51
|
Dabrowski-Tumanski P, Jarmolinska AI, Sulkowska JI. Prediction of the optimal set of contacts to fold the smallest knotted protein. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354109. [PMID: 26291339 DOI: 10.1088/0953-8984/27/35/354109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map.
Collapse
Affiliation(s)
- P Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland. Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | | | | |
Collapse
|
52
|
Chwastyk M, Cieplak M. Cotranslational folding of deeply knotted proteins. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354105. [PMID: 26292194 DOI: 10.1088/0953-8984/27/35/354105] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.
Collapse
Affiliation(s)
- Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | | |
Collapse
|
53
|
Faísca PF. Knotted proteins: A tangled tale of Structural Biology. Comput Struct Biotechnol J 2015; 13:459-68. [PMID: 26380658 PMCID: PMC4556803 DOI: 10.1016/j.csbj.2015.08.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/31/2015] [Accepted: 08/07/2015] [Indexed: 01/19/2023] Open
Abstract
Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research.
Collapse
|
54
|
Computing Reaction Pathways of Rare Biomolecular Transitions using Atomistic Force-Fields. Biophys Chem 2015; 208:62-7. [PMID: 26320390 DOI: 10.1016/j.bpc.2015.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/23/2015] [Accepted: 06/23/2015] [Indexed: 02/02/2023]
Abstract
The Dominant Reaction Pathway (DRP) method is an approximate variational scheme which can be used to compute reaction pathways in conformational transitions undergone by large biomolecules (up to ~10(3) amino-acids) using realistic all-atom force fields. We first review the status of development of this method. Next, we discuss its validation against the results of plain MD protein folding simulations performed by the DE-Shaw group using the Anton supercomputer. Finally, we review a few representative applications of the DRP approach to study reactions which are far too complex and rare to be investigated by plain MD, even on the Anton machine.
Collapse
|
55
|
Najafi S, Potestio R. Two Adhesive Sites Can Enhance the Knotting Probability of DNA. PLoS One 2015; 10:e0132132. [PMID: 26136125 PMCID: PMC4489926 DOI: 10.1371/journal.pone.0132132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/10/2015] [Indexed: 01/05/2023] Open
Abstract
Self-entanglement, or knotting, is entropically favored in long polymers. Relatively short polymers such as proteins can knot as well, but in this case the entanglement is mainly driven by fine-tuned, sequence-specific interactions. The relation between the sequence of a long polymer and its topological state is here investigated by means of a coarse-grained model of DNA. We demonstrate that the introduction of two adhesive regions along the sequence of a self-avoiding chain substantially increases the probability of forming a knot.
Collapse
Affiliation(s)
- Saeed Najafi
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Raffaello Potestio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
56
|
Shih PM, Wang I, Lee YTC, Hsieh SJ, Chen SY, Wang LW, Huang CT, Chien CT, Chang CY, Hsu STD. Random-Coil Behavior of Chemically Denatured Topologically Knotted Proteins Revealed by Small-Angle X-ray Scattering. J Phys Chem B 2015; 119:5437-43. [DOI: 10.1021/acs.jpcb.5b01984] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Po-Min Shih
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Iren Wang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Yun-Tzai Cloud Lee
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
| | - Shu-Ju Hsieh
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Szu-Yu Chen
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Liang-Wei Wang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
| | - Chih-Ting Huang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Chih-Ta Chien
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Department
of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Chia-Yun Chang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
| | - Shang-Te Danny Hsu
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
| |
Collapse
|
57
|
Wang I, Chen SY, Hsu STD. Unraveling the Folding Mechanism of the Smallest Knotted Protein, MJ0366. J Phys Chem B 2015; 119:4359-70. [DOI: 10.1021/jp511029s] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Iren Wang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Szu-Yu Chen
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 10617, Taiwan
| |
Collapse
|
58
|
A Beccara S, Fant L, Faccioli P. Variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent. PHYSICAL REVIEW LETTERS 2015; 114:098103. [PMID: 25793854 DOI: 10.1103/physrevlett.114.098103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Indexed: 05/26/2023]
Abstract
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against MD simulations of the folding of an α and a β protein performed with the same all-atom force field on the Anton supercomputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.
Collapse
Affiliation(s)
- S A Beccara
- European Centre for Theoretical Nuclear Physics and Related Areas (ECT*-FBK), Strada delle Tabarelle 287, Villazzano (Trento) 38123, Italy
- Trento Institute for Fundamental Physics and Applications (INFN-TIFPA), Via Sommarive 14, Povo (Trento) 38123, Italy
| | - L Fant
- Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, Povo (Trento) 38123, Italy
| | - P Faccioli
- Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, Povo (Trento) 38123, Italy
- Trento Institute for Fundamental Physics and Applications (INFN-TIFPA), Via Sommarive 14, Povo (Trento) 38123, Italy
| |
Collapse
|
59
|
Abstract
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also, abound in viral DNA packaged inside bacteriophages. RNA molecules, however, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the several thousand RNA structures present in the Protein Data Bank (PDB). The search identified no more than three deeply knotted RNA molecules. These entries are rRNAs of about 3,000 nt solved by cryo-EM. Their genuine knotted state is, however, doubtful based on the detailed structural comparison with homologs of higher resolution, which are all unknotted. Compared with the case of proteins and viral DNA, the observed incidence of knots in available RNA structures is, therefore, practically negligible. This fact suggests that either evolutionary selection or thermodynamic and kinetic folding mechanisms act toward minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. A possible general strategy for designing synthetic RNA sequences capable of self-tying in a twist-knot fold is finally proposed.
Collapse
|
60
|
Jamroz M, Niemyska W, Rawdon EJ, Stasiak A, Millett KC, Sułkowski P, Sulkowska JI. KnotProt: a database of proteins with knots and slipknots. Nucleic Acids Res 2014; 43:D306-14. [PMID: 25361973 PMCID: PMC4383900 DOI: 10.1093/nar/gku1059] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints.
Collapse
Affiliation(s)
- Michal Jamroz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Wanda Niemyska
- Institute of Mathematics, University of Silesia, Bankowa 14, 40-007 Katowice, Poland
| | - Eric J Rawdon
- Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
| | - Kenneth C Millett
- Department of Mathematics, University of California, Santa Barbara, CA 93106, USA
| | - Piotr Sułkowski
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland California Institute of Technology, Pasadena, CA 91125, USA
| | - Joanna I Sulkowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| |
Collapse
|
61
|
Abstract
Protease inhibition by serpins requires a large conformational transition from an active, metastable state to an inactive, stable state. Similar reactions can also occur in the absence of proteases, and these latency transitions take hours, making their time scales many orders of magnitude larger than are currently accessible using conventional molecular dynamics simulations. Using a variational path sampling algorithm, we simulated the entire serpin active-to-latent transition in all-atom detail with a physically realistic force field using a standard computing cluster. These simulations provide a unifying picture explaining existing experimental data for the latency transition of the serpin plasminogen activator inhibitor-1 (PAI-1). They predict a long-lived intermediate that resembles a previously proposed, partially loop-inserted, prelatent state; correctly predict the effects of PAI-1 mutations on the kinetics; and provide a potential means to identify ligands able to accelerate the latency transition. Interestingly, although all of the simulated PAI-1 variants readily access the prelatent intermediate, this conformation is not populated in the active-to-latent transition of another serpin, α1-antitrypsin, which does not readily go latent. Thus, these simulations also help elucidate why some inhibitory serpin families are more conformationally labile than others.
Collapse
|
62
|
Ghosh R, Roy S, Bagchi B. Multidimensional free energy surface of unfolding of HP-36: Microscopic origin of ruggedness. J Chem Phys 2014; 141:135101. [DOI: 10.1063/1.4896762] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
63
|
He C, Lamour G, Xiao A, Gsponer J, Li H. Mechanically Tightening a Protein Slipknot into a Trefoil Knot. J Am Chem Soc 2014; 136:11946-55. [DOI: 10.1021/ja503997h] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chengzhi He
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Guillaume Lamour
- Center
for High Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Adam Xiao
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Joerg Gsponer
- Center
for High Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Hongbin Li
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| |
Collapse
|
64
|
Soler MA, Nunes A, Faísca PFN. Effects of knot type in the folding of topologically complex lattice proteins. J Chem Phys 2014; 141:025101. [DOI: 10.1063/1.4886401] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
|
65
|
Haglund E, Sulkowska JI, Noel JK, Lammert H, Onuchic JN, Jennings PA. Pierced Lasso Bundles are a new class of knot-like motifs. PLoS Comput Biol 2014; 10:e1003613. [PMID: 24945798 PMCID: PMC4063663 DOI: 10.1371/journal.pcbi.1003613] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/26/2014] [Indexed: 01/11/2023] Open
Abstract
A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins). We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB) and the knot-like threaded structural motif a Pierced Lasso (PL). In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso) in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets.
Collapse
Affiliation(s)
- Ellinor Haglund
- Center for Theoretical Biological Physics (CTBP) and Department of Physics, University of California at San Diego (UCSD), La Jolla, California, United States of America
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | | | - Jeffrey K. Noel
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Heiko Lammert
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Patricia A. Jennings
- Departments of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
66
|
Tubiana L. Computational study on the progressive factorization of composite polymer knots into separated prime components. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:052602. [PMID: 25353821 DOI: 10.1103/physreve.89.052602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Indexed: 06/04/2023]
Abstract
Using Monte Carlo simulations and advanced knot localization methods, we analyze the length and distribution of prime components in composite knots tied on freely jointed rings. For increasing contour length, we observe the progressive factorization of composite knots into separated prime components. However, we observe that a complete factorization, equivalent to the "decorated ring" picture, is not obtained even for rings of contour lengths N ≃ 3 N(0), about tens of times the most probable length of the prime knots tied on the rings. The decorated ring hypothesis has been used in the literature to justify the factorization of composite knot probabilities into the knotting probabilities of their prime components. Following our results, we suggest that such a hypothesis may not be necessary to explain the factorization of the knotting probabilities, at least when polymers excluding volume is not relevant. We rationalize the behavior of the system through a simple one-dimensional model in which prime knots are replaced by slip links randomly placed on a circle, with the only constraint being that the length of the loops has the same distribution as that of the length of the corresponding prime knots.
Collapse
Affiliation(s)
- Luca Tubiana
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana (Slovenia) and SISSA-Scuola Internazionale Superiore di Studi Avanzati Via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|
67
|
Piana S, Klepeis JL, Shaw DE. Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. Curr Opin Struct Biol 2014; 24:98-105. [DOI: 10.1016/j.sbi.2013.12.006] [Citation(s) in RCA: 294] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 01/15/2023]
|
68
|
Covino R, Skrbić T, Beccara SA, Faccioli P, Micheletti C. The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations. Biomolecules 2013; 4:1-19. [PMID: 24970203 PMCID: PMC4030985 DOI: 10.3390/biom4010001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/10/2013] [Accepted: 12/20/2013] [Indexed: 12/14/2022] Open
Abstract
For several decades, the presence of knots in naturally-occurring proteins was largely ruled out a priori for its supposed incompatibility with the efficiency and robustness of folding processes. For this very same reason, the later discovery of several unrelated families of knotted proteins motivated researchers to look into the physico-chemical mechanisms governing the concerted sequence of folding steps leading to the consistent formation of the same knot type in the same protein location. Besides experiments, computational studies are providing considerable insight into these mechanisms. Here, we revisit a number of such recent investigations within a common conceptual and methodological framework. By considering studies employing protein models with different structural resolution (coarse-grained or atomistic) and various force fields (from pure native-centric to realistic atomistic ones), we focus on the role of native and non-native interactions. For various unrelated instances of knotted proteins, non-native interactions are shown to be very important for favoring the emergence of conformations primed for successful self-knotting events.
Collapse
Affiliation(s)
- Roberto Covino
- Department of Physics, University of Trento, Via Sommarive 14, Trento 38123, Italy.
| | - Tatjana Skrbić
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, Trieste 34136, Italy.
| | - Silvio A Beccara
- Interdisciplinary Laboratory for Computational Science, FBK-CMM and University of Trento,Trento 38123, Italy.
| | - Pietro Faccioli
- Department of Physics, University of Trento, Via Sommarive 14, Trento 38123, Italy.
| | - Cristian Micheletti
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, Trieste 34136, Italy.
| |
Collapse
|
69
|
Unfolding thermodynamics of cysteine-rich proteins and molecular thermal-adaptation of marine ciliates. Biomolecules 2013; 3:967-85. [PMID: 24970199 PMCID: PMC4030967 DOI: 10.3390/biom3040967] [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: 09/09/2013] [Revised: 10/28/2013] [Accepted: 10/29/2013] [Indexed: 11/17/2022] Open
Abstract
Euplotes nobilii and Euplotes raikovi are phylogenetically closely allied species of marine ciliates, living in polar and temperate waters, respectively. Their evolutional relation and the sharply different temperatures of their natural environments make them ideal organisms to investigate thermal-adaptation. We perform a comparative study of the thermal unfolding of disulfide-rich protein pheromones produced by these ciliates. Recent circular dichroism (CD) measurements have shown that the two psychrophilic (E. nobilii) and mesophilic (E. raikovi) protein families are characterized by very different melting temperatures, despite their close structural homology. The enhanced thermal stability of the E. raikovi pheromones is realized notwithstanding the fact that these proteins form, as a rule, a smaller number of disulfide bonds. We perform Monte Carlo (MC) simulations in a structure-based coarse-grained (CG) model to show that the higher stability of the E. raikovi pheromones is due to the lower locality of the disulfide bonds, which yields a lower entropy increase in the unfolding process. Our study suggests that the higher stability of the mesophilic E. raikovi phermones is not mainly due to the presence of a strongly hydrophobic core, as it was proposed in the literature. In addition, we argue that the molecular adaptation of these ciliates may have occurred from cold to warm, and not from warm to cold. To provide a testable prediction, we identify a point-mutation of an E. nobilii pheromone that should lead to an unfolding temperature typical of that of E. raikovi pheromones.
Collapse
|
70
|
Native contacts determine protein folding mechanisms in atomistic simulations. Proc Natl Acad Sci U S A 2013; 110:17874-9. [PMID: 24128758 DOI: 10.1073/pnas.1311599110] [Citation(s) in RCA: 420] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent availability of long equilibrium simulations of protein folding in atomistic detail for more than 10 proteins allows us to identify the key interactions driving folding. We find that the collective fraction of native amino acid contacts, Q, captures remarkably well the transition states for all the proteins with a folding free energy barrier. Going beyond this global picture, we devise two different measures to quantify the importance of individual interresidue contacts in the folding mechanism: (i) the log-ratio of lifetimes of contacts during folding transition paths and in the unfolded state and (ii) a Bayesian measure of how predictive the formation of each contact is for being on a transition path. Both of these measures indicate that native, or near-native, contacts are important for determining mechanism, as might be expected. More remarkably, however, we found that for almost all the proteins, with the designed protein α3D being a notable exception, nonnative contacts play no significant part in determining folding mechanisms.
Collapse
|