1
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Especial JNC, Faísca PFN. Effects of sequence-dependent non-native interactions in equilibrium and kinetic folding properties of knotted proteins. J Chem Phys 2023; 159:065101. [PMID: 37551809 DOI: 10.1063/5.0160886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023] Open
Abstract
Determining the role of non-native interactions in folding dynamics, kinetics, and mechanisms is a classic problem in protein folding. More recently, this question has witnessed a renewed interest in light of the hypothesis that knotted proteins require the assistance of non-native interactions to fold efficiently. Here, we conduct extensive equilibrium and kinetic Monte Carlo simulations of a simple off-lattice C-alpha model to explore the role of non-native interactions in the thermodynamics and kinetics of three proteins embedding a trefoil knot in their native structure. We find that equilibrium knotted conformations are stabilized by non-native interactions that are non-local, and proximal to native ones, thus enhancing them. Additionally, non-native interactions increase the knotting frequency at high temperatures, and in partially folded conformations below the transition temperatures. Although non-native interactions clearly enhance the efficiency of transition from an unfolded conformation to a partially folded knotted one, they are not required to efficiently fold a knotted protein. Indeed, a native-centric interaction potential drives the most efficient folding transition, provided that the simulation temperature is well below the transition temperature of the considered model system.
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Affiliation(s)
- João N C Especial
- Departamento de Física, Faculdade de Ciências, Ed. C8, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Patrícia F N Faísca
- Departamento de Física, Faculdade de Ciências, Ed. C8, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
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2
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Dahlstrom TJ, Capraro DT, Jennings PA, Finke JM. Knotting Optimization and Folding Pathways of a Go-Model with a Deep Knot. J Phys Chem B 2022; 126:10221-10236. [PMID: 36424347 DOI: 10.1021/acs.jpcb.2c05588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Formation of protein knots is an intriguing offshoot of the protein folding problem. Since experimental resolution on knot formation is limited, theoretical methods currently provide the most detailed insights into the knotting process. While suitable for shallow knots, molecular dynamics simulations have faced challenges capturing the formation of deep knots in proteins such as the minimally tied trefoil α/β methyltransferase from Thermotoga maritima (MTTTM). To improve the efficiency of MTTTM knotting in Cα Go-model simulations, mutant variants of the MTTTM Go-model were investigated. Through a structure-based analysis of knotted and unknotted states, four residues (K71, R72, E75, V76) were identified to increase the knotting efficiency from 2% to 83% when their contact energies were doubled and dihedral strength around the knot loop increased. The key features of this model are (i) a C-terminal slipknot intermediate that threads the knot in a highly unstructured intermediate, (ii) the inability to knot in native-like intermediate states, and (iii) a minor population in a long-lived trap that cannot knot. Examination of residue 71-76 contacts provides a small set of potential mutants that can directly test the model's validity. In addition, the knotting optimization process developed here has broad applicability in generating knotting-efficient models of other knotted proteins.
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Affiliation(s)
- Thomas J Dahlstrom
- Division of Sciences and Mathematics, Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington98402, United States
| | - Dominique T Capraro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California92093, United States
| | - Particia A Jennings
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California92093, United States
| | - John M Finke
- Division of Sciences and Mathematics, Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington98402, United States
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3
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A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins. Int J Mol Sci 2022; 23:ijms232213871. [PMID: 36430350 PMCID: PMC9695063 DOI: 10.3390/ijms232213871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Monte Carlo simulations are a powerful technique and are widely used in different fields. When applied to complex molecular systems with long chains, such as those in synthetic polymers and proteins, they have the advantage of providing a fast and computationally efficient way to sample equilibrium ensembles and calculate thermodynamic and structural properties under desired conditions. Conformational Monte Carlo techniques employ a move set to perform the transitions in the simulation Markov chain. While accepted conformations must preserve the sequential bonding of the protein chain model and excluded volume among its units, the moves themselves may take the chain across itself. We call this a break in linear topology preservation. In this manuscript, we show, using simple protein models, that there is no difference in equilibrium properties calculated with a move set that preserves linear topology and one that does not. However, for complex structures, such as those of deeply knotted proteins, the preservation of linear topology provides correct equilibrium results but only after long relaxation. In any case, to analyze folding pathways, knotting mechanisms and folding kinetics, the preservation of linear topology may be an unavoidable requirement.
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4
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Zhu H, Tian F, Sun L, Zhu Y, Qiu Q, Dai L. Computational Design of Extraordinarily Stable Peptide Structures through Side-Chain-Locked Knots. J Phys Chem Lett 2022; 13:7741-7748. [PMID: 35969173 DOI: 10.1021/acs.jpclett.2c02385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Extraordinarily stable protein and peptide structures are critically demanded in many applications. Typical approaches to enhance protein and peptide stability are strengthening certain interactions. Here, we develop a very different approach: stabilizing peptide structures through side-chain-locked knots. More specifically, a peptide core consists of a knot, which is prevented from unknotting and unfolding by large side chains of amino acids at knot boundaries. These side chains impose free energy barriers for unknotting. The free energy barriers are quantified using all-atom and coarse-grained simulations. The barriers become infinitely high for large side chains and tight knot cores, resulting in stable peptide structures, which never unfold unless one chemical bond is broken. The extraordinary stability is essentially kinetic stability. Our new approach lifts the thermodynamic restriction in designing peptide structures, provides extra freedom in selecting sequence and structural motifs that are thermodynamically unstable, and should expand the functionality of peptides. This work also provides a bottom-up understanding of how knotting enhances protein stability.
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Affiliation(s)
- Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Yongjian Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Qiyuan Qiu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
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5
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6
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Especial JNC, Faísca PFN. A Specific Set of Heterogeneous Native Interactions Yields Efficient Knotting in Protein Folding. J Phys Chem B 2021; 125:7359-7367. [PMID: 34197706 DOI: 10.1021/acs.jpcb.1c03127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Native interactions are crucial for folding, and non-native interactions appear to be critical for efficiently knotting proteins. Therefore, it is important to understand both their roles in the folding of knotted proteins. It has been proposed that non-native interactions drive the correct order of contact formation, which is essential to avoid backtracking and efficiently self-tie. In this study, we ask if non-native interactions are strictly necessary to tangle a protein or if the correct order of contact formation can be assured by a specific set of native, but otherwise heterogeneous (i.e., having distinct energies), interactions. In order to address this problem, we conducted extensive Monte Carlo simulations of lattice models of protein-like sequences designed to fold into a preselected knotted conformation embedding a trefoil knot. We were able to identify a specific set of heterogeneous native interactions that drives efficient knotting and is able to fold the protein when combined with the remaining native interactions modeled as homogeneous. This specific set of heterogeneous native interactions is strictly enough to efficiently self-tie. A distinctive feature of these native interactions is that they do not backtrack because their energies ensure the correct order of contact formation. Furthermore, they stabilize a knotted intermediate state, which is en route to the native structure. Our results thus show that-at least in the context of the adopted model-non-native interactions are not necessary to knot a protein. However, when they are taken into account in protein energetics, it is possible to find specific, nonlocal non-native interactions that operate as a scaffold that assists the knotting step.
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Affiliation(s)
- João N C Especial
- Departamento de Física, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.,BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal
| | - Patrícia F N Faísca
- Departamento de Física, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.,BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal
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7
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Abstract
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here, we investigate the relation between knotoids differing only by small perturbations of the direction of projection. Since such knotoids are connected by at most a single forbidden move, we characterize forbidden moves in terms of equivariant band attachment between strongly invertible knots and of strand passages between
θ
-curves. This allows for the determination of the optimal sample size needed to produce a well-approximated knotoid distribution. Based on that and on topological properties of the distribution, we probe the depth of knotted proteins with the trefoil as the predominant knot type without using subchain analysis.
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Affiliation(s)
- Agnese barbensi
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
| | - Dimos Goundaroulis
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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8
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Simien JM, Haglund E. Topological Twists in Nature. Trends Biochem Sci 2021; 46:461-471. [PMID: 33419636 DOI: 10.1016/j.tibs.2020.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 11/25/2022]
Abstract
The first entangled protein was observed about 30 years ago, resulting in an increased interest for uncovering the biological functions and biophysical properties of these complex topologies. Recently, the Pierced Lasso Topology (PLT) was discovered in which a covalent bond forms an intramolecular loop, leaving one or both termini free to pierce the loop. This topology is related to knots and other entanglements. PLTs exist in many well-researched systems where the PLTs have previously been unnoticed. PLTs represents 18% of all disulfide containing proteins across all kingdoms of life. In this review, we investigate the biological implications of this specific topology in which the PLT-forming disulfide may act as a molecular switch for protein function and consequently human health.
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Affiliation(s)
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, USA.
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9
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Piejko M, Niewieczerzal S, Sulkowska JI. The Folding of Knotted Proteins: Distinguishing the Distinct Behavior of Shallow and Deep Knots. Isr J Chem 2020. [DOI: 10.1002/ijch.202000036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maciej Piejko
- Faculty of ChemistryUniversity of Warsaw Pasteura 1 Warsaw 02-093 Poland
- Centre of New TechnologiesUniversity of Warsaw Banacha 2c Warsaw 02-097 Poland
| | | | - Joanna I. Sulkowska
- Faculty of ChemistryUniversity of Warsaw Pasteura 1 Warsaw 02-093 Poland
- Centre of New TechnologiesUniversity of Warsaw Banacha 2c Warsaw 02-097 Poland
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10
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Perego C, Potestio R. Computational methods in the study of self-entangled proteins: a critical appraisal. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:443001. [PMID: 31269476 DOI: 10.1088/1361-648x/ab2f19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The existence of self-entangled proteins, the native structure of which features a complex topology, unveils puzzling, and thus fascinating, aspects of protein biology and evolution. The discovery that a polypeptide chain can encode the capability to self-entangle in an efficient and reproducible way during folding, has raised many questions, regarding the possible function of these knots, their conservation along evolution, and their role in the folding paradigm. Understanding the function and origin of these entanglements would lead to deep implications in protein science, and this has stimulated the scientific community to investigate self-entangled proteins for decades by now. In this endeavour, advanced experimental techniques are more and more supported by computational approaches, that can provide theoretical guidelines for the interpretation of experimental results, and for the effective design of new experiments. In this review we provide an introduction to the computational study of self-entangled proteins, focusing in particular on the methodological developments related to this research field. A comprehensive collection of techniques is gathered, ranging from knot theory algorithms, that allow detection and classification of protein topology, to Monte Carlo or molecular dynamics strategies, that constitute crucial instruments for investigating thermodynamics and kinetics of this class of proteins.
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Affiliation(s)
- Claudio Perego
- Max Panck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
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11
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Kumar Sharma R, Agrawal I, Dai L, Doyle PS, Garaj S. Complex DNA knots detected with a nanopore sensor. Nat Commun 2019; 10:4473. [PMID: 31578328 PMCID: PMC6775256 DOI: 10.1038/s41467-019-12358-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/27/2019] [Indexed: 01/15/2023] Open
Abstract
Equilibrium knots are common in biological polymers-their prevalence, size distribution, structure, and dynamics have been extensively studied, with implications to fundamental biological processes and DNA sequencing technologies. Nanopore microscopy is a high-throughput single-molecule technique capable of detecting the shape of biopolymers, including DNA knots. Here we demonstrate nanopore sensors that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding. We show the occurrence of both tight and loose knots, reconciling previous contradictory results from different experimental techniques. We evidence the occurrence of two quantitatively different modes of knot translocation through the nanopores, involving very different tension forces. With large statistics, we explore the complex knots and, for the first time, reveal the existence of rare composite knots. We use parametrized complexity, in concert with simulations, to test the theoretical assumptions of the models, further asserting the relevance of nanopores in future investigation of knots.
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Affiliation(s)
- Rajesh Kumar Sharma
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
- Singapore-MIT Alliance for Research and Technology Centre, 1 CREATE Way, Singapore, 138602, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore
| | - Ishita Agrawal
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
| | - Liang Dai
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Patrick S Doyle
- Singapore-MIT Alliance for Research and Technology Centre, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Slaven Garaj
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore.
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore.
- Department of Physics, National University of Singapore, Singapore, Science Drive 3, Singapore, 117551, Singapore.
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12
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Especial J, Nunes A, Rey A, Faísca PF. Hydrophobic confinement modulates thermal stability and assists knotting in the folding of tangled proteins. Phys Chem Chem Phys 2019; 21:11764-11775. [PMID: 31114834 DOI: 10.1039/c9cp01701a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
There is growing support for the idea that the in vivo folding process of knotted proteins is assisted by chaperonins, but the mechanism of chaperonin assisted folding remains elusive. Here, we conduct extensive Monte Carlo simulations of lattice and off-lattice models to explore the effects of confinement and hydrophobic intermolecular interactions with the chaperonin cage in the folding and knotting processes. We find that moderate to high protein-cavity interactions (which are likely to be established in the beginning of the chaperonin working cycle) cause an energetic destabilization of the protein that overcomes the entropic stabilization driven by excluded volume, and leads to a decrease of the melting temperature relative to bulk conditions. Moreover, mild-to-moderate hydrophobic interactions with the cavity (which would be established later in the cycle) lead to a significant enhancement of knotting probability in relation to bulk conditions while simultaneously moderating the effect of steric confinement in the enhancement of thermal stability. Our results thus indicate that the chaperonin may be able to assist knotting without simultaneously thermally stabilizing potential misfolded states to a point that would hamper productive folding thus compromising its functional role.
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Affiliation(s)
- João Especial
- Departamento de Física, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.
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13
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14
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Sriramoju MK, Chen Y, Lee YTC, Hsu STD. Topologically knotted deubiquitinases exhibit unprecedented mechanostability to withstand the proteolysis by an AAA+ protease. Sci Rep 2018; 8:7076. [PMID: 29728659 PMCID: PMC5935755 DOI: 10.1038/s41598-018-25470-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/23/2018] [Indexed: 01/03/2023] Open
Abstract
More than one thousand knotted protein structures have been identified so far, but the functional roles of these knots remain elusive. It has been postulated that backbone entanglement may provide additional mechanostability. Here, we employed a bacterial proteasome, ClpXP, to mechanically unfold 52-knotted human ubiquitin C-terminal hydrolase (UCH) paralogs from their C-termini, followed by processive translocation into the proteolytic chamber for degradation. Our results revealed unprecedentedly slow kinetics of ClpXP-mediated proteolysis for the proteasome-associated UCHL5: ten thousand times slower than that of a green fluorescence protein (GFP), which has a comparable size to the UCH domain but much higher chemical and thermal stabilities. The ClpXP-dependent mechanostability positively correlates with the intrinsic unfolding rates of the substrates, spanning over several orders of magnitude for the UCHs. The broad range of mechanostability within the same protein family may be associated with the functional requirements for their differential malleabilities.
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Affiliation(s)
| | - Yen Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun-Tzai Cloud Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
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15
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Soler MA, Rey A, Faísca PFN. Steric confinement and enhanced local flexibility assist knotting in simple models of protein folding. Phys Chem Chem Phys 2018; 18:26391-26403. [PMID: 27722468 DOI: 10.1039/c6cp05086g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The chaperonin complex GroEL-GroES is able to accelerate the folding process of knotted proteins considerably. However, the folding mechanism inside the chaperonin cage is elusive. Here we use a combination of lattice and off-lattice Monte Carlo simulations of simple Gō models to study the effect of physical confinement and local flexibility on the folding process of protein model systems embedding a trefoil knot in their native structure. This study predicts that steric confinement plays a specific role in the folding of knotted proteins by increasing the knotting probability for very high degrees of confinement. This effect is observed for protein MJ0366 even above the melting temperature for confinement sizes compatible with the size of the GroEL/GroES chaperonin cage. An enhanced local flexibility produces the same qualitative effects on the folding process. In particular, we observe that knotting probability increases up to 40% in the transition state of protein MJ0366 when flexibility is enhanced. This is underlined by a structural change in the transition state, which becomes devoid of helical content. No relation between the knotting mechanism and flexibility was found in the context of the off-lattice model adopted in this work.
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Affiliation(s)
- Miguel A Soler
- Dipartimento di Scienze Mediche e Biologiche, Universita' di Udine, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Antonio Rey
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain.
| | - Patrícia F N Faísca
- Departamento de Física and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.
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16
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The energy cost of polypeptide knot formation and its folding consequences. Nat Commun 2017; 8:1581. [PMID: 29146980 PMCID: PMC5691195 DOI: 10.1038/s41467-017-01691-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 10/09/2017] [Indexed: 11/08/2022] Open
Abstract
Knots are natural topologies of chains. Yet, little is known about spontaneous knot formation in a polypeptide chain—an event that can potentially impair its folding—and about the effect of a knot on the stability and folding kinetics of a protein. Here we used optical tweezers to show that the free energy cost to form a trefoil knot in the denatured state of a polypeptide chain of 120 residues is 5.8 ± 1 kcal mol−1. Monte Carlo dynamics of random chains predict this value, indicating that the free energy cost of knot formation is of entropic origin. This cost is predicted to remain above 3 kcal mol−1 for denatured proteins as large as 900 residues. Therefore, we conclude that naturally knotted proteins cannot attain their knot randomly in the unfolded state but must pay the cost of knotting through contacts along their folding landscape. The effect of knots on protein stability and folding kinetics is not well understood. Here the authors combine optical tweezer experiments and calculations to experimentally determine the energy cost for knot formation, which indicates that knotted proteins evolved specific folding pathways because knot formation in unfolded chains is unfavorable.
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17
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Dabrowski-Tumanski P, Sulkowska JI. To Tie or Not to Tie? That Is the Question. Polymers (Basel) 2017; 9:E454. [PMID: 30965758 PMCID: PMC6418553 DOI: 10.3390/polym9090454] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 12/18/2022] Open
Abstract
In this review, we provide an overview of entangled proteins. Around 6% of protein structures deposited in the PBD are entangled, forming knots, slipknots, lassos and links. We present theoretical methods and tools that enabled discovering and classifying such structures. We discuss the advantages and disadvantages of the non-trivial topology in proteins, based on available data about folding, stability, biological properties and evolutionary conservation. We also formulate intriguing and challenging questions on the border of biophysics, bioinformatics, biology and mathematics, which arise from the discovery of an entanglement in proteins. Finally, we discuss possible applications of entangled proteins in medicine and nanotechnology, such as the chance to design super stable proteins, whose stability could be controlled by chemical potential.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.
- Faculty of Chemistry, University of Warsaw, Warsaw 02-093, Poland.
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.
- Faculty of Chemistry, University of Warsaw, Warsaw 02-093, Poland.
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18
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Zhang H, Jackson SE. Characterization of the Folding of a 5 2-Knotted Protein Using Engineered Single-Tryptophan Variants. Biophys J 2017; 111:2587-2599. [PMID: 28002735 DOI: 10.1016/j.bpj.2016.10.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 11/16/2022] Open
Abstract
An increasing number of proteins that contain topological knots have been identified over the past two decades; however, their folding mechanisms are still not well understood. UCH-L1 has a 52-knotted topology. Here, we constructed a series of variants that contain a single tryptophan at different locations along the polypeptide chain. A study of the thermodynamic properties of the variants shows that the structure of UCH-L1 is remarkably tolerant to incorporation of bulky tryptophan side chains. Comprehensive kinetic studies of the variants reveal that they fold via parallel pathways on which there are two intermediate states very similar to wild-type UCH-L1. The structures of the intermediate states do not change significantly with mutation and therefore occupy local minima on the energy landscape that have relatively narrow basins. The kinetic studies also establish that there are considerably more tertiary interactions in the intermediate states than results from previous NMR studies suggested. The two intermediates differ from each other in the extent to which tertiary interactions between the highly stable central β-sheet and flanking α-helices and loop regions are formed. There is strong evidence that these states are aggregation prone. The transition states from both I1 and I2 to the native state are plastic and change with mutation and denaturant concentration. Previous studies indicated that the threading event that creates the 52 knot occurs during these steps, suggesting that there is a broad energy barrier consistent with the chain undergoing some searching of conformational space as the threading takes place.
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Affiliation(s)
- Hongyu Zhang
- Department of Chemistry, Cambridge University, Cambridge, United Kingdom; St. Edmund's College, Cambridge University, Cambridge, United Kingdom
| | - Sophie E Jackson
- Department of Chemistry, Cambridge University, Cambridge, United Kingdom.
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19
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Soler MA, Fortuna S. Influence of Linker Flexibility on the Binding Affinity of Bidentate Binders. J Phys Chem B 2017; 121:3918-3924. [PMID: 28379693 DOI: 10.1021/acs.jpcb.6b12627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The design of responsive nanosensors typically relies on the availability of probes capable of capturing their target with high affinity and specificity. This can be achieved by coupling two or more binding units through a linker. In this work, we study the dependence on the binder architecture of the binding affinity between a target molecule and a semirigid bidentate binder. Using two different binder architectures, central-rigid and extreme-rigid, and modifying the length and the flexibility degree of the linker we generated 153 different architectures. We computed their dissociation free energies by means of Monte Carlo simulations and thermodynamic integration. We found that central-rigid bidentate binders are a poor choice, as they dissociate more easily than analogous fully flexible bidentate binders. On the other hand, molecular architectures presenting extreme-rigid units were shown effective for a wide range of set-ups.
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Affiliation(s)
- Miguel A Soler
- Molecular Nanotechnology for Life Science Applications Theory Group, Department of Medical and Biological Sciences, University of Udine , Udine, 33100, Italy.,SISSA , Via Bonomea 265, Trieste, Italy
| | - Sara Fortuna
- Molecular Nanotechnology for Life Science Applications Theory Group, Department of Medical and Biological Sciences, University of Udine , Udine, 33100, Italy.,SISSA , Via Bonomea 265, Trieste, Italy.,Center for Biomedical Sciences and Engineering, University of Nova Gorica , Nova Gorica, Goriška 5000, Slovenia
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20
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Haglund E, Pilko A, Wollman R, Jennings PA, Onuchic JN. Pierced Lasso Topology Controls Function in Leptin. J Phys Chem B 2017; 121:706-718. [PMID: 28035835 DOI: 10.1021/acs.jpcb.6b11506] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein engineering is a powerful tool in drug design and therapeutics, where disulphide bridges are commonly introduced to stabilize proteins. However, these bonds also introduce covalent loops, which are often neglected. These loops may entrap the protein backbone on opposite sides, leading to a "knotted" topology, forming a so-called Pierced Lasso (PL). In this elegant system, the "knot" is held together with a single disulphide bridge where part of the polypeptide chain is threaded through. The size and position of these covalent loops can be manipulated through protein design in vitro, whereas nature uses polymorphism to switch the PL topology. The PL protein leptin shows genetic modification of an N-terminal residue, adding a third cysteine to the same sequence. In an effort to understand the mechanism of threading of these diverse topologies, we designed three loop variants to mimic the polymorphic sequence. This adds elegance to the system under study, as it allows the generation of three possible covalent loops; they are the original wild-type C-terminal loop protein, the fully circularized unthreaded protein, and the N-terminal loop protein, responsible for different lasso topologies. The size of the loop changes the threading mechanism from a slipknotting to a plugging mechanism, with increasing loop size. Interestingly, the ground state of the native protein structure is largely unaffected, but biological assays show that the activity is maximized by properly controlled dynamics in the threaded state. A threaded topology with proper conformational dynamics is important for receptor interaction and activation of the signaling pathways in vivo.
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Affiliation(s)
- Ellinor Haglund
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biosciences, Rice University , Houston, Texas, United States
| | - Anna Pilko
- Department of Chemistry and Biochemistry, The University of California, San Diego (UCSD) , La Jolla, California, United States
| | - Roy Wollman
- Department of Chemistry and Biochemistry, The University of California, San Diego (UCSD) , La Jolla, California, United States
| | - Patricia Ann Jennings
- Department of Chemistry and Biochemistry, The University of California, San Diego (UCSD) , La Jolla, California, United States
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biosciences, Rice University , Houston, Texas, United States
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21
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Untangling the Influence of a Protein Knot on Folding. Biophys J 2016; 110:1044-51. [PMID: 26958882 DOI: 10.1016/j.bpj.2016.01.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 01/01/2016] [Accepted: 01/14/2016] [Indexed: 10/22/2022] Open
Abstract
Entanglement and knots occur across all aspects of the physical world. Despite the common belief that knots are too complicated for incorporation into proteins, knots have been identified in the native fold of a growing number of proteins. The discovery of proteins with this unique backbone characteristic has challenged the preconceptions about the complexity of biological structures, as well as current folding theories. Given the intricacies of the knotted geometry, the interplay between a protein's fold, structure, and function is of particular interest. Interestingly, for most of these proteins, the knotted region appears critical both in folding and function, although full understanding of these contributions is still incomplete. Here, we experimentally reveal the impact of the knot on the landscape, the origin of the bistable nature of the knotted protein, and broaden the view of knot formation as uniquely decoupled from folding.
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22
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Najafi S, Potestio R. Folding of small knotted proteins: Insights from a mean field coarse-grained model. J Chem Phys 2016; 143:243121. [PMID: 26723606 DOI: 10.1063/1.4934541] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.
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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
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23
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Baiesi M, Orlandini E, Trovato A, Seno F. Linking in domain-swapped protein dimers. Sci Rep 2016; 6:33872. [PMID: 27659606 PMCID: PMC5034241 DOI: 10.1038/srep33872] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/05/2016] [Indexed: 11/24/2022] Open
Abstract
The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, makes such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter G', termed Gaussian entanglement, is strongly correlated with the linking number. Based on 110 non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with |G'| > 1. We report that Nature promotes configurations with negative mutual entanglement and surprisingly, it seems to suppress intertwining in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties.
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Affiliation(s)
- Marco Baiesi
- Department of Physics and Astronomy, University of Padova, Padova, Italy
- INFN-Sezione di Padova, Padova, Italy
| | - Enzo Orlandini
- Department of Physics and Astronomy, University of Padova, Padova, Italy
- INFN-Sezione di Padova, Padova, Italy
| | - Antonio Trovato
- Department of Physics and Astronomy, University of Padova, Padova, Italy
- CNISM-Unità di Padova, Padova, Italy
| | - Flavio Seno
- Department of Physics and Astronomy, University of Padova, Padova, Italy
- CNISM-Unità di Padova, Padova, Italy
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24
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Folding analysis of the most complex Stevedore's protein knot. Sci Rep 2016; 6:31514. [PMID: 27527519 PMCID: PMC4985754 DOI: 10.1038/srep31514] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022] Open
Abstract
DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore's protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I'. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I' to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures.
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25
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Lim NCH, Jackson SE. Molecular knots in biology and chemistry. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354101. [PMID: 26291690 DOI: 10.1088/0953-8984/27/35/354101] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.
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Affiliation(s)
- Nicole C H Lim
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. Faculty of Sciences, Universiti Brunei Darussalam, Gadong BE 1410, Brunei Darussalam
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26
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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.
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27
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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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28
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An intramolecular lock facilitates folding and stabilizes the tertiary structure of Streptococcus mutans adhesin P1. Proc Natl Acad Sci U S A 2014; 111:15746-51. [PMID: 25331888 DOI: 10.1073/pnas.1413018111] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cariogenic bacterium Streptococcus mutans uses adhesin P1 to adhere to tooth surfaces, extracellular matrix components, and other bacteria. A composite model of P1 based on partial crystal structures revealed an unusual complex architecture in which the protein forms an elongated hybrid alpha/polyproline type II helical stalk by folding back on itself to display a globular head at the apex and a globular C-terminal region at the base. The structure of P1's N terminus and the nature of its critical interaction with the C-terminal region remained unknown, however. We have cocrystallized a stable complex of recombinant N- and C-terminal fragments and here describe a previously unidentified topological fold in which these widely discontinuous domains are intimately associated. The structure reveals that the N terminus forms a stabilizing scaffold by wrapping behind the base of P1's elongated stalk and physically "locking" it into place. The structure is stabilized through a highly favorable ΔG(solvation) on complex formation, along with extensive hydrogen bonding. We confirm the functional relevance of this intramolecular interaction using differential scanning calorimetry and circular dichroism to show that disruption of the proper spacing of residues 989-1001 impedes folding and diminishes stability of the full-length molecule, including the stalk. Our findings clarify previously unexplained functional and antigenic properties of P1.
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29
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Mashaghi A, van Wijk R, Tans S. Circuit Topology of Proteins and Nucleic Acids. Structure 2014; 22:1227-1237. [DOI: 10.1016/j.str.2014.06.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 05/10/2014] [Accepted: 06/17/2014] [Indexed: 01/19/2023]
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30
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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
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31
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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
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32
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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.
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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.
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