1
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Magi Meconi G, Sasselli IR, Bianco V, Onuchic JN, Coluzza I. Key aspects of the past 30 years of protein design. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:086601. [PMID: 35704983 DOI: 10.1088/1361-6633/ac78ef] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Proteins are the workhorse of life. They are the building infrastructure of living systems; they are the most efficient molecular machines known, and their enzymatic activity is still unmatched in versatility by any artificial system. Perhaps proteins' most remarkable feature is their modularity. The large amount of information required to specify each protein's function is analogically encoded with an alphabet of just ∼20 letters. The protein folding problem is how to encode all such information in a sequence of 20 letters. In this review, we go through the last 30 years of research to summarize the state of the art and highlight some applications related to fundamental problems of protein evolution.
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Affiliation(s)
- Giulia Magi Meconi
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | - Ivan R Sasselli
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | | | - Jose N Onuchic
- Center for Theoretical Biological Physics, Department of Physics & Astronomy, Department of Chemistry, Department of Biosciences, Rice University, Houston, TX 77251, United States of America
| | - Ivan Coluzza
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Bld. Martina Casiano, UPV/EHU Science Park, Barrio Sarriena s/n, 48940 Leioa, Spain
- Basque Foundation for Science, Ikerbasque, 48009, Bilbao, Spain
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2
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Takahashi T, Chikenji G, Tokita K. Lattice protein design using Bayesian learning. Phys Rev E 2021; 104:014404. [PMID: 34412286 DOI: 10.1103/physreve.104.014404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/11/2021] [Indexed: 01/01/2023]
Abstract
Protein design is the inverse approach of the three-dimensional (3D) structure prediction for elucidating the relationship between the 3D structures and amino acid sequences. In general, the computation of the protein design involves a double loop: A loop for amino acid sequence changes and a loop for an exhaustive conformational search for each amino acid sequence. Herein, we propose a novel statistical mechanical design method using Bayesian learning, which can design lattice proteins without the exhaustive conformational search. We consider a thermodynamic hypothesis of the evolution of proteins and apply it to the prior distribution of amino acid sequences. Furthermore, we take the water effect into account in view of the grand canonical picture. As a result, on applying the 2D lattice hydrophobic-polar (HP) model, our design method successfully finds an amino acid sequence for which the target conformation has a unique ground state. However, the performance was not as good for the 3D lattice HP models compared to the 2D models. The performance of the 3D model improves on using a 20-letter lattice proteins. Furthermore, we find a strong linearity between the chemical potential of water and the number of surface residues, thereby revealing the relationship between protein structure and the effect of water molecules. The advantage of our method is that it greatly reduces computation time, because it does not require long calculations for the partition function corresponding to an exhaustive conformational search. As our method uses a general form of Bayesian learning and statistical mechanics and is not limited to lattice proteins, the results presented here elucidate some heuristics used successfully in previous protein design methods.
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Affiliation(s)
- Tomoei Takahashi
- Graduate School of Informatics, Nagoya University, Nagoya 464-8601, Japan
| | - George Chikenji
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Kei Tokita
- Graduate School of Informatics, Nagoya University, Nagoya 464-8601, Japan
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3
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Škrbić T, Hoang TX, Giacometti A, Maritan A, Banavar JR. Spontaneous dimensional reduction and ground state degeneracy in a simple chain model. Phys Rev E 2021; 104:L012101. [PMID: 34412247 DOI: 10.1103/physreve.104.l012101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/08/2021] [Indexed: 11/07/2022]
Abstract
Chain molecules play a key role in the polymer field and in living cells. Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interaction promoting compactness. We analyze the model using simple analytic arguments complemented by extensive computer simulations. We find several striking results: there is a first-order transition from a high-temperature random coil phase to a highly unusual low-temperature phase; the modular ground states exhibit significant degeneracy; the ground state structures exhibit spontaneous dimensional reduction and have a two-layer structure; and the ground states are assembled from secondary motifs of helices and strands connected by tight loops. We discuss the similarities and notable differences between the ground state structures [we call these PoSSuM (Planar Structures with Secondary Motifs)] in the phase and protein native state structures.
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Affiliation(s)
- Tatjana Škrbić
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, USA and Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy
| | - Trinh Xuan Hoang
- Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Ba Dinh, Hanoi 11108, Vietnam
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy and European Center for Living Technologies (ECLT), Ca' Bottacin, Dorsoduro 3911 Calle Crosera, 30123 Venezia, Italy
| | - Amos Maritan
- Dipartimento di Fisica e Astronomia, Università di Padova and INFN, via Marzolo 8, 35131 Padova, Italy
| | - Jayanth R Banavar
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, USA
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4
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Giulini M, Rigoli M, Mattiotti G, Menichetti R, Tarenzi T, Fiorentini R, Potestio R. From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules. Front Mol Biosci 2021; 8:676976. [PMID: 34164432 PMCID: PMC8215203 DOI: 10.3389/fmolb.2021.676976] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/06/2021] [Indexed: 12/18/2022] Open
Abstract
The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.
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Affiliation(s)
- Marco Giulini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Marta Rigoli
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Giovanni Mattiotti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Roberto Menichetti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Thomas Tarenzi
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaele Fiorentini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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5
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Sormani G, Harteveld Z, Rosset S, Correia B, Laio A. A Rosetta-based protein design protocol converging to natural sequences. J Chem Phys 2021; 154:074114. [DOI: 10.1063/5.0039240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
| | - Zander Harteveld
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne CH-1015, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Stéphane Rosset
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne CH-1015, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Bruno Correia
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne CH-1015, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
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6
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Nerattini F, Figliuzzi M, Cardelli C, Tubiana L, Bianco V, Dellago C, Coluzza I. Identification of Protein Functional Regions. Chemphyschem 2020; 21:335-347. [PMID: 31944517 DOI: 10.1002/cphc.201900898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/01/2019] [Indexed: 11/12/2022]
Abstract
Protein sequence stores the information relative to both functionality and stability, thus making it difficult to disentangle the two contributions. However, the identification of critical residues for function and stability has important implications for the mapping of the proteome interactions, as well as for many pharmaceutical applications, e. g. the identification of ligand binding regions for targeted pharmaceutical protein design. In this work, we propose a computational method to identify critical residues for protein functionality and stability and to further categorise them in strictly functional, structural and intermediate. We evaluate single site conservation and use Direct Coupling Analysis (DCA) to identify co-evolved residues both in natural and artificial evolution processes. We reproduce artificial evolution using protein design and base our approach on the hypothesis that artificial evolution in the absence of any functional constraint would exclusively lead to site conservation and co-evolution events of the structural type. Conversely, natural evolution intrinsically embeds both functional and structural information. By comparing the lists of conserved and co-evolved residues, outcomes of the analysis on natural and artificial evolution, we identify the functional residues without the need of any a priori knowledge of the biological role of the analysed protein.
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Affiliation(s)
- Francesca Nerattini
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Matteo Figliuzzi
- Sorbonne Universites, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative UMR, 7238, Paris, France
| | - Chiara Cardelli
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Luca Tubiana
- Physics Department, Universitá degli studi di Trento, via Sommarive 14, 38123, Trento, IT
| | - Valentino Bianco
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria.,Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, Madrid, 28040, Spain
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Ivan Coluzza
- CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain, and IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain
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7
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Nerattini F, Tubiana L, Cardelli C, Bianco V, Dellago C, Coluzza I. Protein design under competing conditions for the availability of amino acids. Sci Rep 2020; 10:2684. [PMID: 32060385 PMCID: PMC7021711 DOI: 10.1038/s41598-020-59401-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 12/08/2019] [Indexed: 11/09/2022] Open
Abstract
Isolating the properties of proteins that allow them to convert sequence into the structure is a long-lasting biophysical problem. In particular, studies focused extensively on the effect of a reduced alphabet size on the folding properties. However, the natural alphabet is a compromise between versatility and optimisation of the available resources. Here, for the first time, we include the impact of the relative availability of the amino acids to extract from the 20 letters the core necessary for protein stability. We present a computational protein design scheme that involves the competition for resources between a protein and a potential interaction partner that, additionally, gives us the chance to investigate the effect of the reduced alphabet on protein-protein interactions. We devise a scheme that automatically identifies the optimal reduced set of letters for the design of the protein, and we observe that even alphabets reduced down to 4 letters allow for single protein folding. However, it is only with 6 letters that we achieve optimal folding, thus recovering experimental observations. Additionally, we notice that the binding between the protein and a potential interaction partner could not be avoided with the investigated reduced alphabets. Therefore, we suggest that aggregation could have been a driving force in the evolution of the large protein alphabet.
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Affiliation(s)
- Francesca Nerattini
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Luca Tubiana
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Chiara Cardelli
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Valentino Bianco
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Ivan Coluzza
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 182, 20014, San Sebastian, Spain. .,IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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8
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Kaushik AC, Mehmood A, Khan MT, Kumar A, Dai X, Wei DQ. RETRACTED ARTICLE: Protein blueprint and their interactions while approachability struggle for amino acids. J Biomol Struct Dyn 2020; 39:i-ix. [PMID: 31914855 DOI: 10.1080/07391102.2020.1713894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | - Aamir Mehmood
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Ajay Kumar
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung City, Taiwan
| | - Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Dong-Qing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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9
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Škrbić T, Hoang TX, Maritan A, Banavar JR, Giacometti A. Local symmetry determines the phases of linear chains: a simple model for the self-assembly of peptides. SOFT MATTER 2019; 15:5596-5613. [PMID: 31259346 DOI: 10.1039/c9sm00851a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We discuss the relation between the emergence of new phases with broken symmetry within the framework of simple models of biopolymers. We start with a classic model for a chain molecule of spherical beads tethered together, with the steric constraint that non-consecutive beads cannot overlap, and with a pairwise attractive square well potential accounting for the hydrophobic effect and promoting compaction. We then discuss the consequences of the successive breaking of spurious symmetries. First, we allow the partial interpenetration of consecutive beads. In addition to the standard high temperature coil phase and the low temperature collapsed phase, this results in a new class of marginally compact ground states comprising conformations reminiscent of α-helices and β-sheets, the building blocks of the native states of globular proteins. We then discuss the effect of a further symmetry breaking of the cylindrical symmetry on attaching a side-sphere to the backbone beads along the negative normal of the chain, to mimic the presence of side chains in real proteins. This leads to the emergence of a novel phase within the previously obtained marginally compact phase, with the appearance of more complex secondary structure assemblies. The potential importance of this new phase in the de novo design of self-assembled peptides is highlighted.
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Affiliation(s)
- Tatjana Škrbić
- Department of Physics and Institute for Theoretical Science, 1274 University of Oregon, Eugene, OR 97403-1274, USA. and Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.
| | - Trinh Xuan Hoang
- Center for Computational Physics Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan St., Hanoi, Vietnam.
| | - Amos Maritan
- Dipartimento di Fisica e Astronomia, Università di Padova, and INFN, via Marzolo 8, I-35131 Padova, Italy.
| | - Jayanth R Banavar
- Department of Physics and Institute for Theoretical Science, 1274 University of Oregon, Eugene, OR 97403-1274, USA.
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.
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10
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Cardelli C, Nerattini F, Tubiana L, Bianco V, Dellago C, Sciortino F, Coluzza I. General Methodology to Identify the Minimum Alphabet Size for Heteropolymer Design. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chiara Cardelli
- Faculty of PhysicsUniversity of ViennaBoltzmanngasse 5 1090 Vienna Austria
| | | | - Luca Tubiana
- Faculty of PhysicsUniversity of ViennaBoltzmanngasse 5 1090 Vienna Austria
| | - Valentino Bianco
- Faculty of ChemistryChemical Physics DepartmentUniversidad Complutense de Madrid, Plaza de las Ciencias, Ciudad UniversitariaMadrid 28040 Spain
| | - Christoph Dellago
- Faculty of PhysicsUniversity of ViennaBoltzmanngasse 5 1090 Vienna Austria
| | - Francesco Sciortino
- Dipartimento di FisicaSapienza Università di RomaPiazzale Aldo Moro 2 00185 Rome Italy
| | - Ivan Coluzza
- CIC biomaGUNEPaseo Miramon 182 20014 San Sebastian Spain
- IKERBASQUEBasque Foundation for Science48013 Bilbao Spain
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11
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Nerattini F, Tubiana L, Cardelli C, Bianco V, Dellago C, Coluzza I. Design of Protein–Protein Binding Sites Suggests a Rationale for Naturally Occurring Contact Areas. J Chem Theory Comput 2018; 15:1383-1392. [DOI: 10.1021/acs.jctc.8b00667] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesca Nerattini
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Luca Tubiana
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Chiara Cardelli
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Valentino Bianco
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Ivan Coluzza
- CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain
- IKERBASQUE,
Basque Foundation for Science, 48013 Bilbao, Spain
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12
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Škrbić T, Hoang TX, Maritan A, Banavar JR, Giacometti A. The elixir phase of chain molecules. Proteins 2018; 87:176-184. [PMID: 30371948 DOI: 10.1002/prot.25619] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/26/2018] [Accepted: 10/16/2018] [Indexed: 11/08/2022]
Abstract
A phase of matter is a familiar notion for inanimate physical matter. The nature of a phase of matter transcends the microscopic material properties. For example, materials in the liquid phase have certain common properties independent of the chemistry of the constituents: liquids take the shape of the container; they flow; and they can be poured-alcohol, oil, and water as well as a Lennard-Jones computer model exhibit similar behavior when poised in the liquid phase. Here, we identify a hitherto unstudied "phase" of matter, the elixir phase, in a simple model of a polymeric chain whose backbone has the correct local cylindrical symmetry induced by the tangent to the chain. The elixir phase appears on breaking the cylindrical symmetry by adding side spheres along the negative normal direction, as in proteins. This phase, nestled between other phases, has multiple ground states made up of building blocks of helices and almost planar sheets akin to protein native folds. We discuss the similarities of this "phase" of a finite size system to the liquid crystal and spin glass phases. Our findings are relevant for understanding proteins; the creation of novel bioinspired nanomachines; and also may have implications for life elsewhere in the cosmos.
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Affiliation(s)
- Tatjana Škrbić
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia Campus Scientifico, Edificio Alfa, Venezia Mestre, Italy.,Department of Physics and Institute for Theoretical Science, University of Oregon, Eugene, Oregon
| | - Trinh X Hoang
- Center for Computational Physics, Institute of Physics, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Amos Maritan
- Dipartimento di Fisica e Astronomia, Università di Padova, and INFN, Padova, Italy
| | - Jayanth R Banavar
- Department of Physics and Institute for Theoretical Science, University of Oregon, Eugene, Oregon
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia Campus Scientifico, Edificio Alfa, Venezia Mestre, Italy
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13
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Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering von Proteinen an Oberflächen: Von komplementärer Charakterisierung zu Materialoberflächen mit maßgeschneiderten Funktionen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Svenja Morsbach
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Grazia Gonella
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Volker Mailänder
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Dermatologie; Universitätsmedizin der Johannes Gutenberg-Universität Mainz; Langenbeckstraße 1 55131 Mainz Deutschland
| | - Seraphine Wegner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Si Wu
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tobias Weidner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Chemie; Universität Aarhus; Langelandsgade 140 8000 Aarhus C Dänemark
| | - Rüdiger Berger
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kaloian Koynov
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Doris Vollmer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Noemí Encinas
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Seah Ling Kuan
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tristan Bereau
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kurt Kremer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Mischa Bonn
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Hans-Jürgen Butt
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Katharina Landfester
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
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14
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Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering Proteins at Interfaces: From Complementary Characterization to Material Surfaces with Designed Functions. Angew Chem Int Ed Engl 2018; 57:12626-12648. [PMID: 29663610 PMCID: PMC6391961 DOI: 10.1002/anie.201712448] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/13/2018] [Indexed: 01/17/2023]
Abstract
Once materials come into contact with a biological fluid containing proteins, proteins are generally—whether desired or not—attracted by the material's surface and adsorb onto it. The aim of this Review is to give an overview of the most commonly used characterization methods employed to gain a better understanding of the adsorption processes on either planar or curved surfaces. We continue to illustrate the benefit of combining different methods to different surface geometries of the material. The thus obtained insight ideally paves the way for engineering functional materials that interact with proteins in a predetermined manner.
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Affiliation(s)
- Svenja Morsbach
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Grazia Gonella
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Volker Mailänder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Dermatology, University Medical Center Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Seraphine Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Si Wu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Rüdiger Berger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Doris Vollmer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Noemí Encinas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Seah Ling Kuan
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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15
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Tubiana L, Jurásek M, Coluzza I. Implementing efficient concerted rotations using Mathematica and C code ⋆. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:87. [PMID: 30022359 DOI: 10.1140/epje/i2018-11694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
In this article we demonstrate a general and efficient metaprogramming implementation of concerted rotations using Mathematica. Concerted rotations allow the movement of a fixed portion of a polymer backbone with fixed bending angles, like a protein, while maintaining the correct geometry of the backbone and the initial and final points of the portion fixed. Our implementation uses Mathematica to generate a C code which is then wrapped in a library by a Python script. The user can modify the Mathematica notebook to generate a set of concerted rotations suited for a particular backbone geometry, without having to write the C code himself. The resulting code is highly optimized, performing on the order of thousands of operations per second.
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Affiliation(s)
- Luca Tubiana
- Computational Physics Department, University of Vienna, Sensengasse 8/10, 1090, Vienna, Austria.
| | - Miroslav Jurásek
- Faculty of Science, Masaryk University, Kotlářská 2, 602 00, Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Kamenice 5, 625 00, Brno, Czech Republic
| | - Ivan Coluzza
- CIC biomaGUNE Parque Cientfico y Tecnolgico de Gipuzkoa, Paseo Miramn 182, 20014, Donostia / San Sebastin, Gipuzkoa, Spain
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16
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Bianco V, Pagès-Gelabert N, Coluzza I, Franzese G. How the stability of a folded protein depends on interfacial water properties and residue-residue interactions. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.08.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Perspectives on the Future of Ice Nucleation Research: Research Needs and Unanswered Questions Identified from Two International Workshops. ATMOSPHERE 2017. [DOI: 10.3390/atmos8080138] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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The role of directional interactions in the designability of generalized heteropolymers. Sci Rep 2017; 7:4986. [PMID: 28694466 PMCID: PMC5504045 DOI: 10.1038/s41598-017-04720-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/18/2017] [Indexed: 12/31/2022] Open
Abstract
Heteropolymers are important examples of self-assembling systems. However, in the design of artificial heteropolymers the control over the single chain self-assembling properties does not reach that of the natural bio-polymers, and in particular proteins. Here, we introduce a sufficiency criterion to identify polymers that can be designed to adopt a predetermined structure and show that it is fulfilled by polymers made of monomers interacting through directional (anisotropic) interactions. The criterion is based on the appearance of a particular peak in the radial distribution function, that we show being a universal feature of all designable heteropolymers, as it is present also in natural proteins. Our criterion can be used to engineer new self-assembling modular polymers that will open new avenues for applications in materials science.
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19
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Coluzza I. Computational protein design: a review. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:143001. [PMID: 28140371 DOI: 10.1088/1361-648x/aa5c76] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins are one of the most versatile modular assembling systems in nature. Experimentally, more than 110 000 protein structures have been identified and more are deposited every day in the Protein Data Bank. Such an enormous structural variety is to a first approximation controlled by the sequence of amino acids along the peptide chain of each protein. Understanding how the structural and functional properties of the target can be encoded in this sequence is the main objective of protein design. Unfortunately, rational protein design remains one of the major challenges across the disciplines of biology, physics and chemistry. The implications of solving this problem are enormous and branch into materials science, drug design, evolution and even cryptography. For instance, in the field of drug design an effective computational method to design protein-based ligands for biological targets such as viruses, bacteria or tumour cells, could give a significant boost to the development of new therapies with reduced side effects. In materials science, self-assembly is a highly desired property and soon artificial proteins could represent a new class of designable self-assembling materials. The scope of this review is to describe the state of the art in computational protein design methods and give the reader an outline of what developments could be expected in the near future.
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Affiliation(s)
- Ivan Coluzza
- Computational Physics, Faculty of Physics, University of Vienna, Vienna, Austria
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20
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Taylor MP, Paul W, Binder K. On the polymer physics origins of protein folding thermodynamics. J Chem Phys 2017; 145:174903. [PMID: 27825238 DOI: 10.1063/1.4966645] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavior is also typical for flexible homopolymer chains with sufficiently short range interactions. Two-state behavior arises from the presence of a low entropy ground (folded) state separated from a set of high entropy disordered (unfolded) states by a free energy barrier. This homopolymer model exhibits a funneled free energy landscape that reveals a complex underlying dynamics involving competition between folding and non-folding pathways. Despite the presence of multiple pathways, this simple physics model gives the robust result of two-state thermodynamics for both the cases of folding from a basin of expanded coil states and from a basin of compact globule states.
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Affiliation(s)
- Mark P Taylor
- Department of Physics, Hiram College, Hiram, Ohio 44234, USA
| | - Wolfgang Paul
- Institut für Physik, Martin-Luther-Universität, D-06099 Halle (Saale), Germany
| | - Kurt Binder
- Institut für Physik, Johannes-Gutenberg-Universität, Staudinger Weg 7, D-55099 Mainz, Germany
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21
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Bianchi E, Capone B, Coluzza I, Rovigatti L, van Oostrum PDJ. Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules. Phys Chem Chem Phys 2017; 19:19847-19868. [DOI: 10.1039/c7cp03149a] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Artistic representation of limited valance units consisting of a soft core (in blue) and a small number of flexible bonding patches (in orange).
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Affiliation(s)
- Emanuela Bianchi
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
- Institute for Theoretical Physics
| | - Barbara Capone
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
- Dipartimento di Scienze
| | - Ivan Coluzza
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
| | - Lorenzo Rovigatti
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
- Rudolf Peierls Centre for Theoretical Physics
| | - Peter D. J. van Oostrum
- Department of Nanobiotechnology
- Institute for Biologically Inspired Materials
- University of Natural Resources and Life Sciences
- A-1190 Vienna
- Austria
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22
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Škrbić T, Badasyan A, Hoang TX, Podgornik R, Giacometti A. From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang-Landau approach. SOFT MATTER 2016; 12:4783-4793. [PMID: 27137225 DOI: 10.1039/c6sm00542j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We use a micro-canonical Wang-Landau technique to study the equilibrium properties of a single flexible homopolymer where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well potential. To mimic the characteristics of a protein-like system, the model is then refined in two different directions. Firstly, by allowing partial overlap between consecutive beads, we break the spherical symmetry and thus provide a severe constraint on the possible conformations of the chain. Alternatively, we introduce additional spherical beads at specific positions in the direction normal to the backbone, to represent the steric hindrance of the side chains in real proteins. Finally, we consider also a combination of these two ingredients. In all three systems, we obtain the full phase diagram in the temperature-interaction range plane and find the presence of helicoidal structures at low temperatures in the intermediate range of interactions. The effect of the range of the square-well attraction is highlighted, and shown to play a role similar to that found in simple liquids and polymers. Perspectives in terms of protein folding are finally discussed.
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Affiliation(s)
- Tatjana Škrbić
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.
| | - Artem Badasyan
- Material Research Laboratory, University of Nova Gorica, SI-5270 Ajdovscina, Slovenia.
| | - Trinh Xuan Hoang
- Center for Computational Physics Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan St., Hanoi, Vietnam.
| | - Rudolf Podgornik
- Department of Theoretical Physics, J. Stefan Institute and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia.
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.
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23
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van Dijk E, Varilly P, Knowles TPJ, Frenkel D, Abeln S. Consistent Treatment of Hydrophobicity in Protein Lattice Models Accounts for Cold Denaturation. PHYSICAL REVIEW LETTERS 2016; 116:078101. [PMID: 26943560 DOI: 10.1103/physrevlett.116.078101] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 05/04/2023]
Abstract
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavorable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here, we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.
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Affiliation(s)
- Erik van Dijk
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit, De Boelelaan 1081A, 1081 HV Amsterdam, Netherlands
| | - Patrick Varilly
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Sanne Abeln
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit, De Boelelaan 1081A, 1081 HV Amsterdam, Netherlands
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24
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Kukic P, Kannan A, Dijkstra MJJ, Abeln S, Camilloni C, Vendruscolo M. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations. PLoS Comput Biol 2015; 11:e1004435. [PMID: 26505754 PMCID: PMC4624779 DOI: 10.1371/journal.pcbi.1004435] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 07/06/2015] [Indexed: 12/02/2022] Open
Abstract
It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. Modelling protein behaviour using computer simulations has progressively emerged in the last 50 years as a powerful strategy in structural and molecular biology. Over this period there has been a continuing interest in pushing the boundaries of this approach in terms of the size of the systems and the timescale of the processes that can be studied. Coarse-grained models offer in principle great opportunities in this context, but it has been extremely challenging to obtain force fields of accuracy comparable to that typical of fully atomistic models. We show here that the representation of protein molecules as self-avoiding tubes within the CamTube model enables the comprehensive, accurate and very fast exploration of the conformational space of proteins in molecular dynamics simulations. We illustrate in particular how the comprehensive mapping of the protein fold universe obtained using the CamTube model offers the possibility of analysing the behaviour of proteins in a wide range of non-native states.
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Affiliation(s)
- Predrag Kukic
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Arvind Kannan
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Departments of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Maurits J. J. Dijkstra
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Computer Science, Vrije Universiteit, Amsterdam, The Netherlands
| | - Sanne Abeln
- Department of Computer Science, Vrije Universiteit, Amsterdam, The Netherlands
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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25
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Bianco V, Franzese G. Contribution of Water to Pressure and Cold Denaturation of Proteins. PHYSICAL REVIEW LETTERS 2015; 115:108101. [PMID: 26382703 DOI: 10.1103/physrevlett.115.108101] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 05/28/2023]
Abstract
The mechanisms of cold and pressure denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here, we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering.
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Affiliation(s)
- Valentino Bianco
- Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Giancarlo Franzese
- Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
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26
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Affiliation(s)
- Ivan Coluzza
- Department of Computational Physics, Faculty of Physics, University of Vienna , Vienna, Austria
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27
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28
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Rutter GO, Brown AH, Quigley D, Walsh TR, Allen MP. Testing the transferability of a coarse-grained model to intrinsically disordered proteins. Phys Chem Chem Phys 2015; 17:31741-9. [DOI: 10.1039/c5cp05652g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The coarse-grained PLUM model is shown to capture structural and dimerization behaviour of the intrinsically disordered biomineralisation peptide n16N.
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Affiliation(s)
- Gil O. Rutter
- Department of Physics
- University of Warwick
- Coventry CV4 7AL
- UK
| | - Aaron H. Brown
- Department of Chemistry and Centre for Scientific Computing
- University of Warwick
- Coventry
- UK
- Institute for Frontier Materials
| | - David Quigley
- Department of Physics and Centre for Scientific Computing
- University of Warwick
- Coventry CV4 7AL
- UK
| | - Tiffany R. Walsh
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Michael P. Allen
- Department of Physics
- University of Warwick
- Coventry CV4 7AL
- UK
- H. H. Wills Physics Laboratory
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29
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Coluzza I. Transferable coarse-grained potential for de novo protein folding and design. PLoS One 2014; 9:e112852. [PMID: 25436908 PMCID: PMC4249799 DOI: 10.1371/journal.pone.0112852] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here we provide evidence of how a novel parametrization of the Caterpillar model may be used for both quantitative protein design and folding. With computer simulations it is shown that, for a large set of real protein structures, the model produces designed sequences with similar physical properties to the corresponding natural occurring sequences. The designed sequences require further experimental testing. For an independent set of proteins, previously used as benchmark, the correct folded structure of both the designed and the natural sequences is also demonstrated. The equilibrium folding properties are characterized by free energy calculations. The resulting free energy profiles not only are consistent among natural and designed proteins, but also show a remarkable precision when the folded structures are compared to the experimentally determined ones. Ultimately, the updated Caterpillar model is unique in the combination of its fundamental three features: its simplicity, its ability to produce natural foldable designed sequences, and its structure prediction precision. It is also remarkable that low frustration sequences can be obtained with such a simple and universal design procedure, and that the folding of natural proteins shows funnelled free energy landscapes without the need of any potentials based on the native structure.
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Affiliation(s)
- Ivan Coluzza
- Faculty of Physics, University of Vienna, Vienna, Austria
- * E-mail:
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30
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Abeln S, Vendruscolo M, Dobson CM, Frenkel D. A simple lattice model that captures protein folding, aggregation and amyloid formation. PLoS One 2014; 9:e85185. [PMID: 24454816 PMCID: PMC3893179 DOI: 10.1371/journal.pone.0085185] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 12/03/2013] [Indexed: 01/01/2023] Open
Abstract
The ability of many proteins to convert from their functional soluble state to amyloid fibrils can be attributed to inter-molecular beta strand formation. Such amyloid formation is associated with neurodegenerative disorders like Alzheimer's and Parkinson's. Molecular modelling can play a key role in providing insight into the factors that make proteins prone to fibril formation. However, fully atomistic models are computationally too expensive to capture the length and time scales associated with fibril formation. As the ability to form fibrils is the rule rather than the exception, much insight can be gained from the study of coarse-grained models that capture the key generic features associated with amyloid formation. Here we present a simple lattice model that can capture both protein folding and beta strand formation. Unlike standard lattice models, this model explicitly incorporates the formation of hydrogen bonds and the directionality of side chains. The simplicity of our model makes it computationally feasible to investigate the interplay between folding, amorphous aggregation and fibril formation, and maintains the capability of classic lattice models to simulate protein folding with high specificity. In our model, the folded proteins contain structures that resemble naturally occurring beta-sheets, with alternating polar and hydrophobic amino acids. Moreover, fibrils with intermolecular cross-beta strand conformations can be formed spontaneously out of multiple short hydrophobic peptide sequences. Both the formation of hydrogen bonds in folded structures and in fibrils is strongly dependent on the amino acid sequence, indicating that hydrogen-bonding interactions alone are not strong enough to initiate the formation of beta sheets. This result agrees with experimental observations that beta sheet and amyloid formation is strongly sequence dependent, with hydrophobic sequences being more prone to form such structures. Our model should open the way to a systematic study of the interplay between the factors that lead to amyloid formation.
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Affiliation(s)
- Sanne Abeln
- IBIVU - Deptartment of Computer Science, VU University, Amsterdam, The Netherlands
| | - Michele Vendruscolo
- Deptartment of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Daan Frenkel
- Deptartment of Chemistry, University of Cambridge, Cambridge, United Kingdom
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31
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Abstract
The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes.
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Affiliation(s)
- Ryan Bradley
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-215-898-0487; Fax: +1-215-573-2071
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32
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MacDonald JT, Kelley LA, Freemont PS. Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling. PLoS One 2013; 8:e65770. [PMID: 23824634 PMCID: PMC3688807 DOI: 10.1371/journal.pone.0065770] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/26/2013] [Indexed: 12/02/2022] Open
Abstract
Coarse-grained (CG) methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using -carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific /-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C++ source code is available for download from http://www.sbg.bio.ic.ac.uk/phyre2/PD2/.
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Affiliation(s)
- James T. MacDonald
- Division of Molecular Biosciences, Imperial College London, London, United Kingdom
- * E-mail:
| | - Lawrence A. Kelley
- Division of Molecular Biosciences, Imperial College London, London, United Kingdom
| | - Paul S. Freemont
- Division of Molecular Biosciences, Imperial College London, London, United Kingdom
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33
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Coluzza I, van Oostrum PDJ, Capone B, Reimhult E, Dellago C. Sequence controlled self-knotting colloidal patchy polymers. PHYSICAL REVIEW LETTERS 2013; 110:075501. [PMID: 25166382 DOI: 10.1103/physrevlett.110.075501] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Indexed: 06/03/2023]
Abstract
Knotted chains are a promising class of polymers with many applications for materials science and drug delivery. Here we introduce an experimentally realizable model for the design of chains with controllable topological properties. Recently, we have developed a systematic methodology to construct self-assembling chains of simple particles, with final structures fully controlled by the sequence of particles along the chain. The individual particles forming the chain are colloids decorated with mutually interacting patches, which can be manufactured in the laboratory with current technology. Our methodology is applied to the design of sequences folding into self-knotting chains, in which the end monomers are by construction always close together in space. The knotted structure can then be externally locked simply by controlling the interaction between the end monomers, paving the way to applications in the design and synthesis of active materials and novel carriers for drugs delivery.
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Affiliation(s)
- Ivan Coluzza
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Peter D J van Oostrum
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Barbara Capone
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Erik Reimhult
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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Coluzza I, Dellago C. The configurational space of colloidal patchy polymers with heterogeneous sequences. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:284111. [PMID: 22738904 DOI: 10.1088/0953-8984/24/28/284111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this work we characterize the configurational space of a short chain of colloidal particles as a function of the range of directional and heterogeneous isotropic interactions. The individual particles forming the chain are colloids decorated with patches that act as interaction sites between them. We show, using computer simulations, that it is possible to sample the relative probability of occurrence of a structure with a sequence in the space of all possible realizations of the chain. The results presented here represent a first attempt to map the space of possible configurations that a chain of colloidal particles may adopt. Knowledge of such a space is crucial for a possible application of colloidal chains as models for designable self-assembling systems.
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Affiliation(s)
- Ivan Coluzza
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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Analytic markovian rates for generalized protein structure evolution. PLoS One 2012; 7:e34228. [PMID: 22693543 PMCID: PMC3367531 DOI: 10.1371/journal.pone.0034228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/26/2012] [Indexed: 12/24/2022] Open
Abstract
A general understanding of the complex phenomenon of protein evolution requires the accurate description of the constraints that define the sub-space of proteins with mutations that do not appreciably reduce the fitness of the organism. Such constraints can have multiple origins, in this work we present a model for constrained evolutionary trajectories represented by a Markovian process throughout a set of protein-like structures artificially constructed to be topological intermediates between the structure of two natural occurring proteins. The number and type of intermediate steps defines how constrained the total evolutionary process is. By using a coarse-grained representation for the protein structures, we derive an analytic formulation of the transition rates between each of the intermediate structures. The results indicate that compact structures with a high number of hydrogen bonds are more probable and have a higher likelihood to arise during evolution. Knowledge of the transition rates allows for the study of complex evolutionary pathways represented by trajectories through a set of intermediate structures.
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Rubenstein BM, Coluzza I, Miller MA. Controlling the folding and substrate-binding of proteins using polymer brushes. PHYSICAL REVIEW LETTERS 2012; 108:208104. [PMID: 23003194 DOI: 10.1103/physrevlett.108.208104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Revised: 03/09/2012] [Indexed: 06/01/2023]
Abstract
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully upon binding. In this Letter, we use Monte Carlo simulations to investigate how disordered polymer chains grafted around a binding site affect the folding and binding of three model proteins. The protein that approaches the substrate fully folded is more hindered during the binding process than those whose folding and binding are cooperative. The polymer chains act as localized crowding agents and can select correctly folded and bound configurations in favor of nonspecifically adsorbed states. The free energy change for forming all intraprotein and protein-substrate contacts can depend nonmonotonically on the polymer length.
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Affiliation(s)
- Brenda M Rubenstein
- Department of Chemistry, Columbia University, MC 3178, 3000 Broadway, New York, NY 10027, USA
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