Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy.

The dimensions of unfolded and intrinsically disordered proteins are highly dependent on their amino acid composition and solution conditions, especially salt and denaturant concentration. However, the quantitative implications of this behavior have remained unclear, largely because the effective theta-state, the central reference point for the underlying polymer collapse transition, has eluded experimental determination. Here, we used single-molecule fluorescence spectroscopy and two-focus correlation spectroscopy to determine the theta points for six different proteins. While the scaling exponents of all proteins converge to 0.62 ± 0.03 at high denaturant concentrations, as expected for a polymer in good solvent, the scaling regime in water strongly depends on sequence composition. The resulting average scaling exponent of 0.46 ± 0.05 for the four foldable protein sequences in our study suggests that the aqueous cellular milieu is close to effective theta conditions for unfolded proteins. In contrast, two intrinsically disordered proteins do not reach the Θ-point under any of our solvent conditions, which may reflect the optimization of their expanded state for the interactions with cellular partners. Sequence analyses based on our results imply that foldable sequences with more compact unfolded states are a more recent result of protein evolution.

Identification of a bis-molybdopterin intermediate in molybdenum cofactor biosynthesis in Escherichia coli.

The molybdenum cofactor is an important cofactor, and its biosynthesis is essential for many organisms, including humans. Its basic form comprises a single molybdopterin (MPT) unit, which binds a molybdenum ion bearing three oxygen ligands via a dithiolene function, thus forming Mo-MPT. In bacteria, this form is modified to form the bis-MPT guanine dinucleotide cofactor with two MPT units coordinated at one molybdenum atom, which additionally contains GMPs bound to the terminal phosphate group of the MPTs (bis-MGD). The MobA protein catalyzes the nucleotide addition to MPT, but the mechanism of the biosynthesis of the bis-MGD cofactor has remained enigmatic. We have established an in vitro system for studying bis-MGD assembly using purified compounds. Quantification of the MPT/molybdenum and molybdenum/phosphorus ratios, time-dependent assays for MPT and MGD detection, and determination of the numbers and lengths of Mo-S and Mo-O bonds by X-ray absorption spectroscopy enabled identification of a novel bis-Mo-MPT intermediate on MobA prior to nucleotide attachment. The addition of Mg-GTP to MobA loaded with bis-Mo-MPT resulted in formation and release of the final bis-MGD product. This cofactor was fully functional and reconstituted the catalytic activity of apo-TMAO reductase (TorA). We propose a reaction sequence for bis-MGD formation, which involves 1) the formation of bis-Mo-MPT, 2) the addition of two GMP units to form bis-MGD on MobA, and 3) the release and transfer of the mature cofactor to the target protein TorA, in a reaction that is supported by the specific chaperone TorD, resulting in an active molybdoenzyme.

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins.

We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With single-molecule FRET, this question can be addressed even under near-native conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both the presence and the absence of denaturant, with good agreement between the results from single-molecule FRET and dynamic light scattering. Although dissociation of denaturant from the polypeptide chain with increasing temperature accounts for part of the compaction, the results indicate an important role for additional temperature-dependent interactions within the unfolded chain. The observation of a collapse of a similar extent in the extremely hydrophilic, intrinsically disordered protein prothymosin alpha suggests that the hydrophobic effect is not the sole source of the underlying interactions. Circular dichroism spectroscopy and replica exchange molecular dynamics simulations in explicit water show changes in secondary structure content with increasing temperature and suggest a contribution of intramolecular hydrogen bonding to unfolded state collapse.

Three-dimensional mapping of the B1 field using an optimized phase-based method: application to hyperpolarized 3He in lungs.

A novel method is presented for the three-dimensional mapping of the B(1) -field of a transmit radio-frequency MR coil. The method is based on the acquisition of phase images, where the effective flip angle is encoded in the phase of the nonselective hard pulse excitation. The method involves the application of a rectangular composite pulse as excitation in a three-dimensional gradient recall echo to produce measurable phase angle variation. However, such a pulse may significantly increase the radio-frequency power deposition in excess of the standard acceptable SAR limits, imposing extremely long TRs (>100 msec), which would result in acquisition times significantly greater than a single breath-hold. In this study, the phases of the radio-frequency excitation are modified, resulting in a different pulse sequence scheme. It is shown that the new method increases sensitivity with respect to radio-frequency inhomogeneities by up to 10 times, and reduces the total duration of the pulse so that three-dimensional B(1) mapping is possible with (3) He in lungs within a single breath-hold. Computer simulations demonstrate the increase in sensitivity. Phantom results with (1) H MRI are used for validation. In vivo results are presented with hyperpolarized (3) He in human lungs at 1.5T.

A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4.

Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix-helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers.

Early stages of misfolding and association of beta2-microglobulin: insights from infrared spectroscopy and dynamic light scattering.

Conformational changes associated with the assembly of recombinant beta 2-microglobulin in vitro under acidic conditions were investigated using infrared spectroscopy and static and dynamic light scattering. In parallel, the morphology of the different aggregated species obtained under defined conditions was characterized by electron microscopy. The initial salt-induced aggregate form of beta 2-microglobulin, composed of small oligomers (dimers to tetramers), revealed the presence of beta-strands organized in an intramolecular-like fashion. Further particle growth was accompanied by the formation of intermolecular beta-sheet structure and led to short curved forms. An increase in temperature by only 25 degrees C was able to disaggregate these assemblies, followed by the formation of longer filamentous structures. In contrast, a rise in temperature up to 100 degrees C was associated with a reorganization of the short curved forms at the level of secondary structure and the state of assembly, leading to a species with a characteristic infrared spectrum different from those of all the other aggregates observed before, suggesting a unique overall structure. The infrared spectral features of this species were nearly identical to those of beta 2-microglobulin assemblies formed at low ionic strength with agitation, indicating the presence of fibrils, which was confirmed by electron microscopy. The observed spectroscopic changes suggest that the heat-triggered conversion of the short curved assemblies into fibrils involves a reorganization of the beta-strands from an antiparallel arrangement to a parallel arrangement, with the latter being characteristic of amyloid fibrils of beta 2-microglobulin.

Intrapulmonary 3He gas distribution depending on bolus size and temporal bolus placement.

OBJECTIVE: Dynamic ventilation (3)He-MRI is a new method to assess pulmonary gas inflow. As differing airway diameters throughout the ventilatory cycle can influence gas inflow this study intends to investigate the influence of volume and timing of a He gas bolus with respect to the beginning of the tidal volume on inspiratory gas distribution. MATERIALS AND METHODS: An ultrafast 2-dimensional spoiled gradient echo sequence (temporal resolution 100 milliseconds) was used for dynamic ventilation (3)He-MRI of 11 anesthetized and mechanically ventilated pigs. The applied (3)He gas bolus was varied in volume between 100 and 200 mL. A 150-mL bolus was varied in its application time after the beginning of the tidal volume between 0 and 1200 milliseconds. Signal kinetics were evaluated using an in-house developed software after definition of parameters for the quantitative description of (3)He gas inflow. RESULTS: The signal rise time (time interval between signal in the parenchyma reaches 10% and 90% of its maximum) was prolonged with increasing bolus volume. The parameter was shortened with increasing delay of (3)He application after the beginning of the tidal volume. Timing variation as well as volume variation showed no clear interrelation to the signal delay time 10 (time interval between signal in the trachea reaches 50% of its maximum and signal in the parenchyma reaches 10% of its maximum). CONCLUSIONS: Dynamic ventilation (3)He-MRI is able to detect differences in bolus geometry performed by volume variation. Pulmonary gas inflow as investigated by dynamic ventilation (3)He-MRI tends to be accelerated by an increasing application delay of a (3)He gas bolus after the beginning of the tidal volume.

Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".

Riback et al (Reports, 13 October 2017, p. 238) used small-angle x-ray scattering (SAXS) experiments to infer a degree of compaction for unfolded proteins in water versus chemical denaturant that is highly consistent with the results from Förster resonance energy transfer (FRET) experiments. There is thus no "contradiction" between the two methods, nor evidence to support their claim that commonly used FRET fluorophores cause protein compaction.

Involvement of jugular valve insufficiency in cerebral venous air embolism.

BACKGROUND: Cerebral venous air entrapment is a rare finding on cranial computed tomography (CT) scan. Peripheral air embolism is discussed as a potential cause. However, the mechanism of retrograde passage through internal jugular valves and veins is unclear. CASE REPORT: The case of a patient is reported, who had air entrapment in the left cavernous sinus. Prior to CT scanning, a peripheral intravenous line had been placed. Ultrasound revealed excessive insufficiency of the left internal jugular valve. To further study the mechanism of embolism, an echo contrast agent was injected into the cubital vein. A Valsalva maneuver resulted in retrograde transition of microbubbles across the insufficient valve. Valvular function on the unaffected right side was intact. CONCLUSIONS: This case report gives insight into the mechanism of cerebral venous air embolism. This is the firstcase describing jugular valve insufficiency as the missing link between peripheral air embolism and cerebral venous air entrapment.

[Microstructure of the lung: diffusion measurement of hyperpolarized 3Helium]. / Mikrostruktur der Lunge: Untersuchung mittels Diffusionsmessung von hochpolarisiertem 3Helium.

Imaging methods to study the lung are traditionally based on x-ray or on radioactive contrast agents. Conventional magnetic resonance imaging (MRI) has only limited applications for lung imaging because of the low tissue density of protons concentration of hydrogen atoms, which are usually the basis for the imaging. The introduction of hyperpolarized noble gases as a contrast agent in MRI has opened new possibilities for lung diagnosis. The present paper describes this new technique. Diffusion-weighted MRI for assessment of the lung microstructure is presented here as an example of the new possibilities of functional imaging. Studies to determine the sensitivity of the diffusion measurement and regarding the correlation with traditionally established methods are also presented, along with results of the measurement of the reproducibility determined in a clinical pilot study on healthy volunteers and patients. Furthermore, a pilot measurement of the 3He diffusion tensor in the lung is presented.

Assessment of lung microstructure with magnetic resonance imaging of hyperpolarized Helium-3.

Magnetic resonance imaging of the apparent diffusion coefficient (ADC) of hyperpolarized Helium-3 is a new technique for probing pulmonary microstructure in vivo. The aim of this study was the assessment of potential sources of systematic errors of the ADC measurement. The influence of macroscopic motion was determined by measurements at two different delays after initiating the breath-hold, and before and after cardiac arrest. An intercentre comparison was performed in two age- and lung function-matched groups of lung-healthy volunteers at two research sites. Moreover, measurements of diffusion anisotropy were performed. We found no dependency of the ADC as a function of the delay after stop of inspiration. The influence of cardiac motion was less than 10%. In the intercentre comparison study, an excellent agreement between the two sites was found. First measurements of the diffusion tensor of intrapulmonary Helium-3 are shown.

[Hyperpolarized (3)helium gas for functional magnetic resonance imaging of the lung]. / Funktionelle MRT der Lunge unter Verwendung von hyperpolarisiertem 3Helium-Gas.

Lung imaging is traditionally done using X-ray-based methods, since MRI is limited by low proton density as well as inherent magnetic field inhomogeneities of the lung tissue. After introduction of MRI using hyperpolarized noble gases, a totally new field of MRI of the chest has rapidly evolved. These techniques reveal new functional information of the lungs, which could not be obtained before. The first part of this review describes the underlying MR technology explaining distribution of static ventilation, dynamic distribution of ventilation, lung microstructure (apparent diffusion coefficient [ADC]), measurement of oxygen partial pressure (pO(2)), and safety. The clinical potential is afterwards demonstrated in the second part. Therefore, the effort in normal lungs and the mainly focused diseases chronic obstructive pulmonary disease (COPD), smoker's lung, cystic fibrosis, asthma, lung transplantation, and pulmonary embolism are reported.

Functional analysis in single-lung transplant recipients: a comparative study of high-resolution CT, 3He-MRI, and pulmonary function tests.

OBJECTIVE: To develop and evaluate a postprocessing tool to quantify ventilated split-lung volumes on the basis of (3)He-MRI and to apply it in patients after single-lung transplantation (SLTX). High-resolution CT (HRCT) was employed as a reference modality providing split air-filled lung volumes. Lung volumes derived from pulmonary function test results served as clinical parameters and were used as the "gold standard." MATERIAL AND METHODS: Eight patients (mean age, 54 years) with emphysema and six patients (mean age, 58 years) with idiopathic pulmonary fibrosis. All patients were evaluated following SLTX. HRCT was performed during inspiration (slice thickness, 1 mm; increment, 10 mm). For correlation with (3)He-MRI, HRCT images were reconstructed in coronal orientation to match the same anatomic levels. Aerated lung was determined by threshold-based segmentation of CT. (3)He-MRI was performed on a 1.5-T scanner using a two-dimensional, fast low-angle shot sequence in coronal orientation covering the whole lung after inhalation of a 300-mL bolus of hyperpolarized (3)He gas followed by normal room air for the rest of the tidal volume. Lung segmentation on (3)He-MRI was done using different thresholds. RESULTS: In emphysematous patients, (3)He-MRI showed excellent correlation (r = 0.9) with vital capacity, while CT correlated (r = 0.8) with total lung capacity. (3)He-MRI correlated well with CT (r > 0.8) for grafts and native fibrotic lungs. In emphysematous lungs, MRI showed a good correlation (r = 0.7) with the nonemphysematous lung volume from CT. Increasing thresholds in (3)He-MRI reveal differences between aerated and ventilated lung areas with a different distribution in emphysema and fibrosis. CONCLUSIONS: (3)He-MRI is superior to CT in emphysema to demonstrate ventilated lung areas that participate in gas exchange. In fibrosis, (3)He-MRI and CT have a similar impact. The decrease pattern and the intraindividual ratio between ventilation of native and transplanted lungs will have to be investigated as a new surrogate for the ventilatory follow-up in patients undergoing SLTX.

Functional evaluation of emphysema using diffusion-weighted 3Helium-magnetic resonance imaging, high-resolution computed tomography, and lung function tests.

PURPOSE: To assess the emphysematous enlargement of distal airspaces and concomitant large and small airway disease using diffusion-weighted Helium-magnetic resonance imaging (MRI), high-resolution computed tomography (HRCT), and lung function tests (LFT). METHODS: Seven patients were examined after single lung transplantation (LTx) and 1 before double LTx for various forms of emphysema. Five patients after double LTx served as controls. Patients were assessed by Helium-MRI (apparent diffusion coefficient [ADC]), HRCT (mean lung density [MLD], emphysema index [EI]), and LFT. RESULTS: Transplanted lungs: mean ADC = 0.17 cm/s, MLD = -848 H, EI = 22%. Emphysematous lungs: mean ADC = 0.33 cm/s, MLD = -922 H; EI = 54%. Good correlations were found between ADC and MLD (r = 0.6), EI (r = 0.8), intrathoracic gas volume (r = 0.7), forced expiratory volume in 1 second (r = 0.7), and forced expiratory flows (r = 0.7). In contrast, HRCT only provided moderate correlations with LFT (EI: r = 0.5; MLD: r [le] 0.4). CONCLUSION: In this initial study, He-MRI yield good correlations with HRCT and agrees better than HRCT with the functional characterization of emphysema regarding hyperinflation, large and small airway disease as provided by LFT.

Distribution of ventilation in lung transplant recipients: evaluation by dynamic 3He-MRI with lung motion correction.

RATIONALE AND OBJECTIVES: The ability of motion corrected dynamic 3He-magnetic resonance imaging (MRI) to discriminate distributional patterns of inhaled hyperpolarized 3He between different groups of lung transplant recipients was evaluated. METHODS: An ultrafast low-angle shot 2D sequence (temporal resolution 128 ms) was used for ventilation 3He-MRI of 11 single and 6 double lung transplant recipients. After digital motion correction, signal kinetics were evaluated in a tracheal and 7 pulmonary regions of interest. Results from grafts and native lungs as well as from normal and rejected grafts were compared with each other and to reference values from healthy subjects. RESULTS: In emphysema patients, median alveolar rise time, a parameter for increase of alveolar signal, was 0.28 seconds for the graft and 0.48 seconds for the native lung, in fibrosis patients its median was 0.46 seconds for the graft and 0.21 seconds for the native lung. In double lung recipients, alveolar rise time was 0.29 seconds in normal and clinically rejected grafts. CONCLUSIONS: Dynamic ventilation 3He-MRI discriminated normal lung grafts from diseased native lungs in single lung recipients. Graft rejection in double lung recipients could not be discriminated.

Dynamic ventilation (3)He-magnetic resonance imaging with lung motion correction: gas flow distribution analysis.

RATIONALE AND OBJECTIVES: Software was developed to correct for lung motion to improve the description of hyperpolarized (3)He gas distribution in the lung. METHODS: Five volunteers were studied by dynamic ventilation (3)He-MRI using an ultrafast FLASH 2D sequence with a temporal resolution of 128 milliseconds. Signal kinetics were evaluated in the trachea and seven parenchymal Regions of Interest. Reference ranges for healthy subjects were defined for motion-corrected and uncorrected images. RESULTS: Motion correction was successfully performed. Reference ranges were 0.11-1.21 seconds for tracheal transit time, 0-0.02 seconds for trachea-alveolar interval, 0.22-0.62 seconds for alveolar rise time and 0-76.6 arbitrary units for alveolar amplitude for motion corrected images, and 0-1.09 seconds, 0-0.11 seconds, 0.26-0.85 seconds, 46.4-99.8 arbitrary units for uncorrected images. CONCLUSIONS: Evaluation of (3)He-distribution in the lung using motion correction of dynamic (3)He-ventilation imaging is feasible and gives more narrow reference ranges.

Polymerization of proteins into amyloid protofibrils shares common critical oligomeric states but differs in the mechanisms of their formation.

Amyloid protofibril formation of phosphoglycerate kinase (PGK) and Syrian hamster prion protein (SHaPrP(90-232)) were investigated by static and dynamic light scattering, size exclusion chromatography and electron microscopy. Changes in secondary structure were monitored by Fourier transform infrared spectroscopy and by circular dichroism. Protofibril formation of the two proteins is found to be a two-stage process. At the beginning, an ensemble of critical oligomers is built up. These critical oligomeric states possess a predominant beta-sheet structure and do not interact considerably with monomers. Initial oligomerization and transition to beta-sheet structure are coupled events differing in their details for both proteins. Intermediate oligomeric states (dimers, trimers, etc.) are populated in case of PGK, whereas SHaPrP(90-232) behaves according to an apparent two-state reaction between monomers and octamers rich in beta-structure with a reaction order varying between 2 and 4. All oligomers coalesce to PGK protofibrils in the second stage, while SHaPrP(90-232) protofibrils are only formed by a subpopulation. The rates of both growth stages can be tuned in case of PGK by different salts preserving the underlying generalized diffusion-collision mechanism. The different kinetics of the early misfolding and oligomerization events of the two proteins argue against a common mechanism of protofibril formation. A classification scheme for misassembly mechanisms of proteins based on energy landscapes is presented. It includes scenarios of downhill polymerization to which protofibril formation of PGK and SHaPrP(90-232) belong.