51
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Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences. PLoS Comput Biol 2015; 11:e1004207. [PMID: 25905910 PMCID: PMC4407897 DOI: 10.1371/journal.pcbi.1004207] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/20/2015] [Indexed: 12/28/2022] Open
Abstract
Design of proteins with desired thermal properties is important for scientific and biotechnological applications. Here we developed a theoretical approach to predict the effect of mutations on protein stability from non-equilibrium unfolding simulations. We establish a relative measure based on apparent simulated melting temperatures that is independent of simulation length and, under certain assumptions, proportional to equilibrium stability, and we justify this theoretical development with extensive simulations and experimental data. Using our new method based on all-atom Monte-Carlo unfolding simulations, we carried out a saturating mutagenesis of Dihydrofolate Reductase (DHFR), a key target of antibiotics and chemotherapeutic drugs. The method predicted more than 500 stabilizing mutations, several of which were selected for detailed computational and experimental analysis. We find a highly significant correlation of r = 0.65–0.68 between predicted and experimentally determined melting temperatures and unfolding denaturant concentrations for WT DHFR and 42 mutants. The correlation between energy of the native state and experimental denaturation temperature was much weaker, indicating the important role of entropy in protein stability. The most stabilizing point mutation was D27F, which is located in the active site of the protein, rendering it inactive. However for the rest of mutations outside of the active site we observed a weak yet statistically significant positive correlation between thermal stability and catalytic activity indicating the lack of a stability-activity tradeoff for DHFR. By combining stabilizing mutations predicted by our method, we created a highly stable catalytically active E. coli DHFR mutant with measured denaturation temperature 7.2°C higher than WT. Prediction results for DHFR and several other proteins indicate that computational approaches based on unfolding simulations are useful as a general technique to discover stabilizing mutations. All-atom molecular simulations have provided valuable insight into the workings of molecular machines and the folding and unfolding of proteins. However, commonly employed molecular dynamics simulations suffer from a limitation in accessible time scale, making it difficult to model large-scale unfolding events in a realistic amount of simulation time without employing unrealistically high temperatures. Here, we describe a rapid all-atom Monte Carlo simulation approach to simulate unfolding of the essential bacterial enzyme Dihydrofolate Reductase (DHFR) and all possible single point-mutants. We use these simulations to predict which mutants will be more thermodynamically stable (i.e., reside more often in the native folded state vs. the unfolded state) than the wild-type protein, and we confirm our predictions experimentally, creating several highly stable and catalytically active mutants. Thermally stable active engineered proteins can be used as a starting point in directed evolution experiments to evolve new functions on the background of this additional “reservoir of stability.” The stabilized enzyme may be able to accumulate a greater number of destabilizing yet functionally important mutations before unfolding, protease digestion, and aggregation abolish its activity.
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Kim SB, Dsilva CJ, Kevrekidis IG, Debenedetti PG. Systematic characterization of protein folding pathways using diffusion maps: Application to Trp-cage miniprotein. J Chem Phys 2015; 142:085101. [DOI: 10.1063/1.4913322] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Carmeline J. Dsilva
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Ioannis G. Kevrekidis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
| | - Pablo G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
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53
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Krobath H, Rey A, Faísca PFN. How determinant is N-terminal to C-terminal coupling for protein folding? Phys Chem Chem Phys 2015; 17:3512-24. [DOI: 10.1039/c4cp05178e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The existence of native interactions between the protein termini is a major determinant of the free energy barrier in a two-state folding transition being therefore a critical modulator of protein folding cooperativity.
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Affiliation(s)
- Heinrich Krobath
- Centro de Física da Matéria Condensada and Departamento de Física
- Faculdade de Ciências da Universidade de Lisboa
- Portugal
| | - Antonio Rey
- Departamento de Química Física I
- Facultad de Ciencias Químicas
- Universidad Complutense
- Madrid
- Spain
| | - Patrícia F. N. Faísca
- Centro de Física da Matéria Condensada and Departamento de Física
- Faculdade de Ciências da Universidade de Lisboa
- Portugal
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54
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Banerjee PR, Deniz AA. Shedding light on protein folding landscapes by single-molecule fluorescence. Chem Soc Rev 2014; 43:1172-88. [PMID: 24336839 DOI: 10.1039/c3cs60311c] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Single-molecule (SM) fluorescence methods have been increasingly instrumental in our current understanding of a number of key aspects of protein folding and aggregation landscapes over the past decade. With the advantage of a model free approach and the power of probing multiple subpopulations and stochastic dynamics directly in a heterogeneous structural ensemble, SM methods have emerged as a principle technique for studying complex systems such as intrinsically disordered proteins (IDPs), globular proteins in the unfolded basin and during folding, and early steps of protein aggregation in amyloidogenesis. This review highlights the application of these methods in investigating the free energy landscapes, folding properties and dynamics of individual protein molecules and their complexes, with an emphasis on inherently flexible systems such as IDPs.
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Affiliation(s)
- Priya R Banerjee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
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55
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Sinner C, Lutz B, John S, Reinartz I, Verma A, Schug A. Simulating Biomolecular Folding and Function by Native-Structure-Based/Go-Type Models. Isr J Chem 2014. [DOI: 10.1002/ijch.201400012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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56
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Matsuoka M, Kikuchi T. Sequence analysis on the information of folding initiation segments in ferredoxin-like fold proteins. BMC STRUCTURAL BIOLOGY 2014; 14:15. [PMID: 24884463 PMCID: PMC4055915 DOI: 10.1186/1472-6807-14-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/15/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND While some studies have shown that the 3D protein structures are more conservative than their amino acid sequences, other experimental studies have shown that even if two proteins share the same topology, they may have different folding pathways. There are many studies investigating this issue with molecular dynamics or Go-like model simulations, however, one should be able to obtain the same information by analyzing the proteins' amino acid sequences, if the sequences contain all the information about the 3D structures. In this study, we use information about protein sequences to predict the location of their folding segments. We focus on proteins with a ferredoxin-like fold, which has a characteristic topology. Some of these proteins have different folding segments. RESULTS Despite the simplicity of our methods, we are able to correctly determine the experimentally identified folding segments by predicting the location of the compact regions considered to play an important role in structural formation. We also apply our sequence analyses to some homologues of each protein and confirm that there are highly conserved folding segments despite the homologues' sequence diversity. These homologues have similar folding segments even though the homology of two proteins' sequences is not so high. CONCLUSION Our analyses have proven useful for investigating the common or different folding features of the proteins studied.
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Affiliation(s)
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan.
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57
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Shao Q. Probing Sequence Dependence of Folding Pathway of α-Helix Bundle Proteins through Free Energy Landscape Analysis. J Phys Chem B 2014; 118:5891-900. [DOI: 10.1021/jp5043393] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qiang Shao
- Drug Discovery and Design
Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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58
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Orevi T, Rahamim G, Shemesh S, Ben Ishay E, Amir D, Haas E. Fast closure of long loops at the initiation of the folding transition of globular proteins studied by time-resolved FRET-based methods. BIO-ALGORITHMS AND MED-SYSTEMS 2014. [DOI: 10.1515/bams-2014-0018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe protein folding problem would be considered “solved” when it will be possible to “read genes”, i.e., to predict the native fold of proteins, their dynamics, and the mechanism of fast folding based solely on sequence data. The long-term goal should be the creation of an algorithm that would simulate the stepwise mechanism of folding, which constrains the conformational space and in which random search for stable interactions is possible. Here, we focus attention on the initial phases of the folding transition starting with the compact disordered collapsed ensemble, in search of the initial sub-domain structural biases that direct the otherwise stochastic dynamics of the backbone. Our studies are designed to test the “loop hypothesis”, which suggests that fast closure of long loop structures by non-local interactions between clusters of mainly non-polar residues is an essential conformational step at the initiation of the folding transition of globular proteins. We developed and applied experimental methods based on time-resolved resonance excitation energy transfer (trFRET) measurements combined with fast mixing methods and studied the initial phases of the folding of
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59
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Krobath H, Shakhnovich EI, Faísca PFN. Structural and energetic determinants of co-translational folding. J Chem Phys 2014; 138:215101. [PMID: 23758397 DOI: 10.1063/1.4808044] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We performed extensive lattice Monte Carlo simulations of ribosome-bound stalled nascent chains (RNCs) to explore the relative roles of native topology and non-native interactions in co-translational folding of small proteins. We found that the formation of a substantial part of the native structure generally occurs towards the end of protein synthesis. However, multi-domain structures, which are rich in local interactions, are able to develop gradually during chain elongation, while those with proximate chain termini require full protein synthesis to fold. A detailed assessment of the conformational ensembles populated by RNCs with different lengths reveals that the directionality of protein synthesis has a fine-tuning effect on the probability to populate low-energy conformations. In particular, if the participation of non-native interactions in folding energetics is mild, the formation of native-like conformations is majorly determined by the properties of the contact map around the tethering terminus. Likewise, a pair of RNCs differing by only 1-2 residues can populate structurally well-resolved low energy conformations with significantly different probabilities. An interesting structural feature of these low-energy conformations is that, irrespective of native structure, their non-native interactions are always long-ranged and marginally stabilizing. A comparison between the conformational spectra of RNCs and chain fragments folding freely in the bulk reveals drastic changes amongst the two set-ups depending on the native structure. Furthermore, they also show that the ribosome may enhance (up to 20%) the population of low energy conformations for chains folding to native structures dominated by local interactions. In contrast, a RNC folding to a non-local topology is forced to remain largely unstructured but can attain low energy conformations in bulk.
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Affiliation(s)
- Heinrich Krobath
- Centro de Física da Matéria Condensada and Departamento de Física, Universidade de Lisboa, Av. Prof. Gama Pinto 2, 1649-003 Lisboa, Portugal
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60
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Kumar TKS, Sivaraman T, Samuel D, Srisailam S, Ganesh G, Hsieh HC, Hung KW, Peng HJ, Ho MC, Arunkumar AI, Yu C. Protein Folding and β-Sheet Proteins. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200000141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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61
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Abstract
This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin) can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation.
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Affiliation(s)
- Miguel A. Soler
- Centro de Física da Matéria Condensada, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Física, Universidade de Lisboa, Lisboa, Portugal
| | - Patrícia F. N. Faísca
- Centro de Física da Matéria Condensada, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Física, Universidade de Lisboa, Lisboa, Portugal
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62
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63
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Finkelstein AV, Bogatyreva NS, Garbuzynskiy SO. Restrictions to protein folding determined by the protein size. FEBS Lett 2013; 587:1884-90. [DOI: 10.1016/j.febslet.2013.04.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 04/28/2013] [Indexed: 10/26/2022]
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64
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Orevi T, Rahamim G, Hazan G, Amir D, Haas E. The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways. Biophys Rev 2013; 5:85-98. [PMID: 28510159 DOI: 10.1007/s12551-013-0113-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/01/2013] [Indexed: 12/12/2022] Open
Abstract
The extremely fast and efficient folding transition (in seconds) of globular proteins led to the search for some unifying principles embedded in the physics of the folding polypeptides. Most of the proposed mechanisms highlight the role of local interactions that stabilize secondary structure elements or a folding nucleus as the starting point of the folding pathways, i.e., a "bottom-up" mechanism. Non-local interactions were assumed either to stabilize the nucleus or lead to the later steps of coalescence of the secondary structure elements. An alternative mechanism was proposed, an "up-down" mechanism in which it was assumed that folding starts with the formation of very few non-local interactions which form closed long loops at the initiation of folding. The possible biological advantage of this mechanism, the "loop hypothesis", is that the hydrophobic collapse is associated with ordered compactization which reduces the chance for degradation and misfolding. In the present review the experiments, simulations and theoretical consideration that either directly or indirectly support this mechanism are summarized. It is argued that experiments monitoring the time-dependent development of the formation of specifically targeted early-formed sub-domain structural elements, either long loops or secondary structure elements, are necessary. This can be achieved by the time-resolved FRET-based "double kinetics" method in combination with mutational studies. Yet, attempts to improve the time resolution of the folding initiation should be extended down to the sub-microsecond time regime in order to design experiments that would resolve the classes of proteins which first fold by local or non-local interactions.
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Affiliation(s)
- Tomer Orevi
- The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel, 52900
| | - Gil Rahamim
- The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel, 52900
| | - Gershon Hazan
- The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel, 52900
| | - Dan Amir
- The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel, 52900
| | - Elisha Haas
- The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel, 52900.
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65
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Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy. Nat Commun 2013; 3:1195. [PMID: 23149740 PMCID: PMC3514500 DOI: 10.1038/ncomms2204] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 10/15/2012] [Indexed: 11/09/2022] Open
Abstract
Theory, simulations and experimental results have suggested an important role of internal friction in the kinetics of protein folding. Recent experiments on spectrin domains provided the first evidence for a pronounced contribution of internal friction in proteins that fold on the millisecond timescale. However, it has remained unclear how this contribution is distributed along the reaction and what influence it has on the folding dynamics. Here we use a combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, microfluidic mixing and denaturant- and viscosity-dependent protein-folding kinetics to probe internal friction in the unfolded state and at the early and late transition states of slow- and fast-folding spectrin domains. We find that the internal friction affecting the folding rates of spectrin domains is highly localized to the early transition state, suggesting an important role of rather specific interactions in the rate-limiting conformational changes.
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66
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Raoof S, Heo M, Shakhnovich EI. A one-shot germinal center model under protein structural stability constraints. Phys Biol 2013; 10:025001. [PMID: 23492682 DOI: 10.1088/1478-3975/10/2/025001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The germinal center reaction is the process by which low-affinity B cells evolve into potent, immunoglobulin-secreting plasma and memory B cells. Since the recycling hypothesis was created, experimental studies have both tracked movement of a small population of B cells from the light zone into the dark zone, supporting the recycling model, and parallel to the light zone-dark zone interface, indicating a one-way trajectory. We present a novel, sequence-based ab initio model of protein stability and protein interactions. Our model contains a dark zone region of clonal expansion and somatic hypermutation and a light zone site of antigenic selection. We show not only that a one-shot model is sufficient to achieve biologically-realistic rates of affinity growth, population dynamics, and silent:non-silent mutation ratios in the complementary determining region and framework region of antibodies, but also that a stochastic recycling program with or without realistic constraints on the structural stabilities of GC antibodies cannot produce biologically-observed affinity growth, population dynamics or silent:non-silent mutation profiles. The effect of recycling erases affinity gains made by potent antibodies cycling back from the light zone and causes B cells to pool in the dark zone under high replication rates.
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Affiliation(s)
- Sana Raoof
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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67
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Udgaonkar JB. Polypeptide chain collapse and protein folding. Arch Biochem Biophys 2013; 531:24-33. [DOI: 10.1016/j.abb.2012.10.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/01/2012] [Accepted: 10/08/2012] [Indexed: 12/11/2022]
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68
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Mohazab AR, Plotkin SS. Polymer uncrossing and knotting in protein folding, and their role in minimal folding pathways. PLoS One 2013; 8:e53642. [PMID: 23365638 PMCID: PMC3554774 DOI: 10.1371/journal.pone.0053642] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 11/30/2012] [Indexed: 11/19/2022] Open
Abstract
We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the minimal uncrossing cost that would have been required to avoid such events. A depth-first tree search algorithm is applied to find minimal transformations to fold [Formula: see text], [Formula: see text], [Formula: see text], and knotted proteins. In all cases, the extra uncrossing/non-crossing distance is a small fraction of the total distance travelled by a ghost chain. Different structural classes may be distinguished by the amount of extra uncrossing distance, and the effectiveness of such discrimination is compared with other order parameters. It was seen that non-crossing distance over chain length provided the best discrimination between structural and kinetic classes. The scaling of non-crossing distance with chain length implies an inevitable crossover to entanglement-dominated folding mechanisms for sufficiently long chains. We further quantify the minimal folding pathways by collecting the sequence of uncrossing moves, which generally involve leg, loop, and elbow-like uncrossing moves, and rendering the collection of these moves over the unfolded ensemble as a multiple-transformation "alignment". The consensus minimal pathway is constructed and shown schematically for representative cases of an [Formula: see text], [Formula: see text], and knotted protein. An overlap parameter is defined between pathways; we find that [Formula: see text] proteins have minimal overlap indicating diverse folding pathways, knotted proteins are highly constrained to follow a dominant pathway, and [Formula: see text] proteins are somewhere in between. Thus we have shown how topological chain constraints can induce dominant pathway mechanisms in protein folding.
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Affiliation(s)
- Ali R. Mohazab
- Department of Physics and Astronomy, University of British Columbia, Vancouver, B.C, Canada
| | - Steven S. Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, B.C, Canada
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69
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Krobath H, Faísca PFN. Interplay between native topology and non-native interactions in the folding of tethered proteins. Phys Biol 2013; 10:016002. [DOI: 10.1088/1478-3975/10/1/016002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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70
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Gridnev DK, Ojeda-May P, Garcia ME. Selecting fast-folding proteins by their rate of convergence. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:012714. [PMID: 23410366 DOI: 10.1103/physreve.87.012714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 11/26/2012] [Indexed: 06/01/2023]
Abstract
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using only the very initial parts of the dynamical trajectories. It does not require any preliminary knowledge of the native state and can be applied to different kinds of models, including atomistic descriptions. We tested the method within both the lattice and off-lattice model frameworks and obtained several so far unknown good folders. The unbiased algorithm also allows one to determine the optimal folding temperature and takes at least 3-4 orders of magnitude fewer time steps than those needed to compute folding times.
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71
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Soler MA, Faísca PFN. How difficult is it to fold a knotted protein? In silico insights from surface-tethered folding experiments. PLoS One 2012; 7:e52343. [PMID: 23284997 PMCID: PMC3527535 DOI: 10.1371/journal.pone.0052343] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 11/14/2012] [Indexed: 11/25/2022] Open
Abstract
We explore the effect of surface tethering on the folding process of a lattice protein that contains a trefoil knot in its native structure via Monte Carlo simulations. We show that the outcome of the tethering experiment depends critically on which terminus is used to link the protein to a chemically inert plane. In particular, if surface tethering occurs at the bead that is closer to the knotted core the folding rate becomes exceedingly slow and the protein is not able to find the native structure in all the attempted folding trajectories. Such low folding efficiency is also apparent from the analysis of the probability of knot formation, p(knot), as a function of nativeness. Indeed, p(knot) increases abruptly from ∼0 to ∼1 only when the protein has more than 80% of its native contacts formed, showing that a highly compact conformation must undergo substantial structural re-arrangement in order to get effectively knotted. When the protein is surface tethered by the bead that is placed more far away from the knotted core p(knot) is higher than in the other folding setups (including folding in the bulk), especially if conformations are highly native-like. These results show that the mobility of the terminus closest to the knotted core is critical for successful folding of trefoil proteins, which, in turn, highlights the importance of a knotting mechanism that is based on a threading movement of this terminus through a knotting loop. The results reported here predict that if this movement is blocked, knotting occurs via an alternative mechanism, the so-called spindle mechanism, which is prone to misfolding. Our simulations show that in the three considered folding setups the formation of the knot is typically a late event in the folding process. We discuss the implications of our findings for co-translational folding of knotted trefoils.
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Affiliation(s)
- Miguel A. Soler
- Centro de Física da Matéria Condensada, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Física, Universidade de Lisboa, Lisboa, Portugal
| | - Patrícia F. N. Faísca
- Centro de Física da Matéria Condensada, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Física, Universidade de Lisboa, Lisboa, Portugal
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72
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Abstract
The ability of protein chains to spontaneously form their spatial structures is a long-standing puzzle in molecular biology. Experimentally measured rates of spontaneous folding of single-domain globular proteins range from microseconds to hours: the difference (11 orders of magnitude) is akin to the difference between the life span of a mosquito and the age of the universe. Here, we show that physical theory with biological constraints outlines a "golden triangle" limiting the possible range of folding rates for single-domain globular proteins of various size and stability, and that the experimentally measured folding rates fall within this narrow triangle built without any adjustable parameters, filling it almost completely. In addition, the golden triangle predicts the maximal size of protein domains that fold under solely thermodynamic (rather than kinetic) control. It also predicts the maximal allowed size of the "foldable" protein domains, and the size of domains found in known protein structures is in a good agreement with this limit.
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73
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Ben Ishay E, Rahamim G, Orevi T, Hazan G, Amir D, Haas E. Fast Subdomain Folding Prior to the Global Refolding Transition of E. coli Adenylate Kinase: A Double Kinetics Study. J Mol Biol 2012; 423:613-23. [DOI: 10.1016/j.jmb.2012.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 07/31/2012] [Accepted: 08/07/2012] [Indexed: 11/16/2022]
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74
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Krobath H, Estácio S, Faísca P, Shakhnovich E. Identification of a Conserved Aggregation-Prone Intermediate State in the Folding Pathways of Spc-SH3 Amyloidogenic Variants. J Mol Biol 2012; 422:705-722. [DOI: 10.1016/j.jmb.2012.06.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 06/11/2012] [Accepted: 06/11/2012] [Indexed: 01/30/2023]
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75
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Folding pathways of proteins with increasing degree of sequence identities but different structure and function. Proc Natl Acad Sci U S A 2012; 109:17772-6. [PMID: 22652570 DOI: 10.1073/pnas.1201794109] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Much experimental work has been devoted in comparing the folding behavior of proteins sharing the same fold but different sequence. The recent design of proteins displaying very high sequence identities but different 3D structure allows the unique opportunity to address the protein-folding problem from a complementary perspective. Here we explored by Φ-value analysis the pathways of folding of three different heteromorphic pairs, displaying increasingly high-sequence identity (namely, 30%, 77%, and 88%), but different structures called G(A) (a 3-α helix fold) and G(B) (an α/β fold). The analysis, based on 132 site-directed mutants, is fully consistent with the idea that protein topology is committed very early along the pathway of folding. Furthermore, data reveals that when folding approaches a perfect two-state scenario, as in the case of the G(A) domains, the structural features of the transition state appear very robust to changes in sequence composition. On the other hand, when folding is more complex and multistate, as for the G(B)s, there are alternative nuclei or accessible pathways that can be alternatively stabilized by altering the primary structure. The implications of our results in the light of previous work on the folding of different members belonging to the same protein family are discussed.
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76
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Faísca PFN, Travasso RDM, Parisi A, Rey A. Why do protein folding rates correlate with metrics of native topology? PLoS One 2012; 7:e35599. [PMID: 22558173 PMCID: PMC3338708 DOI: 10.1371/journal.pone.0035599] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 03/20/2012] [Indexed: 12/02/2022] Open
Abstract
For almost 15 years, the experimental correlation between protein folding rates and the contact order parameter has been under scrutiny. Here, we use a simple simulation model combined with a native-centric interaction potential to investigate the physical roots of this empirical observation. We simulate a large set of circular permutants, thus eliminating dependencies of the folding rate on other protein properties (e.g. stability). We show that the rate-contact order correlation is a consequence of the fact that, in high contact order structures, the contact order of the transition state ensemble closely mirrors the contact order of the native state. This happens because, in these structures, the native topology is represented in the transition state through the formation of a network of tertiary interactions that are distinctively long-ranged.
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Affiliation(s)
- Patrícia F N Faísca
- Centro de Física da Matéria Condensada, Universidade de Lisboa, Lisboa, Portugal.
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77
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Wales DJ, Head-Gordon T. Evolution of the potential energy landscape with static pulling force for two model proteins. J Phys Chem B 2012; 116:8394-411. [PMID: 22432920 DOI: 10.1021/jp211806z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The energy landscape is analyzed for off-lattice bead models of protein L and protein G as a function of a static pulling force. Two different pairs of attachment points (pulling directions) are compared in each case, namely, residues 1/56 and 10/32. For the terminal residue pulling direction 1/56, the distinct global minimum structures are all extended, aside from the compact geometry that correlates with zero force. The helical turns finally disappear at the highest pulling forces considered. For the 10/32 pulling direction, the changes are more complicated, with a variety of competing arrangements for beads outside the region where the force is directly applied. These alternatives produce frustrated energy landscapes, with low-lying minima separated by high barriers. The calculated folding pathways in the absence of force are in good agreement with previous work. The N-terminal hairpin folds first for protein L and the C-terminal hairpin for protein G, which exhibits an intermediate. However, for a relatively low static force, where the global minimum retains its structure, the folding mechanisms change, sometimes dramatically, depending on the protein and the attachment points. The scaling relations predicted by catastrophe theory are found to hold in the limit of short path lengths.
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Affiliation(s)
- David J Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK.
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78
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Moreno-Hernández S, Levitt M. Comparative modeling and protein-like features of hydrophobic-polar models on a two-dimensional lattice. Proteins 2012; 80:1683-93. [PMID: 22411636 DOI: 10.1002/prot.24067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 02/26/2012] [Accepted: 03/03/2012] [Indexed: 11/07/2022]
Abstract
Lattice models of proteins have been extensively used to study protein thermodynamics, folding dynamics, and evolution. Our study considers two different hydrophobic-polar (HP) models on the 2D square lattice: the purely HP model and a model where a compactness-favoring term is added. We exhaustively enumerate all the possible structures in our models and perform the study of their corresponding folds, HP arrangements in space and shapes. The two models considered differ greatly in their numbers of structures, folds, arrangements, and shapes. Despite their differences, both lattice models have distinctive protein-like features: (1) Shapes are compact in both models, especially when a compactness-favoring energy term is added. (2) The residue composition is independent of the chain length and is very close to 50% hydrophobic in both models, as we observe in real proteins. (3) Comparative modeling works well in both models, particularly in the more compact one. The fact that our models show protein-like features suggests that lattice models incorporate the fundamental physical principles of proteins. Our study supports the use of lattice models to study questions about proteins that require exactness and extensive calculations, such as protein design and evolution, which are often too complex and computationally demanding to be addressed with more detailed models.
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Affiliation(s)
- Sergio Moreno-Hernández
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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79
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Lu Y, Ye X, Li J, Li C, Liu S. Kinetics of Laser-Heating-Induced Phase Transition of Poly(N-isopropylacrylamide) Chains in Dilute and Semidilute Solutions. J Phys Chem B 2011; 115:12001-6. [DOI: 10.1021/jp204853p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yijie Lu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaodong Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Junfang Li
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 LingLing Road, Shanghai 200032, China
| | - Chunliang Li
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shilin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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80
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Vasilevskaya VV, Ermilov VA. Computer simulation of macromolecular systems with amphiphilic monomer units: Biomimetic models. POLYMER SCIENCE SERIES A 2011. [DOI: 10.1134/s0965545x11090148] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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81
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Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations. PLoS Comput Biol 2011; 7:e1002137. [PMID: 21931542 PMCID: PMC3169518 DOI: 10.1371/journal.pcbi.1002137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 06/09/2011] [Indexed: 11/25/2022] Open
Abstract
Small globular proteins and peptides commonly exhibit two-state folding kinetics in which the rate limiting step of folding is the surmounting of a single free energy barrier at the transition state (TS) separating the folded and the unfolded states. An intriguing question is whether the polypeptide chain reaches, and leaves, the TS by completely random fluctuations, or whether there is a directed, stepwise process. Here, the folding TS of a 15-residue β-hairpin peptide, Peptide 1, is characterized using independent 2.5 μs-long unbiased atomistic molecular dynamics (MD) simulations (a total of 15 μs). The trajectories were started from fully unfolded structures. Multiple (spontaneous) folding events to the NMR-derived conformation are observed, allowing both structural and dynamical characterization of the folding TS. A common loop-like topology is observed in all the TS structures with native end-to-end and turn contacts, while the central segments of the strands are not in contact. Non-native sidechain contacts are present in the TS between the only tryptophan (W11) and the turn region (P7-G9). Prior to the TS the turn is found to be already locked by the W11 sidechain, while the ends are apart. Once the ends have also come into contact, the TS is reached. Finally, along the reactive folding paths the cooperative loss of the W11 non-native contacts and the formation of the central inter-strand native contacts lead to the peptide rapidly proceeding from the TS to the native state. The present results indicate a directed stepwise process to folding the peptide. The folding dynamics of many small protein/peptides investigated recently are in terms of simple two-state model in which only two populations exist (folded and unfolded), separated by a single free energy barrier with only one kinetically important transition state (TS). However, dynamical characterization of the folding TS is challenging. We have used independent unbiased atomistic molecular dynamics simulations with clear folding-unfolding transitions to characterize structural and dynamical features of transition state ensemble of Peptide 1. A common loop-like topology is observed in all TS structures extracted from multiple simulations. The trajectories were used to examine the mechanism by which the TS is reached and subsequent events in folding pathways. The folding TS is reached and crossed in a directed stagewise process rather than through random fluctuations. Specific structures are formed before, during, and after the transition state, indicating a clear structured folding pathway.
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82
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Jelinska C, Davis P, Kenig M, Žerovnik E, Kokalj S, Gunčar G, Turk D, Turk V, Clarke D, Waltho J, Staniforth R. Modulation of contact order effects in the two-state folding of stefins A and B. Biophys J 2011; 100:2268-74. [PMID: 21539796 PMCID: PMC3149235 DOI: 10.1016/j.bpj.2011.03.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 03/09/2011] [Accepted: 03/15/2011] [Indexed: 11/25/2022] Open
Abstract
It is well established that contact order and folding rates are correlated for small proteins. The folding rates of stefins A and B differ by nearly two orders of magnitude despite sharing an identical native fold and hence contact order. We break down the determinants of this behavior and demonstrate that the modulation of contact order effects can be accounted for by the combined contributions of a framework-like mechanism, characterized by intrinsic helix stabilities, together with nonnative helical backbone conformation and nonnative hydrophobic interactions within the folding transition state. These contributions result in the formation of nonnative interactions in the transition state as evidenced by the opposing effects on folding rate and stability of these proteins.
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Affiliation(s)
- Clare Jelinska
- Department of Molecular Biology and Biotechnology, Krebs Institute, Western Bank, University of Sheffield, Sheffield, United Kingdom
| | - Peter J. Davis
- Department of Molecular Biology and Biotechnology, Krebs Institute, Western Bank, University of Sheffield, Sheffield, United Kingdom
| | - Manca Kenig
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Saša Jenko Kokalj
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Gregor Gunčar
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - David T. Clarke
- Council for the Central Laboratory of the Research Councils Daresbury Laboratory, Daresbury, Warrington, United Kingdom
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute, Western Bank, University of Sheffield, Sheffield, United Kingdom
- Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Rosemary A. Staniforth
- Department of Molecular Biology and Biotechnology, Krebs Institute, Western Bank, University of Sheffield, Sheffield, United Kingdom
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83
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Faísca PFN, Nunes A, Travasso RDM, Shakhnovich EI. Non-native interactions play an effective role in protein folding dynamics. Protein Sci 2011; 19:2196-209. [PMID: 20836137 DOI: 10.1002/pro.498] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Systematic Monte Carlo simulations of simple lattice models show that the final stage of protein folding is an ordered process where native contacts get locked (i.e., the residues come into contact and remain in contact for the duration of the folding process) in a well-defined order. The detailed study of the folding dynamics of protein-like sequences designed as to exhibit different contact energy distributions, as well as different degrees of sequence optimization (i.e., participation of non-native interactions in the folding process), reveals significant differences in the corresponding locking scenarios--the collection of native contacts and their average locking times, which are largely ascribable to the dynamics of non-native contacts. Furthermore, strong evidence for a positive role played by non-native contacts at an early folding stage was also found. Interestingly, for topologically simple target structures, a positive interplay between native and non-native contacts is observed also toward the end of the folding process, suggesting that non-native contacts may indeed affect the overall folding process. For target models exhibiting clear two-state kinetics, the relation between the nucleation mechanism of folding and the locking scenario is investigated. Our results suggest that the stabilization of the folding transition state can be achieved through the establishment of a very small network of native contacts that are the first to lock during the folding process.
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Affiliation(s)
- Patrícia F N Faísca
- Centro de Física da Matéria Condensada, Universidade de Lisboa, Av. Prof. Gama Pinto 2, 1649-003 Lisboa, Portugal.
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84
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Naganathan AN, Orozco M. The protein folding transition-state ensemble from a Gō-like model. Phys Chem Chem Phys 2011; 13:15166-74. [DOI: 10.1039/c1cp20964g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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85
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Sosnick TR, Barrick D. The folding of single domain proteins--have we reached a consensus? Curr Opin Struct Biol 2010; 21:12-24. [PMID: 21144739 DOI: 10.1016/j.sbi.2010.11.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 11/03/2010] [Accepted: 11/04/2010] [Indexed: 10/18/2022]
Abstract
Rather than stressing the most recent advances in the field, this review highlights the fundamental topics where disagreement remains and where adequate experimental data are lacking. These topics include properties of the denatured state and the role of residual structure, the nature of the fundamental steps and barriers, the extent of pathway heterogeneity and non-native interactions, recent comparisons between theory and experiment, and finally, dynamical properties of the folding reaction.
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Affiliation(s)
- Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.
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86
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Travasso RDM, Faísca PFN, Rey A. The protein folding transition state: Insights from kinetics and thermodynamics. J Chem Phys 2010; 133:125102. [DOI: 10.1063/1.3485286] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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87
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Abstract
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances in theory and experiments have resulted in a conceptual framework for describing the folding mechanisms of globular proteins. The sizes of proteins in the denatured and folded states, cooperativity of the folding transition, dispersions in the melting temperatures at the residue level, and timescales of folding are, to a large extent, determined by N, the number of residues. The intricate details of folding as a function of denaturant concentration can be predicted by using a novel coarse-grained molecular transfer model. By watching one molecule fold at a time, using single-molecule methods, investigators have established the validity of the theoretically anticipated heterogeneity in the folding routes and the N-dependent timescales for the three stages in the approach to the native state. Despite the successes of theory, of which only a few examples are documented here, we conclude that much remains to be done to solve the protein folding problem in the broadest sense.
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Affiliation(s)
- D Thirumalai
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
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88
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Ivankov DN, Finkelstein AV. Protein Folding as Flow across a Network of Folding−Unfolding Pathways. 2. The “In-Water” Case. J Phys Chem B 2010; 114:7930-4. [DOI: 10.1021/jp912187w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmitry N. Ivankov
- Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region 142290, Russia
| | - Alexei V. Finkelstein
- Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region 142290, Russia
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89
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Borrero EE, Contreras Martínez LM, DeLisa MP, Escobedo FA. Kinetics and reaction coordinates of the reassembly of protein fragments via forward flux sampling. Biophys J 2010; 98:1911-20. [PMID: 20441755 PMCID: PMC2862158 DOI: 10.1016/j.bpj.2009.12.4329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 12/07/2009] [Accepted: 12/15/2009] [Indexed: 11/16/2022] Open
Abstract
We studied the mechanism of the reassembly and folding process of two fragments of a split lattice protein by using forward flux sampling (FFS). Our results confirmed previous thermodynamics and kinetics analyses that suggested that the disruption of the critical core (of an unsplit protein that folds by a nucleation mechanism) plays a key role in the reassembly mechanism of the split system. For several split systems derived from a parent 48-mer model, we estimated the reaction coordinates in terms of collective variables by using the FFS least-square estimation method and found that the reassembly transition is best described by a combination of the total number of native contacts, the number of interchain native contacts, and the total conformational energy of the split system. We also analyzed the transition path ensemble obtained from FFS simulations using the estimated reaction coordinates as order parameters to identify the microscopic features that differentiate the reassembly of the different split systems studied. We found that in the fastest folding split system, a balanced distribution of the original-core amino acids (of the unsplit system) between protein fragments propitiates interchain interactions at early stages of the folding process. Only this system exhibits a different reassembly mechanism from that of the unsplit protein, involving the formation of a different folding nucleus. In the slowest folding system, the concentration of the folding nucleus in one fragment causes its early prefolding, whereas the second fragment tends to remain as a detached random coil. We also show that the reassembly rate can be either increased or decreased by tuning interchain cooperativeness via the introduction of a single point mutation that either strengthens or weakens one of the native interchain contacts (prevalent in the transition state ensemble).
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Affiliation(s)
| | | | | | - Fernando A. Escobedo
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York
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90
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Insights into protein folding mechanisms from large scale analysis of mutational effects. Proc Natl Acad Sci U S A 2010; 107:8611-6. [PMID: 20418505 DOI: 10.1073/pnas.1000988107] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein folding mechanisms are probed experimentally using single-point mutant perturbations. The relative effects on the folding (phi-values) and unfolding (1 - phi) rates are used to infer the detailed structure of the transition-state ensemble (TSE). Here we analyze kinetic data on > 800 mutations carried out for 24 proteins with simple kinetic behavior. We find two surprising results: (i) all mutant effects are described by the equation: DeltaDeltaG(double dagger)(unfold)=0.76DeltaDeltaG(eq) +/- 1.8kJ/mol. Therefore all data are consistent with a single phi-value (0.24) with accuracy comparable to experimental precision, suggesting that the structural information in conventional phi-values is low. (ii) phi-values change with stability, increasing in mean value and spread from native to unfolding conditions, and thus cannot be interpreted without proper normalization. We eliminate stability effects calculating the phi-values at the mutant denaturation midpoints; i.e., conditions of zero stability (phi(0)). We then show that the intrinsic variability is phi(0) = 0.36 +/- 0.11, being somewhat larger for beta-sheet-rich proteins than for alpha-helical proteins. Importantly, we discover that phi(0)-values are proportional to how many of the residues surrounding the mutated site are local in sequence. High phi(0)-values correspond to protein surface sites, which have few nonlocal neighbors, whereas core residues with many tertiary interactions produce the lowest phi(0)-values. These results suggest a general mechanism in which the TSE at zero stability is a broad conformational ensemble stabilized by local interactions and without specific tertiary interactions, reconciling phi-values with many other empirical observations.
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91
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92
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Scaloni F, Federici L, Brunori M, Gianni S. Deciphering the folding transition state structure and denatured state properties of nucleophosmin C-terminal domain. Proc Natl Acad Sci U S A 2010; 107:5447-52. [PMID: 20212148 PMCID: PMC2851762 DOI: 10.1073/pnas.0910516107] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nucleophosmin (NPM1), one of the most abundant nucleolar proteins, is a frequent target of oncogenic mutations in acute myeloid leukaemia (AML). Mutation-induced changes at the C-terminal domain of NPM1 (Cter-NPM1) compromise its stability and cause the aberrant translocation of NPM1 to the cytosol. Hence, this protein represents a suitable candidate to investigate the relations between folding and disease. Since Cter-NPM1 folds via a compact denatured state, stabilization of the folded state of the mutated variants demands detailed structural information on both the native and denatured states. Here, we present the characterization of the complete folding pathway of Cter-NPM1 and provide molecular details for both the transition and the denatured states. The structure of the transition state was assessed by Phi-value analysis, whereas residual structure in the denatured state was mapped by evaluating the effect of mutations as modulated by conditions promoting denatured state compaction. Data reveal that folding of Cter-NPM1 proceeds via an extended nucleus and that the denatured state retains significant malleable structure at the interface between the second and third helices. Our observations constitute the essential prerequisite for structure-based drug-design studies, aimed at identifying molecules that may rescue pathological NPM1 mutants by stabilizing the native-like state.
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Affiliation(s)
- Flavio Scaloni
- Istituto Pasteur–Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università di Roma La Sapienza, Rome, Italy; and
| | - Luca Federici
- Centro Studi sull’Invecchiamento and Dipartimento di Scienze Biomediche, Università di Chieti G. D’Annunzio, Chieti, Italy
| | - Maurizio Brunori
- Istituto Pasteur–Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università di Roma La Sapienza, Rome, Italy; and
| | - Stefano Gianni
- Istituto Pasteur–Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università di Roma La Sapienza, Rome, Italy; and
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93
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A probabilistic approach to the effect of water hydrogen bonds on the kinetics of protein folding and protein denaturation. Adv Colloid Interface Sci 2010; 154:77-90. [PMID: 20163782 DOI: 10.1016/j.cis.2010.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 01/20/2010] [Indexed: 11/23/2022]
Abstract
Previously, we presented a review of our kinetic models for the nucleation mechanism of protein folding and for the protein thermal denaturation in a barrierless way. A protein was treated as a random heteropolymer consisting of hydrophobic, hydrophilic, and neutral beads. As a crucial idea of the model, an overall potential around the cluster of native residues wherein a residue performs a chaotic motion was considered as the combination of the average dihedral, effective pairwise, and confining potentials. The overall potential as a function of the distance from the cluster has a double well shape. This allowed one to develop kinetic models for the nucleation mechanism of protein folding (NMPF) and barrierless protein denaturation (BPD) by using the mean first passage time analysis. In the original models, however, hydrogen bonding effects were taken into account only indirectly which affected the accuracy of the models because hydrogen bonding does play a crucial role in the folding, stability, and denaturation of proteins. To improve the NMPF and BPD models and explicitly take into account the hydrogen bonding "water-water" and "water-protein residue", we have developed a probabilistic hydrogen bond (PHB) model for the effect of hydrogen bond networks of water molecules around two solute particles (immersed in water) on their interaction, and have then combined the PHB model with the NMPF and BPD models. In this paper, that can be regarded as sequel of our previous review, we analyze the modified NMPF and BPD models that explicitly take into account the effect of water-water hydrogen bonding on these processes. As expected, the application of the modified models to the folding/unfolding of two model proteins (one short, consisting of 124 residues and the other large, consisting of 2500 residues) demonstrate that the hydrogen bond networks play a very important role in the protein folding/unfolding phenomena.
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94
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Yan Z, Wang J, Zhang Y, Qin M, Wang W. Nucleation process in the folding of a domain-swapped dimer. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:021910. [PMID: 20365598 DOI: 10.1103/physreve.81.021910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2009] [Revised: 12/07/2009] [Indexed: 05/29/2023]
Abstract
Nucleation processes are important for the understanding in protein dynamics. To evaluate the effect of nucleation mechanism in dimerization process, a domain-swapped dimer (Esp8) is simulated with the symmetrized Gō model and the classical Gō model. The pathways of the dimerization are analyzed with computational phi -analysis method. It is found out that some nuclei are observed in the kinetic steps of the dimeric association though the whole pathway is a process with multiple intermediate states. The key residues in the nuclei are rather similar to those observed in the monomeric folding. The differences with the monomeric cases are also discussed. These differences illustrate the effects of dimeric feature on the nucleation process. Besides, manual mutations are carried out to illustrate the importance of the interactions related to the nuclei. It is observed that the mutations in the nuclei-related interactions apparently change the dynamics while other mutations have little effect on the kinetics. All of these results outline a picture that the nucleation processes act as the fundamental steps of high-order organization of protein systems.
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Affiliation(s)
- Zhiqiang Yan
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
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95
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Dee DR, Yada RY. The prosegment catalyzes pepsin folding to a kinetically trapped native state. Biochemistry 2010; 49:365-71. [PMID: 20000477 DOI: 10.1021/bi9014055] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Investigations of irreversible protein unfolding often assume that alterations to the unfolded state, rather than the nature of the native state itself, are the cause of the irreversibility. However, the present study describes a less common explanation for the irreversible denaturation of pepsin, a zymogen-derived aspartic peptidase. The presence of a large folding barrier combined with the thermodynamically metastable nature of the native state, the formation of which depends on a separate prosegment (PS) domain, is the source of the irreversibility. Pepsin is unable to refold to the native state upon return from denaturing conditions due to a large folding barrier (24.6 kcal/mol) and instead forms a thermodynamically stable, yet inactive, refolded state. The native state is kinetically stabilized by an unfolding activation energy of 24.5 kcal/mol, comparable to the folding barrier, indicating that native pepsin exists as a thermodynamically metastable state. However, in the presence of the PS, the native state becomes thermodynamically stable, and the PS catalyzes pepsin folding by stabilizing the folding transition state by 14.7 kcal/mol. Once folded, the PS is removed, and the native conformation exists as a kinetically trapped state. Thus, while PS-guided folding is thermodynamically driven, without the PS the pepsin energy landscape is dominated by kinetic barriers rather than by free energy differences between native and denatured states. As pepsin is the archetype of a broad class of aspartic peptidases of similar structure and function, and many require their PS for correct folding, these results suggest that the occurrence of native states optimized for kinetic rather than thermodynamic stability may be a common feature of protein design.
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Affiliation(s)
- Derek R Dee
- Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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96
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Djikaev YS, Ruckenstein E. Effect of hydrogen bond networks on the nucleation mechanism of protein folding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:061918. [PMID: 20365201 DOI: 10.1103/physreve.80.061918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/23/2009] [Indexed: 05/29/2023]
Abstract
We have recently developed a kinetic model for the nucleation mechanism of protein folding (NMPF) in terms of ternary nucleation by using the first passage time analysis. A protein was considered as a random heteropolymer consisting of hydrophobic, hydrophilic (some of which are negatively or positively ionizable), and neutral beads. The main idea of the NMPF model consisted of averaging the dihedral potential in which a selected residue is involved over all possible configurations of all neighboring residues along the protein chain. The combination of the average dihedral, effective pairwise (due to Lennard-Jones-type and electrostatic interactions), and confining (due to the polymer connectivity constraint) potentials gives rise to an overall potential around the cluster that, as a function of the distance from the cluster center, has a double-well shape. This allows one to evaluate the protein folding time. In the original NMPF model hydrogen bonding was not taken into account explicitly. To improve the NMPF model and make it more realistic, in this paper we modify our (previously developed) probabilistic hydrogen bond model and combine it with the former. Thus, a contribution due to the disruption of hydrogen bond networks around the interacting particles (cluster of native residues and residue in the protein unfolded part) appears in the overall potential field around a cluster. The modified model is applied to the folding of the same model proteins that were examined in the original model: a short protein consisting of 124 residues (roughly mimicking bovine pancreatic ribonuclease) and a long one consisting of 2500 residues (as a representative of large proteins with superlong polypeptide chains), at pH=8.3 , 7.3, and 6.3. The hydrogen bond contribution now plays a dominant role in the total potential field around the cluster (except for very short distances thereto where the repulsive energy tends to infinity). It is by an order of magnitude stronger for hydrophobic residues than for hydrophilic ones. The range of "residue-cluster" distances, at which the hydrogen bond effect exists, is twice as long for hydrophobic residues as for hydrophilic ones.
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Affiliation(s)
- Y S Djikaev
- Department of Chemical and Biological Engineering, SUNY at Buffalo, Buffalo, New York 14260, USA.
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97
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Stagg L, Samiotakis A, Homouz D, Cheung MS, Wittung-Stafshede P. Residue-specific analysis of frustration in the folding landscape of repeat beta/alpha protein apoflavodoxin. J Mol Biol 2009; 396:75-89. [PMID: 19913555 DOI: 10.1016/j.jmb.2009.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 11/04/2009] [Accepted: 11/05/2009] [Indexed: 11/17/2022]
Abstract
Flavodoxin adopts the common repeat beta/alpha topology and folds in a complex kinetic reaction with intermediates. To better understand this reaction, we analyzed a set of Desulfovibrio desulfuricans apoflavodoxin variants with point mutations in most secondary structure elements by in vitro and in silico methods. By equilibrium unfolding experiments, we first revealed how different secondary structure elements contribute to overall protein resistance to heat and urea. Next, using stopped-flow mixing coupled with far-UV circular dichroism, we probed how individual residues affect the amount of structure formed in the experimentally detected burst-phase intermediate. Together with in silico folding route analysis of the same point-mutated variants and computation of growth in nucleation size during early folding, computer simulations suggested the presence of two competing folding nuclei at opposite sides of the central beta-strand 3 (i.e., at beta-strands 1 and 4), which cause early topological frustration (i.e., misfolding) in the folding landscape. Particularly, the extent of heterogeneity in folding nuclei growth correlates with the in vitro burst-phase circular dichroism amplitude. In addition, phi-value analysis (in vitro and in silico) of the overall folding barrier to apoflavodoxin's native state revealed that native-like interactions in most of the beta-strands must form in transition state. Our study reveals that an imbalanced competition between the two sides of apoflavodoxin's central beta-sheet directs initial misfolding, while proper alignment on both sides of beta-strand 3 is necessary for productive folding.
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Affiliation(s)
- Loren Stagg
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, USA
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98
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Abstract
Progress in understanding protein folding allows to simulate, with atomic detail, the evolution of amino-acid sequences folding to a given native conformation. A particularly attractive example is the HIV-1 protease, main target of therapies to fight AIDS, which under drug pressure is able to develop resistance within few months from the starting of therapy. By comparing the results of simulations of the evolution of the protease with the corresponding proteomic data, one can approximately determine the value of the associated evolution pressure under which the enzyme has become and, as a consequence, map out the energy landscape in sequence space of the HIV-1 protease. It is found that there are several families of sequences folding to the native conformations of the enzyme. Each of these families are characterized by different sets of highly conserved ("hot") amino acids which play a critical role in the folding and stability of the protease. There are two main possibilities for the virus to move from one family to a different one: (a) in a single generation, through the concerted mutations of the hot amino acids, a highly unlikely event, (b) through a folding path (if it exists), again a very improbable event. In fact, the number of generations needed by the virus to change stepwise its sequence from one family to another is astronomically large. These results point to the "hot" segments of the protease as promising targets for a nonconventional inhibition strategy, likely not to create resistance.
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Affiliation(s)
- G Tiana
- Department of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy.
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99
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Gin BC, Garrahan JP, Geissler PL. The Limited Role of Nonnative Contacts in the Folding Pathways of a Lattice Protein. J Mol Biol 2009; 392:1303-14. [DOI: 10.1016/j.jmb.2009.06.058] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 06/19/2009] [Accepted: 06/23/2009] [Indexed: 11/15/2022]
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100
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Faísca PFN. The nucleation mechanism of protein folding: a survey of computer simulation studies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:373102. [PMID: 21832332 DOI: 10.1088/0953-8984/21/37/373102] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The nucleation mechanism of protein folding, originally proposed by Baldwin in the early 1970s, was firstly observed by Shakhnovich and co-workers two decades later in the context of Monte Carlo simulations of a simple lattice model. At about the same time the extensive use of φ-value analysis provided the first experimental evidence that the folding of Chymotrypsin-inhibitor 2, a small single-domain protein, which folds with two-state kinetics, is also driven by a nucleation mechanism. Since then, the nucleation mechanism is generally considered the most common form of folding mechanism amongst two-state proteins. However, recent experimental data has put forward the idea that this may not necessarily be so, since the accuracy of the experimentally determined φ values, which are used to identify the critical (i.e. nucleating) residues, is typically poor. Here, we provide a survey of in silico results on the nucleation mechanism, ranging from simple lattice Monte Carlo to more sophisticated off-lattice molecular dynamics simulations, and discuss them in light of experimental data.
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Affiliation(s)
- Patrícia F N Faísca
- Centro de Física Teórica e Computacional, Universidade de Lisboa, Avenida Professor Gama Pinto 2, 1649-003 Lisboa, Portugal
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