1
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Cea PA, Pérez M, Herrera SM, Muñoz SM, Fuentes-Ugarte N, Coche-Miranda J, Maturana P, Guixé V, Castro-Fernandez V. Deciphering Structural Traits for Thermal and Kinetic Stability across Protein Family Evolution through Ancestral Sequence Reconstruction. Mol Biol Evol 2024; 41:msae127. [PMID: 38913681 PMCID: PMC11229819 DOI: 10.1093/molbev/msae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/17/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
Natural proteins are frequently marginally stable, and an increase in environmental temperature can easily lead to unfolding. As a result, protein engineering to improve protein stability is an area of intensive research. Nonetheless, since there is usually a high degree of structural homology between proteins from thermophilic organisms and their mesophilic counterparts, the identification of structural determinants for thermoadaptation is challenging. Moreover, in many cases, it has become clear that the success of stabilization strategies is often dependent on the evolutionary history of a protein family. In the last few years, the use of ancestral sequence reconstruction (ASR) as a tool for elucidation of the evolutionary history of functional traits of a protein family has gained strength. Here, we used ASR to trace the evolutionary pathways between mesophilic and thermophilic kinases that participate in the biosynthetic pathway of vitamin B1 in bacteria. By combining biophysics approaches, X-ray crystallography, and molecular dynamics simulations, we found that the thermal stability of these enzymes correlates with their kinetic stability, where the highest thermal/kinetic stability is given by an increase in small hydrophobic amino acids that allow a higher number of interatomic hydrophobic contacts, making this type of interaction the main support for stability in this protein architecture. The results highlight the potential benefits of using ASR to explore the evolutionary history of protein sequence and structure to identify traits responsible for the kinetic and thermal stability of any protein architecture.
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Affiliation(s)
- Pablo A Cea
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Myriam Pérez
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Sixto M Herrera
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Sebastián M Muñoz
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Nicolás Fuentes-Ugarte
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - José Coche-Miranda
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Pablo Maturana
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
| | - Victor Castro-Fernandez
- Departamento de Biología, Facultad de Ciencias, Laboratorio de Bioquímica y Biología Molecular, Universidad de Chile, Santiago, Chile
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2
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Nguyen TA, Lee C. Thr-to-Ala Mutation Leads to a Larger Aromatic Pair and Reduced Packing Density in α1,α3-Helices during Thioredoxin Cold Adaptation. ACS OMEGA 2024; 9:10812-10824. [PMID: 38463323 PMCID: PMC10918799 DOI: 10.1021/acsomega.3c09806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/18/2024] [Accepted: 02/08/2024] [Indexed: 03/12/2024]
Abstract
This study investigates the impact of aromatic-aromatic interactions on the cold adaptation of thioredoxin (Trx), a small redox protein with a conserved Trx-fold structure. Two Trx orthologs, one from the psychrophilic Arctic bacterium Sphingomonas sp. (SpTrx) and the other from the mesophilic Escherichia coli (EcTrx), display distinct aromatic interactions in their α1,α3-helices. SpTrx features a larger Trp11-Phe69 pair, while EcTrx employs a smaller Phe12-Tyr70 pair along with an additional Asp9-Thr66 hydrogen bond. Smaller aromatic residues in SpTrx (Phe-Phe or Phe-Tyr pair) lead to decreased thermal and thermodynamic stabilities, increased conformational flexibility, and reduced enzyme activity. In contrast, EcTrx's thermal stability is primarily influenced by the larger Trp residue, especially in the more hydrophobic Trp-Phe pair compared to the Trp-Tyr pair. Both SpTrx and EcTrx exhibit a strengthening of the Asp-Thr hydrogen bond by a Phe-Tyr pair and a weakening by a Trp-Phe pair. Additionally, the Asp8-Thr65 hydrogen bond in SpTrx contributes to the destabilization of the Phe-Phe pair. Molecular dynamics simulations of SpTrx indicate that a smaller aromatic pair or the Asp-Thr hydrogen bond in the α1,α3-helices further destabilizes the α2-helix across the central β-sheet. Our results suggest that the Thr-to-Ala mutation destabilizes the α1,α3-helices, resulting in a larger aromatic pair and reduced packing density in psychrophilic Trxs during cold adaptation. These findings enhance our understanding of Trx's adaptation to colder temperatures.
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Affiliation(s)
- Tu Anh Nguyen
- Department of Biomedical
Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
| | - ChangWoo Lee
- Department of Biomedical
Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
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3
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Van Tran T, Nguyen H, Vu L, Lee C. Structural conservation in the glutathione binding in Sphingomonas sp. glutaredoxin Grx3 and variations for cold adaptation. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140971. [PMID: 37935252 DOI: 10.1016/j.bbapap.2023.140971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/29/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Glutaredoxin 3 (Grx3), a redox protein with a thioredoxin-fold structure, maintains structural integrity and glutathione (GSH) binding capabilities across varying habitat temperatures. The cis-Pro loop, essential for GSH binding, relies on the Arg-Asp salt bridge (α2-α3) and Gln-His hydrogen bond (β3-β4) for its conformation. In some psychrophilic Grx3 variants, Arg in α2 is replaced with Tyr, and His in β4 is replaced with Phe. This study examines the roles of these bonds in Grx3's structure, function, and cold adaptation, using SpGrx3 from the Arctic bacterium Sphingomonas sp. Despite its cold habitat, SpGrx3 maintains the Arg51-Asp69 salt bridge and Gln56-His63 hydrogen bond. The R51Y substitution disrupts the α2-α3 salt bridge, while the H63F and H63Y substitutions hinder the salt bridge through cation-π interactions with Arg51, involving Phe63/Tyr63, thereby enhancing flexibility. Conversely, mutations that disrupt the hydrogen bond (Q56A, H63A, and H63F) reduce thermal stability. In the psychrophilic Grx3 configuration A48T/R51Y/H63F, a Thr48-Gln56 hydrogen bond stabilizes the cis-Pro loop, enhancing flexibility by disrupting both bonds. Furthermore, all mutants exhibit reduced α-helical content and catalytic efficiency. In summary, the highly conserved Arg51-Asp69 salt bridge and Gln56-His63 hydrogen bond are crucial for stabilizing the cis-Pro loop and catalytic activity in SpGrx3. His63 is favored as it avoids cation-π interactions with Arg51, unlike Phe63/Tyr63. Psychrophilic Grx3 variants have adapted to cold environments by reducing GSH binding and increasing structural flexibility. These findings deepen our understanding of the structural conservation in Grx3 for GSH binding and the critical alterations required for cold adaptation.
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Affiliation(s)
- Trang Van Tran
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
| | - Hoa Nguyen
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
| | - Luyen Vu
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan 38453, South Korea.
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4
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Derbyshire MC, Raffaele S. Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors. Nat Commun 2023; 14:5244. [PMID: 37640704 PMCID: PMC10462633 DOI: 10.1038/s41467-023-40949-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Pathogens secrete effector proteins to subvert host physiology and cause disease. Effectors are engaged in a molecular arms race with the host resulting in conflicting evolutionary constraints to manipulate host cells without triggering immune responses. The molecular mechanisms allowing effectors to be at the same time robust and evolvable remain largely enigmatic. Here, we show that 62 conserved structure-related families encompass the majority of fungal orphan effector candidates in the Pezizomycotina subphylum. These effectors diversified through changes in patterns of thermodynamic frustration at surface residues. The underlying mutations tended to increase the robustness of the overall effector protein structure while switching potential binding interfaces. This mechanism could explain how conserved effector families maintained biological activity over long evolutionary timespans in different host environments and provides a model for the emergence of sequence-unrelated effector families with conserved structures.
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Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes Micro-organismes Environnement (LIPME), INRAE, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France.
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5
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Das D, Yadav P, Mitra S, Ainavarapu SRK. Metal-binding and circular permutation-dependent thermodynamic and kinetic stability of azurin. Proteins 2023; 91:634-648. [PMID: 36511110 DOI: 10.1002/prot.26454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
Native topology is known to determine the folding kinetics and the energy landscape of proteins. Furthermore, the circular permutation (CP) of proteins alters the order of the secondary structure connectivity while retaining the three-dimensional structure, making it an elegant and powerful approach to altering native topology. Previous studies elucidated the influence of CP in proteins with different folds such as Greek key β-barrel, β-sandwich, β-α-β, and all α-Greek key. CP mainly affects the protein stability and unfolding kinetics, while folding kinetics remains mostly unaltered. However, the effect of CP on metalloproteins is yet to be elaborately studied. The active site of metalloproteins poses an additional complexity in studying protein folding. Here, we investigate a CP variant (cpN42) of azurin-in both metal-free and metal-bound (holo) forms. As observed earlier in other proteins, apo-forms of wild-type (WT) and cpN42 fold with similar rates. In contrast, zinc-binding accelerates the folding of WT but decelerates the folding of cpN42. On zinc-binding, the spontaneous folding rate of WT increases by >250 times that of cpN42, which is unprecedented and the highest for any CP to date. On the other hand, zinc-binding reduces the spontaneous unfolding rate of cpN42 by ~100 times, making the WT and CP azurins unfold at similar rates. Our study demonstrates metal binding as a novel way to modulate the unfolding and folding rates of CPs compared to their WT counterparts. We hope our study increases the understanding of the effect of CP on the folding mechanism and energy landscape of metalloproteins.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Priya Yadav
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Soumyajit Mitra
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Dr. Homi Bhabha Road, Colaba, Tata Institute of Fundamental Research, Mumbai, India
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6
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Low JYK, Shi X, Anandalakshmi V, Neo D, Peh GSL, Koh SK, Zhou L, Abdul Rahim MK, Boo K, Lee J, Mohanram H, Alag R, Mu Y, Mehta JS, Pervushin K. Release of frustration drives corneal amyloid disaggregation by brain chaperone. Commun Biol 2023; 6:348. [PMID: 36997596 PMCID: PMC10063603 DOI: 10.1038/s42003-023-04725-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/17/2023] [Indexed: 04/01/2023] Open
Abstract
TGFBI-related corneal dystrophy (CD) is characterized by the accumulation of insoluble protein deposits in the corneal tissues, eventually leading to progressive corneal opacity. Here we show that ATP-independent amyloid-β chaperone L-PGDS can effectively disaggregate corneal amyloids in surgically excised human cornea of TGFBI-CD patients and release trapped amyloid hallmark proteins. Since the mechanism of amyloid disassembly by ATP-independent chaperones is unknown, we reconstructed atomic models of the amyloids self-assembled from TGFBIp-derived peptides and their complex with L-PGDS using cryo-EM and NMR. We show that L-PGDS specifically recognizes structurally frustrated regions in the amyloids and releases those frustrations. The released free energy increases the chaperone's binding affinity to amyloids, resulting in local restructuring and breakage of amyloids to protofibrils. Our mechanistic model provides insights into the alternative source of energy utilized by ATP-independent disaggregases and highlights the possibility of using these chaperones as treatment strategies for different types of amyloid-related diseases.
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Affiliation(s)
- Jia Yi Kimberly Low
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, 518172, Shenzhen, China
| | | | - Dawn Neo
- Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore, 168751, Singapore
| | - Gary Swee Lim Peh
- Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore, 168751, Singapore
| | - Siew Kwan Koh
- Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore, 168751, Singapore
| | - Lei Zhou
- School of Optometry, Department of Applied Biology and Chemical Technology, Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong, China
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - M K Abdul Rahim
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Ketti Boo
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - JiaXuan Lee
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Harini Mohanram
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Reema Alag
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Jodhbir S Mehta
- Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore, 168751, Singapore.
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
- Singapore National Eye Centre, 11 Third Hospital Avenue, Singapore, 168751, Singapore.
| | - Konstantin Pervushin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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7
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Tapia-Rojo R, Mora M, Board S, Walker J, Boujemaa-Paterski R, Medalia O, Garcia-Manyes S. Enhanced statistical sampling reveals microscopic complexity in the talin mechanosensor folding energy landscape. NATURE PHYSICS 2023; 19:52-60. [PMID: 36660164 PMCID: PMC7614079 DOI: 10.1038/s41567-022-01808-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Statistical mechanics can describe the major conformational ensembles determining the equilibrium free-energy landscape of a folding protein. The challenge is to capture the full repertoire of low-occurrence conformations separated by high kinetic barriers that define complex landscapes. Computationally, enhanced sampling methods accelerate the exploration of molecular rare events. However, accessing the entire protein's conformational space in equilibrium experiments requires technological developments to enable extended observation times. We developed single-molecule magnetic tweezers to capture over a million individual transitions as a single talin protein unfolds and refolds under force in equilibrium. When observed at classically-probed timescales, talin folds in an apparently uncomplicated two-state manner. As the sampling time extends from minutes to days, the underlying energy landscape exhibits gradually larger signatures of complexity, involving a finite number of well-defined rare conformations. A fluctuation analysis allows us to propose plausible structures of each low-probability conformational state. The physiological relevance of each distinct conformation can be connected to the binding of the cytoskeletal protein vinculin, suggesting an extra layer of complexity in talin-mediated mechanotransduction. More generally, our experiments directly test the fundamental notion that equilibrium dynamics depend on the observation timescale.
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Affiliation(s)
- Rafael Tapia-Rojo
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- Corresponding authors: , ,
| | - Marc Mora
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- Corresponding authors: , ,
| | - Stephanie Board
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
| | - Jane Walker
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
| | - Rajaa Boujemaa-Paterski
- Department of Biochemistry, Zurich University, Winterhurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, Zurich University, Winterhurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Sergi Garcia-Manyes
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- Corresponding authors: , ,
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8
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Bartuzi D, Kaczor AA, Matosiuk D. Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling. Methods Mol Biol 2023; 2627:25-40. [PMID: 36959440 DOI: 10.1007/978-1-0716-2974-1_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Homology modeling was long considered a method of choice in tertiary protein structure prediction. However, it used to provide models of acceptable quality only when templates with appreciable sequence identity with a target could be found. The threshold value was long assumed to be around 20-30%. Below this level, obtained sequence identity was getting dangerously close to values that can be obtained by chance, after aligning any random, unrelated sequences. In these cases, other approaches, including ab initio folding simulations or fragment assembly, were usually employed. The most recent editions of the CASP and CAMEO community-wide modeling methods assessment have brought some surprising outcomes, proving that much more clues can be inferred from protein sequence analyses than previously thought. In this chapter, we focus on recent advances in the field of difficult protein modeling, pushing the threshold deep into the "twilight zone", with particular attention devoted to improvements in applications of machine learning and model evaluation.
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Affiliation(s)
- Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland.
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland
- University of Eastern Finland, School of Pharmacy, Kuopio, Finland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Laboratory, Medical University of Lublin, Lublin, Poland
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9
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Cortez LM, Morrison AJ, Garen CR, Patterson S, Uyesugi T, Petrosyan R, Sekar RV, Harms MJ, Woodside MT, Sim VL. Probing the origin of prion protein misfolding via reconstruction of ancestral proteins. Protein Sci 2022; 31:e4477. [PMID: 36254680 PMCID: PMC9667828 DOI: 10.1002/pro.4477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 12/13/2022]
Abstract
Prion diseases are fatal neurodegenerative diseases caused by pathogenic misfolding of the prion protein, PrP. They are transmissible between hosts, and sometimes between different species, as with transmission of bovine spongiform encephalopathy to humans. Although PrP is found in a wide range of vertebrates, prion diseases are seen only in certain mammals, suggesting that infectious misfolding was a recent evolutionary development. To explore when PrP acquired the ability to misfold infectiously, we reconstructed the sequences of ancestral versions of PrP from the last common primate, primate-rodent, artiodactyl, placental, bird, and amniote. Recombinant ancestral PrPs were then tested for their ability to form β-sheet aggregates, either spontaneously or when seeded with infectious prion strains from human, cervid, or rodent species. The ability to aggregate developed after the oldest ancestor (last common amniote), and aggregation capabilities diverged along evolutionary pathways consistent with modern-day susceptibilities. Ancestral bird PrP could not be seeded with modern-day prions, just as modern-day birds are resistant to prion disease. Computational modeling of structures suggested that differences in helix 2 could account for the resistance of ancestral bird PrP to seeding. Interestingly, ancestral primate PrP could be converted by all prion seeds, including both human and cervid prions, raising the possibility that species descended from an ancestral primate have retained the susceptibility to conversion by cervid prions. More generally, the results suggest that susceptibility to prion disease emerged prior to ~100 million years ago, with placental mammals possibly being generally susceptible to disease.
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Affiliation(s)
- Leonardo M. Cortez
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
- Division of Neurology, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada
- Neuroscience and Mental Health InstituteUniversity of AlbertaEdmontonAlbertaCanada
| | - Anneliese J. Morrison
- Institute of Molecular BiologyUniversity of OregonEugeneOregonUSA
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
| | - Craig R. Garen
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
| | - Sawyer Patterson
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
| | - Toshi Uyesugi
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
| | - Rafayel Petrosyan
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
- Present address:
Zaven & Sonia Akian College of Science and EngineeringAmerican University of ArmeniaYerevanArmenia
| | | | - Michael J. Harms
- Institute of Molecular BiologyUniversity of OregonEugeneOregonUSA
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
| | - Michael T. Woodside
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
- Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Valerie L. Sim
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
- Division of Neurology, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada
- Neuroscience and Mental Health InstituteUniversity of AlbertaEdmontonAlbertaCanada
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10
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Zhou X, Song H, Li J. Residue-Frustration-Based Prediction of Protein-Protein Interactions Using Machine Learning. J Phys Chem B 2022; 126:1719-1727. [PMID: 35170967 DOI: 10.1021/acs.jpcb.1c10525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of protein-protein interactions (PPIs) is important in understanding the function of proteins. However, it is still a challenge to investigate the transient protein-protein interaction by experiments. Hence, the computational prediction for protein-protein interactions draws growing attention. Statistics-based features have been widely used in the studies of protein structure prediction and protein folding. Due to the scarcity of experimental data of PPI, it is difficult to construct a conventional statistical feature for PPI prediction, and the application of statistics-based features is very limited in this field. In this paper, we explored the application of frustration, a statistical potential, in PPI prediction. By comparing the energetic contribution of the extra stabilization energy from a given residue pair in the native protein with the statistics of the energies, we obtained the residue pair's frustration index. By calculating the number of residue pairs with a high frustration index, the highly frustrated density, a residue-frustration-based feature, was then obtained to describe the tendency of residues to be involved in PPI. Highly frustrated density, as well as structure-based features, were then used to describe protein residues and combined with the long short-term memory (LSTM) neural network to predict PPI residue pairs. Our model correctly predicted 75% dimers when only the top 2‰ residue pairs were selected in each dimer. Our model, which considers the statistics-based features, is significantly different from the models based on the chemical features of residues. We found that frustration can effectively describe the tendency of residue to be involved in PPI. Frustration-based features can replace chemical features to combine with machine learning and realize the better performance of PPI prediction. It reveals the great potential of statistical potential such as frustration in PPI prediction.
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Affiliation(s)
- Xiaozhou Zhou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Haoyu Song
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang, China
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11
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Nguyen TT, Hoang T, Tran KN, Kim H, Jang SH, Lee C. Essential roles of buried phenylalanine in the structural stability of thioredoxin from a psychrophilic Arctic bacterium Sphingomonas sp. PLoS One 2021; 16:e0261123. [PMID: 34910731 PMCID: PMC8673628 DOI: 10.1371/journal.pone.0261123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 11/21/2022] Open
Abstract
Thioredoxin (Trx), a small redox protein, exhibits thermal stability at high temperatures regardless of its origin, including psychrophiles. Trxs have a common structure consisting of the central β-sheet flanked by an aliphatic cluster on one side and an aromatic cluster on the other side. Although the roles of aromatic amino acids in the folding and stability of proteins have been studied extensively, the contributions of aromatic residues to the stability and function of Trx, particularly Trxs from cold-adapted organisms, have not been fully elucidated. This study examined the roles of aromatic amino acids in the aromatic cluster of a Trx from the psychrophilic Arctic bacterium Sphingomonas sp. PAMC 26621 (SpTrx). The aromatic cluster of SpTrx was comprised of W11, F26, F69, and F80, in which F26 at the β2 terminus was buried inside. The substitution of tyrosine for F26 changed the SpTrx conformation substantially compared to that of F69 and F80. Further biochemical and spectroscopic investigations on F26 showed that the F26Y, F26W, and F26A mutants resulted in structural instability of SpTrx in both urea- and temperature-induced unfolding and lower insulin reduction activities. The Trx reductase (SpTR) showed lower catalytic efficiencies against F26 mutants compared to the wild-type SpTrx. These results suggest that buried F26 is essential for maintaining the active-site conformation of SpTrx as an oxidoreductase and its structural stability for interactions with SpTR at colder temperatures.
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Affiliation(s)
- Thu-Thuy Nguyen
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Trang Hoang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Kiet N. Tran
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Hyeonji Kim
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
- * E-mail:
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12
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Chu WT, Yan Z, Chu X, Zheng X, Liu Z, Xu L, Zhang K, Wang J. Physics of biomolecular recognition and conformational dynamics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:126601. [PMID: 34753115 DOI: 10.1088/1361-6633/ac3800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Biomolecular recognition usually leads to the formation of binding complexes, often accompanied by large-scale conformational changes. This process is fundamental to biological functions at the molecular and cellular levels. Uncovering the physical mechanisms of biomolecular recognition and quantifying the key biomolecular interactions are vital to understand these functions. The recently developed energy landscape theory has been successful in quantifying recognition processes and revealing the underlying mechanisms. Recent studies have shown that in addition to affinity, specificity is also crucial for biomolecular recognition. The proposed physical concept of intrinsic specificity based on the underlying energy landscape theory provides a practical way to quantify the specificity. Optimization of affinity and specificity can be adopted as a principle to guide the evolution and design of molecular recognition. This approach can also be used in practice for drug discovery using multidimensional screening to identify lead compounds. The energy landscape topography of molecular recognition is important for revealing the underlying flexible binding or binding-folding mechanisms. In this review, we first introduce the energy landscape theory for molecular recognition and then address four critical issues related to biomolecular recognition and conformational dynamics: (1) specificity quantification of molecular recognition; (2) evolution and design in molecular recognition; (3) flexible molecular recognition; (4) chromosome structural dynamics. The results described here and the discussions of the insights gained from the energy landscape topography can provide valuable guidance for further computational and experimental investigations of biomolecular recognition and conformational dynamics.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Xiakun Chu
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
| | - Xiliang Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Li Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Kun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Jin Wang
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
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13
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Localization of Energetic Frustration in Proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2376:387-398. [PMID: 34845622 DOI: 10.1007/978-1-0716-1716-8_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We present a detailed heuristic method to quantify the degree of local energetic frustration manifested by protein molecules. Current applications are realized in computational experiments where a protein structure is visualized highlighting the energetic conflicts or the concordance of the local interactions in that structure. Minimally frustrated linkages highlight the stable folding core of the molecule. Sites of high local frustration, in contrast, often indicate functionally relevant regions such as binding, active, or allosteric sites.
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14
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Caetano-Anollés G, Aziz MF, Mughal F, Caetano-Anollés D. Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution. Expert Rev Proteomics 2021; 18:863-880. [PMID: 34628994 DOI: 10.1080/14789450.2021.1992277] [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] [Indexed: 01/24/2023]
Abstract
INTRODUCTION While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chronologies are series of time events describing the history of biological systems and subsystems and the rise of biological innovations. Together with time-varying networks, these chronologies provide a window into the past. AREAS COVERED Here, we review molecular chronologies and networks built with modern methods of phylogeny reconstruction. We discuss how chronologies of structural domain families uncover the explosive emergence of metabolism, the late rise of translation, the co-evolution of ribosomal proteins and rRNA, and the late development of the ribosomal exit tunnel; events that coincided with a tendency to shorten folding time. Evolving networks described the early emergence of domains and a late 'big bang' of domain combinations. EXPERT OPINION Two processes, folding and recruitment appear central to the evolutionary progression. The former increases protein persistence. The later fosters diversity. Chronologically, protein evolution mirrors folding by combining supersecondary structures into domains, developing translation machinery to facilitate folding speed and stability, and enhancing structural complexity by establishing long-distance interactions in novel structural and architectural designs.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA.,C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Derek Caetano-Anollés
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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15
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Liu S, Rong C. Quantifying Frustrations for Molecular Complexes with Noncovalent Interactions. J Phys Chem A 2021; 125:4910-4917. [PMID: 34056899 DOI: 10.1021/acs.jpca.1c02690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular systems bound together through noncovalent interactions are involved in a lot of life-essential processes such as molecular recognition, signal transduction, and allosteric regulation. While cooperation as an important effect discovered in these systems focuses on the behavior of system's entirety, we need also examine the behavior of individual parts. In this work, using the distortion energy as the descriptor, we quantify frustration as the energetic loss of individual parts due to the formation of nonadditive molecular complexes. The applicability of our approach has been illustrated by a few simple clusters. Our results show that the frustration effect is smaller than the cooperation effect, but same as cooperativity, it can be both positive and negative. The ultimate benefit of a system made of multiple parts is dictated by the balance between the cooperative behavior among parts and the sacrifice from its individuals. This conflicting yet complementary conceptual pair of cooperation and frustration provides us with a different perspective from the systems' viewpoint for molecular complexes. This new angle of appreciating molecular complexes can be applied in conformational changes, enzymatic catalysis, and many more.
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Affiliation(s)
- Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States.,Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), and College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, P. R. China
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16
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Romero-Romero S, Kordes S, Michel F, Höcker B. Evolution, folding, and design of TIM barrels and related proteins. Curr Opin Struct Biol 2021; 68:94-104. [PMID: 33453500 PMCID: PMC8250049 DOI: 10.1016/j.sbi.2020.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/16/2022]
Abstract
Proteins are chief actors in life that perform a myriad of exquisite functions. This diversity has been enabled through the evolution and diversification of protein folds. Analysis of sequences and structures strongly suggest that numerous protein pieces have been reused as building blocks and propagated to many modern folds. This information can be traced to understand how the protein world has diversified. In this review, we discuss the latest advances in the analysis of protein evolutionary units, and we use as a model system one of the most abundant and versatile topologies, the TIM-barrel fold, to highlight the existing common principles that interconnect protein evolution, structure, folding, function, and design.
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Affiliation(s)
| | - Sina Kordes
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Florian Michel
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.
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17
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Marques MA, Landim-Vieira M, Moraes AH, Sun B, Johnston JR, Dieseldorff Jones KM, Cino EA, Parvatiyar MS, Valera IC, Silva JL, Galkin VE, Chase PB, Kekenes-Huskey PM, de Oliveira GAP, Pinto JR. Anomalous structural dynamics of minimally frustrated residues in cardiac troponin C triggers hypertrophic cardiomyopathy. Chem Sci 2021; 12:7308-7323. [PMID: 34163821 PMCID: PMC8171346 DOI: 10.1039/d1sc01886h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/11/2021] [Indexed: 12/13/2022] Open
Abstract
Cardiac TnC (cTnC) is highly conserved among mammals, and genetic variants can result in disease by perturbing Ca2+-regulation of myocardial contraction. Here, we report the molecular basis of a human mutation in cTnC's αD-helix (TNNC1-p.C84Y) that impacts conformational dynamics of the D/E central-linker and sampling of discrete states in the N-domain, favoring the "primed" state associated with Ca2+ binding. We demonstrate cTnC's αD-helix normally functions as a central hub that controls minimally frustrated interactions, maintaining evolutionarily conserved rigidity of the N-domain. αD-helix perturbation remotely alters conformational dynamics of the N-domain, compromising its structural rigidity. Transgenic mice carrying this cTnC mutation exhibit altered dynamics of sarcomere function and hypertrophic cardiomyopathy. Together, our data suggest that disruption of evolutionary conserved molecular frustration networks by a myofilament protein mutation may ultimately compromise contractile performance and trigger hypertrophic cardiomyopathy.
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Affiliation(s)
- Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Adolfo H Moraes
- Department of Chemistry, Federal University of Minas Gerais Belo Horizonte MG Brazil
| | - Bin Sun
- Department of Cell and Molecular Physiology, Loyola University Chicago Maywood IL USA
| | - Jamie R Johnston
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Karissa M Dieseldorff Jones
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Elio A Cino
- Department of Biochemistry and Immunology, Federal University of Minas Gerais Belo Horizonte MG Brazil
| | - Michelle S Parvatiyar
- Department of Nutrition, Food and Exercise Sciences, Florida State University Tallahassee FL USA
| | - Isela C Valera
- Department of Nutrition, Food and Exercise Sciences, Florida State University Tallahassee FL USA
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Vitold E Galkin
- Department of Physiological Sciences, Eastern Virginia Medical School Norfolk VA USA
| | - P Bryant Chase
- Department of Biological Science, Florida State University Tallahassee FL USA
| | | | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Jose Renato Pinto
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
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18
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Sakaguchi R, Fujiyoshi S, Wakai S, Yamanaka M, Sambongi Y. Thermal destabilization mechanism of cytochrome c' from psychrophilic Shewanella violacea. Biosci Biotechnol Biochem 2021; 85:1121-1127. [PMID: 33686411 DOI: 10.1093/bbb/zbab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/06/2021] [Indexed: 02/01/2023]
Abstract
Cytochrome c' is a nitric oxide (NO)-binding heme protein found in Gram negative bacteria. The thermal stability of psychrophilic Shewanella violacea cytochrome c' (SVCP) is lower than those of its homologues from other 2 psychrophilic Shewanella species, indicating that thermal destabilization mechanism for low-temperature adaptation accumulates in SVCP. In order to understand this mechanism at the amino acid level, here the stability and function of SVCP variants, modeled using the 2 homologues, were examined. The variants exhibited increased stability, and they bound NO similar to the wild type. The vulnerability as to the SVCP stability could be attributed to less hydrogen bond at the subunit interface, more flexible loop structure, and less salt bridge on the protein surface, which appear to be its destabilization mechanism. This study provides an example for controlling stability without spoiling function in psychrophilic proteins.
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Affiliation(s)
- Riku Sakaguchi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - So Fujiyoshi
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Japan
| | - Satoshi Wakai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Masaru Yamanaka
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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19
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Zou T, Woodrum BW, Halloran N, Campitelli P, Bobkov AA, Ghirlanda G, Ozkan SB. Local Interactions That Contribute Minimal Frustration Determine Foldability. J Phys Chem B 2021; 125:2617-2626. [PMID: 33687216 DOI: 10.1021/acs.jpcb.1c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Earlier experiments suggest that the evolutionary information (conservation and coevolution) encoded in protein sequences is necessary and sufficient to specify the fold of a protein family. However, there is no computational work to quantify the effect of such evolutionary information on the folding process. Here we explore the role of early folding steps for sequences designed using coevolution and conservation through a combination of computational and experimental methods. We simulated a repertoire of native and designed WW domain sequences to analyze early local contact formation and found that the N-terminal β-hairpin turn would not form correctly due to strong non-native local contacts in unfoldable sequences. Through a maximum likelihood approach, we identified five local contacts that play a critical role in folding, suggesting that a small subset of amino acid pairs can be used to solve the "needle in the haystack" problem to design foldable sequences. Thus, using the contact probability of those five local contacts that form during the early stage of folding, we built a classification model that predicts the foldability of a WW sequence with 81% accuracy. This classification model was used to redesign WW domain sequences that could not fold due to frustration and make them foldable by introducing a few mutations that led to the stabilization of these critical local contacts. The experimental analysis shows that a redesigned sequence folds and binds to polyproline peptides with a similar affinity as those observed for native WW domains. Overall, our analysis shows that evolutionary-designed sequences should not only satisfy the folding stability but also ensure a minimally frustrated folding landscape.
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Affiliation(s)
- Taisong Zou
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Brian W Woodrum
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Halloran
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Andrey A Bobkov
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
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20
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Wang CK, Craik DJ. Linking molecular evolution to molecular grafting. J Biol Chem 2021; 296:100425. [PMID: 33600801 PMCID: PMC8005815 DOI: 10.1016/j.jbc.2021.100425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/01/2022] Open
Abstract
Molecular grafting is a strategy for the engineering of molecular scaffolds into new functional agents, such as next-generation therapeutics. Despite its wide use, studies so far have focused almost exclusively on demonstrating its utility rather than understanding the factors that lead to either poor or successful grafting outcomes. Here, we examine protein evolution and identify parallels between the natural process of protein functional diversification and the artificial process of molecular grafting. We discuss features of natural proteins that are correlated to innovability-the capacity to acquire new functions-and describe their implications to molecular grafting scaffolds. Disulfide-rich peptides are used as exemplars because they are particularly promising scaffolds onto which new functions can be grafted. This article provides a perspective on why some scaffolds are more suitable for grafting than others, identifying opportunities on how molecular grafting might be improved.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
| | - David J Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
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21
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Crippa M, Andreghetti D, Capelli R, Tiana G. Evolution of frustrated and stabilising contacts in reconstructed ancient proteins. EUROPEAN BIOPHYSICS JOURNAL 2021; 50:699-712. [PMID: 33569610 PMCID: PMC8260555 DOI: 10.1007/s00249-021-01500-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/14/2020] [Accepted: 01/13/2021] [Indexed: 11/30/2022]
Abstract
Energetic properties of a protein are a major determinant of its evolutionary fitness. Using a reconstruction algorithm, dating the reconstructed proteins and calculating the interaction network between their amino acids through a coevolutionary approach, we studied how the interactions that stabilise 890 proteins, belonging to five families, evolved for billions of years. In particular, we focused our attention on the network of most strongly attractive contacts and on that of poorly optimised, frustrated contacts. Our results support the idea that the cluster of most attractive interactions extends its size along evolutionary time, but from the data, we cannot conclude that protein stability or that the degree of frustration tends always to decrease.
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Affiliation(s)
- Martina Crippa
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Turin, Italy
| | - Damiano Andreghetti
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy
| | - Riccardo Capelli
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Turin, Italy
| | - Guido Tiana
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, via Celoria 16, 20133, Milan, Italy.
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22
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Hou Q, Pucci F, Ancien F, Kwasigroch JM, Bourgeas R, Rooman M. SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs. Bioinformatics 2021; 37:1963–1971. [PMID: 33471089 DOI: 10.1093/bioinformatics/btab034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/05/2020] [Accepted: 01/15/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Although structured proteins adopt their lowest free energy conformation in physiological conditions, the individual residues are generally not in their lowest free energy conformation. Residues that are stability weaknesses are often involved in functional regions, whereas stability strengths ensure local structural stability. The detection of strengths and weaknesses provides key information to guide protein engineering experiments aiming to modulate folding and various functional processes. RESULTS We developed the SWOTein predictor which identifies strong and weak residues in proteins on the basis of three types of statistical energy functions describing local interactions along the chain, hydrophobic forces and tertiary interactions. The large-scale analysis of the different types of strengths and weaknesses demonstrated their complementarity and the enhancement of the information they provide. Moreover, a good average correlation was observed between predicted and experimental strengths and weaknesses obtained from native hydrogen exchange data. SWOTein application to three test cases further showed its suitability to predict and interpret strong and weak residues in the context of folding, conformational changes and protein-protein binding. In summary, SWOTein is both fast and accurate and can be applied at small and large scale to analyze and modulate folding and molecular recognition processes. AVAILABILITY The SWOTein webserver provides the list of predicted strengths and weaknesses and a protein structure visualization tool that facilitates the interpretation of the predictions. It is freely available for academic use at http://babylone.ulb.ac.be/SWOTein/.
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Affiliation(s)
- Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong 250002, P. R. China.,National Institute of Health Data Science of China, Shandong University, Shandong 250002, P. R. China.,Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - François Ancien
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Jean-Marc Kwasigroch
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
| | - Raphaël Bourgeas
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, 1050 Brussels, Belgium
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23
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Modi T, Campitelli P, Kazan IC, Ozkan SB. Protein folding stability and binding interactions through the lens of evolution: a dynamical perspective. Curr Opin Struct Biol 2020; 66:207-215. [PMID: 33388636 DOI: 10.1016/j.sbi.2020.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/02/2020] [Accepted: 11/26/2020] [Indexed: 01/06/2023]
Abstract
While the function of a protein depends heavily on its ability to fold into a correct 3D structure, billions of years of evolution have tailored proteins from highly stable objects to flexible molecules as they adapted to environmental changes. Nature maintains the fine balance of protein folding and stability while still evolving towards new function through generations of fine-tuning necessary interactions with other proteins and small molecules. Here we focus on recent computational and experimental studies that shed light onto how evolution molds protein folding and the functional landscape from a conformational dynamics' perspective. Particularly, we explore the importance of dynamic allostery throughout protein evolution and discuss how the protein anisotropic network can give rise to allosteric and epistatic interactions.
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Affiliation(s)
- Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Ismail Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
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Kong L, Wang Q, Yang W, Shen J, Li Y, Zheng X, Wang L, Chu Y, Deng Z, Chooi YH, You D. Three Recently Diverging Duplicated Methyltransferases Exhibit Substrate-Dependent Regioselectivity Essential for Xantholipin Biosynthesis. ACS Chem Biol 2020; 15:2107-2115. [PMID: 32649177 DOI: 10.1021/acschembio.0c00296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Polycyclic xanthones are characterized by highly oxygenated, angular hexacyclic frameworks and exhibit diverse biological activities. Although many of them have been isolated and chemically synthesized, the detailed biosynthetic machinery awaits discovery. Recently, xanthone construction in the xantholipin (1) pathway was shown to involve cryptic demethoxylation. This suggested a rationale for the existence of three O-methyltransferase (OMT) genes in the gene cluster, although there are only two O-methyl groups in the structure of 1. Here, in vivo and in vitro analysis have been used to show that the three paralogous OMTs, XanM1-M3, introduce individual methyl groups at specific points in the biosynthetic pathway. Each OMT can to some extent take over the role of the other OMTs, although they exhibit highly substrate-dependent regiospecificity. In addition, phylogenetic analysis suggests their evolution from a common ancestor. Four putative ancestral proteins were constructed, and one of them performed all the functions of XanM1-M3, while the others possessed more limited catalytic functions. The results suggest that a promiscuous common ancestor may have been able to catalyze all three reactions prior to gene duplication and functional divergence. The characterization of XanM1-M3 expands the enzyme inventory for polycyclic xanthone biosynthesis and suggests novel directed evolution approaches to diversifying natural product pathways.
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Affiliation(s)
- Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Weinan Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jufang Shen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaoqing Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Lu Wang
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China
| | - Yiwen Chu
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
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25
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Valente D, Werlang T. Frustration and inhomogeneous environments in relaxation of open chains with Ising-type interactions. Phys Rev E 2020; 102:022114. [PMID: 32942439 DOI: 10.1103/physreve.102.022114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/21/2020] [Indexed: 11/07/2022]
Abstract
Frustration can contribute to very slow relaxation times in large open chains, as in spin glasses and in biopolymers. However, frustration may not be sufficient to produce broken ergodicity in finite systems. Here we employ a system-plus-reservoir approach to investigate how strongly inhomogeneous environments and frustration compete in the relaxation of finite open chains. We find a sufficient condition for our inhomogeneous environments to break ergodicity. We use the microscopic model to derive a Markovian quantum master equation for a generic chain with ultrastrong intrachain couplings. We show that this microscopic model avoids a spurious broken ergodicity we find in the phenomenological model. We work out an explicit example of broken ergodicity due to the inhomogeneous environment of an unfrustrated spin chain as far as simulating a recent experiment on protein denaturation (where environment inhomogeneity is especially relevant). We finally show that an inhomogeneous environment can mitigate the effects of frustration-induced degeneracies.
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Affiliation(s)
- D Valente
- Instituto de Física, Universidade Federal de Mato Grosso, CEP 78060-900, Cuiabá, MT, Brazil
| | - T Werlang
- Instituto de Física, Universidade Federal de Mato Grosso, CEP 78060-900, Cuiabá, MT, Brazil
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26
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Non-conservation of folding rates in the thioredoxin family reveals degradation of ancestral unassisted-folding. Biochem J 2020; 476:3631-3647. [PMID: 31750876 PMCID: PMC6906118 DOI: 10.1042/bcj20190739] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 01/04/2023]
Abstract
Evolution involves not only adaptation, but also the degradation of superfluous features. Many examples of degradation at the morphological level are known (vestigial organs, for instance). However, the impact of degradation on molecular evolution has been rarely addressed. Thioredoxins serve as general oxidoreductases in all cells. Here, we report extensive mutational analyses on the folding of modern and resurrected ancestral bacterial thioredoxins. Contrary to claims from recent literature, in vitro folding rates in the thioredoxin family are not evolutionarily conserved, but span at least a ∼100-fold range. Furthermore, modern thioredoxin folding is often substantially slower than ancestral thioredoxin folding. Unassisted folding, as probed in vitro, thus emerges as an ancestral vestigial feature that underwent degradation, plausibly upon the evolutionary emergence of efficient cellular folding assistance. More generally, our results provide evidence that degradation of ancestral features shapes, not only morphological evolution, but also the evolution of individual proteins.
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27
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Sharpe DJ, Röder K, Wales DJ. Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers. J Phys Chem B 2020; 124:4062-4068. [PMID: 32336100 PMCID: PMC7304908 DOI: 10.1021/acs.jpcb.0c01420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Artificial
analogues of the natural nucleic acids have attracted
interest as a diverse class of information storage molecules capable
of self-replication. In this study, we use the computational potential
energy landscape framework to investigate the structural and dynamical
properties of xylo- and deoxyxylo-nucleic acids (XyNA and dXyNA),
which are derived from their respective RNA and DNA analogues by inversion
of a single chiral center in the sugar moiety of the nucleotides.
For an octameric XyNA sequence and the analogue dXyNA, we observe
facile conformational transitions between a left-handed helix, which
is the free energy global minimum, and a ladder-type structure with
approximately zero helicity. The competing ensembles are better separated
in the dXyNA, making it a more suitable candidate for a molecular
switch, whereas the XyNA exhibits additional flexibility. Both energy
landscapes exhibit greater frustration than we observe in RNA or DNA,
in agreement with the higher degree of optimization expected from
the principle of minimal frustration in evolved biomolecules.
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Affiliation(s)
- Daniel J Sharpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Konstantin Röder
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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28
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Avagyan S, Vasilchuk D, Makhatadze GI. Protein adaptation to high hydrostatic pressure: Computational analysis of the structural proteome. Proteins 2020; 88:584-592. [PMID: 31618488 DOI: 10.1002/prot.25839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/11/2019] [Accepted: 09/21/2019] [Indexed: 11/11/2022]
Abstract
Hydrostatic pressure has a vital role in the biological adaptation of the piezophiles, organisms that live under high hydrostatic pressure. However, the mechanisms by which piezophiles are able to adapt their proteins to high hydrostatic pressure is not well understood. One proposed hypothesis is that the volume changes of unfolding (ΔVTot ) for proteins from piezophiles is distinct from those of nonpiezophilic organisms. Since ΔVTot defines pressure dependence of stability, we performed a comprehensive computational analysis of this property for proteins from piezophilic and nonpiezophilic organisms. In addition, we experimentally measured the ΔVTot of acylphosphatases and thioredoxins belonging to piezophilic and nonpiezophilic organisms. Based on this analysis we concluded that there is no difference in ΔVTot for proteins from piezophilic and nonpiezophilic organisms. Finally, we put forward the hypothesis that increased concentrations of osmolytes can provide a systemic increase in pressure stability of proteins from piezophilic organisms and provide experimental thermodynamic evidence in support of this hypothesis.
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Affiliation(s)
- Samvel Avagyan
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - Daniel Vasilchuk
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York
| | - George I Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York
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29
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Zhang L, Ma H, Qian W, Li H. Protein structure optimization using improved simulated annealing algorithm on a three-dimensional AB off-lattice model. Comput Biol Chem 2020; 85:107237. [PMID: 32109854 DOI: 10.1016/j.compbiolchem.2020.107237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/11/2020] [Accepted: 02/15/2020] [Indexed: 01/01/2023]
Abstract
This paper proposed an improved simulated annealing (ISA) algorithm for protein structure optimization based on a three-dimensional AB off-lattice model. In the algorithm, we provided a general formula used for producing initial solution, and designed a multivariable disturbance term, relating to the parameters of simulated annealing and a tuned constant, to generate neighborhood solution. To avoid missing optimal solution, storage operation was performed in searching process. We applied the algorithm to test artificial protein sequences from literature and constructed a benchmark dataset consisting of 10 real protein sequences from the Protein Data Bank (PDB). Otherwise, we generated Cα space-filling model to represent protein folding conformation. The results indicate our algorithm outperforms the five methods before in searching lower energies of artificial protein sequences. In the testing on real proteins, our method can achieve the energy conformations with Cα-RMSD less than 3.0 Å from the PDB structures. Moreover, Cα space-filling model may simulate dynamic change of protein folding conformation at atomic level.
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Affiliation(s)
- Lizhong Zhang
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China; College of Computer Science and Technology, Shenyang University of Chemical Technology, Shenyang 110142, China
| | - He Ma
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China; Key Laboratory of Medical Image Computing (Northeastern University), Ministry of Education, Shenyang 110169, China.
| | - Wei Qian
- Department of Electrical and Computer Engineering, College of Engineering, University of Texas, El Paso TX 79968, USA
| | - Haiyan Li
- College of Pharmaceutical and Bioengineering, Shenyang University of Chemical Technology, Shenyang 110142, China
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30
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Bigman LS, Levy Y. Proteins: molecules defined by their trade-offs. Curr Opin Struct Biol 2020; 60:50-56. [DOI: 10.1016/j.sbi.2019.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/07/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022]
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31
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Sheik Amamuddy O, Veldman W, Manyumwa C, Khairallah A, Agajanian S, Oluyemi O, Verkhivker GM, Tastan Bishop Ö. Integrated Computational Approaches and Tools forAllosteric Drug Discovery. Int J Mol Sci 2020; 21:E847. [PMID: 32013012 PMCID: PMC7036869 DOI: 10.3390/ijms21030847] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/16/2022] Open
Abstract
Understanding molecular mechanisms underlying the complexity of allosteric regulationin proteins has attracted considerable attention in drug discovery due to the benefits and versatilityof allosteric modulators in providing desirable selectivity against protein targets while minimizingtoxicity and other side effects. The proliferation of novel computational approaches for predictingligand-protein interactions and binding using dynamic and network-centric perspectives has ledto new insights into allosteric mechanisms and facilitated computer-based discovery of allostericdrugs. Although no absolute method of experimental and in silico allosteric drug/site discoveryexists, current methods are still being improved. As such, the critical analysis and integration ofestablished approaches into robust, reproducible, and customizable computational pipelines withexperimental feedback could make allosteric drug discovery more efficient and reliable. In this article,we review computational approaches for allosteric drug discovery and discuss how these tools can beutilized to develop consensus workflows for in silico identification of allosteric sites and modulatorswith some applications to pathogen resistance and precision medicine. The emerging realization thatallosteric modulators can exploit distinct regulatory mechanisms and can provide access to targetedmodulation of protein activities could open opportunities for probing biological processes and insilico design of drug combinations with improved therapeutic indices and a broad range of activities.
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Affiliation(s)
- Olivier Sheik Amamuddy
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Colleen Manyumwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Afrah Khairallah
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Steve Agajanian
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Odeyemi Oluyemi
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
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32
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Mouro PR, Povinelli APR, Leite VBP, Chahine J. Exploring Folding Aspects of Monomeric Superoxide Dismutase. J Phys Chem B 2020; 124:650-661. [DOI: 10.1021/acs.jpcb.9b09640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paulo R. Mouro
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
| | - Ana P. R. Povinelli
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
| | - Vitor B. P. Leite
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Jorge Chahine
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
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33
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Nandi T, Desai A, Ainavarapu SRK. The unfolding transition state of ubiquitin with charged residues has higher energy than that with hydrophobic residues. Phys Chem Chem Phys 2020; 22:23158-23168. [DOI: 10.1039/d0cp03876h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The native-state structure and folding pathways of a protein are encoded in its amino acid sequence.
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Affiliation(s)
- Tathagata Nandi
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400005
- India
| | - Amogh Desai
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400005
- India
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34
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Abstract
Large proteins composed of multiple domains are abundant in all proteomes, but their folding and structural dynamics remain poorly understood. Using single-molecule force spectroscopy, we have defined how stabilizing interfaces among the domains of elongation factor G (EF-G) shape its folding pathway. Contrary to the expectation that multidomain proteins fold sequentially as they emerge from the ribosome, we find that folding cannot be completed until the full protein has been synthesized. This posttranslational folding mechanism results in a propensity for misfolding. It is dictated by an energetic coupling among domains that enables conformational flexibility crucial for EF-G function. EF-G thus provides an example of how distinct biological ends—robust folding and functionally important flexibility—come into conflict during protein biogenesis. Large proteins with multiple domains are thought to fold cotranslationally to minimize interdomain misfolding. Once folded, domains interact with each other through the formation of extensive interfaces that are important for protein stability and function. However, multidomain protein folding and the energetics of domain interactions remain poorly understood. In elongation factor G (EF-G), a highly conserved protein composed of 5 domains, the 2 N-terminal domains form a stably structured unit cotranslationally. Using single-molecule optical tweezers, we have defined the steps leading to fully folded EF-G. We find that the central domain III of EF-G is highly dynamic and does not fold upon emerging from the ribosome. Surprisingly, a large interface with the N-terminal domains does not contribute to the stability of domain III. Instead, it requires interactions with its folded C-terminal neighbors to be stably structured. Because of the directionality of protein synthesis, this energetic dependency of domain III on its C-terminal neighbors disrupts cotranslational folding and imposes a posttranslational mechanism on the folding of the C-terminal part of EF-G. As a consequence, unfolded domains accumulate during synthesis, leading to the extensive population of misfolded species that interfere with productive folding. Domain III flexibility enables large-scale conformational transitions that are part of the EF-G functional cycle during ribosome translocation. Our results suggest that energetic tuning of domain stabilities, which is likely crucial for EF-G function, complicates the folding of this large multidomain protein.
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35
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Nandi T, Yadav A, Ainavarapu SRK. Experimental comparison of energy landscape features of ubiquitin family proteins. Proteins 2019; 88:449-461. [DOI: 10.1002/prot.25822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/05/2019] [Accepted: 09/18/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Tathagata Nandi
- Department of Chemical SciencesTata Institute of Fundamental Research Mumbai India
| | - Anju Yadav
- Department of Chemical SciencesTata Institute of Fundamental Research Mumbai India
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36
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Cheung NJ, Yu W. Sibe: a computation tool to apply protein sequence statistics to predict folding and design in silico. BMC Bioinformatics 2019; 20:455. [PMID: 31492097 PMCID: PMC6728967 DOI: 10.1186/s12859-019-2984-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/03/2019] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Evolutionary information contained in the amino acid sequences of proteins specifies the biological function and fold, but exactly what information contained in the protein sequence drives both of these processes? Considerable progress has been made to answer this fundamental question, but it remains challenging to explore the potential space of cooperative interactions between amino acids. Statistical analysis plays a significant role in studying such interactions and its use has expanded in recent years to studies ranging from coevolution-guided rational protein design to protein folding in silico. RESULTS Here we describe a computational tool named Sibe for use in studies of protein sequence, folding, and design using evolutionary coupling between amino acids as a driving factor. In this study, Sibe is used to identify positionally conserved couplings between pairwise amino acids and aid rational protein design. In this process, pairwise couplings are filtered according to the relative entropy computed from the positional conservations and grouped into several 'blocks', which could contribute to driving protein folding and design. A human β2-adrenergic receptor (β2AR) was used to demonstrate that those 'blocks' contribute the rational design for specifying functional residues. Sibe also provides folding modules based on both the positionally conserved couplings and well-established statistical potentials for simulating protein folding in silico and predicting tertiary structure. Our results show that statistically inferences of basic evolutionary principles, such as conservations and coupled-mutations, can be used to rapidly design a diverse set of proteins and study protein folding. CONCLUSIONS The developed software Sibe provides a computational tool for systematical analysis from protein primary to its tertiary structure using the evolutionary couplings as a driving factor. Sibe, written in C++, accounts for compatibility with the 'big data' era in biological science, and it primarily focuses on protein sequence analysis, but it is also applicable to extend to other modeling and predictions of experimental measurements.
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Affiliation(s)
- Ngaam J. Cheung
- Department of Brain and Cognitive Science, DGIST, Daegu, 42988 South Korea
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HA UK
| | - Wookyung Yu
- Department of Brain and Cognitive Science, DGIST, Daegu, 42988 South Korea
- Core Protein Resources Center, DGIST, Daegu, 42988 South Korea
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37
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Coglitore D, Janot JM, Balme S. Protein at liquid solid interfaces: Toward a new paradigm to change the approach to design hybrid protein/solid-state materials. Adv Colloid Interface Sci 2019; 270:278-292. [PMID: 31306853 DOI: 10.1016/j.cis.2019.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 10/26/2022]
Abstract
This review gives an overview of protein adsorption at solid/liquid interface. Compared to the other ones, we have focus on three main questions with the point of view of the protein. The first question is related to the kinetic and especially the using of Langmuir model to describe the protein adsorption. The second question is about the concept of hard and soft protein. In this part, we report the protein structural modification induced by adsorption regarding their intrinsic structure. This allows formulating of a new concept to classify the protein to predict their behavior at solid/liquid interface. The last question is related to the protein corona. We give an overview about the soft/hard corona and attempt to make correlation with the concept of hard/soft protein.
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38
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Napolitano S, Reber RJ, Rubini M, Glockshuber R. Functional analyses of ancestral thioredoxins provide insights into their evolutionary history. J Biol Chem 2019; 294:14105-14118. [PMID: 31366732 PMCID: PMC6755812 DOI: 10.1074/jbc.ra119.009718] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/29/2019] [Indexed: 12/24/2022] Open
Abstract
Thioredoxin (Trx) is a conserved, cytosolic reductase in all known organisms. The enzyme receives two electrons from NADPH via thioredoxin reductase (TrxR) and passes them on to multiple cellular reductases via disulfide exchange. Despite the ubiquity of thioredoxins in all taxa, little is known about the functions of resurrected ancestral thioredoxins in the context of a modern mesophilic organism. Here, we report on functional in vitro and in vivo analyses of seven resurrected Precambrian thioredoxins, dating back 1–4 billion years, in the Escherichia coli cytoplasm. Using synthetic gene constructs for recombinant expression of the ancestral enzymes, along with thermodynamic and kinetic assays, we show that all ancestral thioredoxins, as today's thioredoxins, exhibit strongly reducing redox potentials, suggesting that thioredoxins served as catalysts of cellular reduction reactions from the beginning of evolution, even before the oxygen catastrophe. A detailed, quantitative characterization of their interactions with the electron donor TrxR from Escherichia coli and the electron acceptor methionine sulfoxide reductase, also from E. coli, strongly hinted that thioredoxins and thioredoxin reductases co-evolved and that the promiscuity of thioredoxins toward downstream electron acceptors was maintained during evolution. In summary, our findings suggest that thioredoxins evolved high specificity for their sole electron donor TrxR while maintaining promiscuity to their multiple electron acceptors.
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Affiliation(s)
- Silvia Napolitano
- Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - Robin J Reber
- Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
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39
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Affiliation(s)
- Michael J Harms
- Institute of Molecular Biology and Chemistry and Biochemistry Department, University of Oregon, Eugene, OR, USA.
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40
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Yan Z, Wang J. Superfunneled Energy Landscape of Protein Evolution Unifies the Principles of Protein Evolution, Folding, and Design. PHYSICAL REVIEW LETTERS 2019; 122:018103. [PMID: 31012725 DOI: 10.1103/physrevlett.122.018103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 11/08/2018] [Indexed: 06/09/2023]
Abstract
Evolution is essential for shaping the biological functions. Darwin proposed the selection as the driving force for evolution upon mutations. While mutations are clear, the quantification of the selection force is still challenging. In this study, we identified and quantified both thermodynamic stability and kinetic accessibility as the selection forces for protein evolution. The protein evolution can be viewed and quantified as a trajectory moving along a superfunneled energy landscape with a line attractor at the bottom. The resulting evolved sequences and structures show strong protein characteristics including the hydrophobic core, high designability, and fast folding. The evolution principle uncovered here is validated on real proteins and sheds light on the protein design.
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Affiliation(s)
- Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, New York 11790, USA
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Trudeau DL, Tawfik DS. Protein engineers turned evolutionists-the quest for the optimal starting point. Curr Opin Biotechnol 2019; 60:46-52. [PMID: 30611116 DOI: 10.1016/j.copbio.2018.12.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/22/2018] [Accepted: 12/03/2018] [Indexed: 12/12/2022]
Abstract
The advent of laboratory directed evolution yielded a fruitful crosstalk between the disciplines of molecular evolution and bio-engineering. Here, we outline recent developments in both disciplines with respect to how one can identify the best starting points for directed evolution, such that highly efficient and robust tailor-made enzymes can be obtained with minimal optimization. Directed evolution studies have highlighted essential features of engineer-able enzymes: highly stable, mutationally robust enzymes with the capacity to accept a broad range of substrates. Robust, evolvable enzymes can be inferred from the natural sequence record. Broad substrate spectrum relates to conformational plasticity and can also be predicted by phylogenetic analyses and/or by computational design. Overall, an increasingly powerful toolkit is becoming available for identifying optimal starting points including network analyses of enzyme superfamilies and other bioinformatics methods.
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Affiliation(s)
- Devin L Trudeau
- Department of Biomolecular Sciences, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel.
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42
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Sun B, Cook EC, Creamer TP, Kekenes-Huskey PM. Electrostatic control of calcineurin's intrinsically-disordered regulatory domain binding to calmodulin. Biochim Biophys Acta Gen Subj 2018; 1862:2651-2659. [PMID: 30071273 PMCID: PMC6317854 DOI: 10.1016/j.bbagen.2018.07.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/13/2018] [Accepted: 07/24/2018] [Indexed: 12/26/2022]
Abstract
Calcineurin (CaN) is a serine/threonine phosphatase that regulates a variety of physiological and pathophysiological processes in mammalian tissue. The calcineurin (CaN) regulatory domain (RD) is responsible for regulating the enzyme's phosphatase activity, and is believed to be highly-disordered when inhibiting CaN, but undergoes a disorder-to-order transition upon diffusion-limited binding with the regulatory protein calmodulin (CaM). The prevalence of polar and charged amino acids in the regulatory domain (RD) suggests electrostatic interactions are involved in mediating calmodulin (CaM) binding, yet the lack of atomistic-resolution data for the bound complex has stymied efforts to probe how the RD sequence controls its conformational ensemble and long-range attractions contribute to target protein binding. In the present study, we investigated via computational modeling the extent to which electrostatics and structural disorder facilitate CaM/CaN association kinetics. Specifically, we examined several RD constructs that contain the CaM binding region (CAMBR) to characterize the roles of electrostatics versus conformational diversity in controlling diffusion-limited association rates, via microsecond-scale molecular dynamics (MD) and Brownian dynamic (BD) simulations. Our results indicate that the RD amino acid composition and sequence length influence both the dynamic availability of conformations amenable to CaM binding, as well as long-range electrostatic interactions to steer association. These findings provide intriguing insight into the interplay between conformational diversity and electrostatically-driven protein-protein association involving CaN, which are likely to extend to wide-ranging diffusion-limited processes regulated by intrinsically-disordered proteins.
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Affiliation(s)
- Bin Sun
- Department of Chemistry, University of Kentucky, 505 Rose St., Chemistry-Physics Building, Lexington, KY, USA 40506
| | - Erik C Cook
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, St. Lexington, KY, USA 40536
| | - Trevor P Creamer
- Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone, St. Lexington, KY, USA 40536
| | - Peter M Kekenes-Huskey
- Department of Chemistry, University of Kentucky, 505 Rose St., Chemistry-Physics Building, Lexington, KY, USA 40506.
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Modi T, Huihui J, Ghosh K, Ozkan SB. Ancient thioredoxins evolved to modern-day stability-function requirement by altering native state ensemble. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170184. [PMID: 29735738 PMCID: PMC5941179 DOI: 10.1098/rstb.2017.0184] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 02/06/2023] Open
Abstract
Thioredoxins (THRXs)-small globular proteins that reduce other proteins-are ubiquitous in all forms of life, from Archaea to mammals. Although ancestral thioredoxins share sequential and structural similarity with the modern-day (extant) homologues, they exhibit significantly different functional activity and stability. We investigate this puzzle by comparative studies of their (ancient and modern-day THRXs') native state ensemble, as quantified by the dynamic flexibility index (DFI), a metric for the relative resilience of an amino acid to perturbations in the rest of the protein. Clustering proteins using DFI profiles strongly resemble an alternative classification scheme based on their activity and stability. The DFI profiles of the extant proteins are substantially different around the α3, α4 helices and catalytic regions. Likewise, allosteric coupling of the active site with the rest of the protein is different between ancient and extant THRXs, possibly explaining the decreased catalytic activity at low pH with evolution. At a global level, we note that the population of low-flexibility (called hinges) and high-flexibility sites increases with evolution. The heterogeneity (quantified by the variance) in DFI distribution increases with the decrease in the melting temperature typically associated with the evolution of ancient proteins to their modern-day counterparts.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85281, USA
| | - Jonathan Huihui
- Department of Physics and Astronomy, University of Denver, Denver, CO 80209, USA
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO 80209, USA
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85281, USA
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44
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Ferreiro DU, Komives EA, Wolynes PG. Frustration, function and folding. Curr Opin Struct Biol 2017; 48:68-73. [PMID: 29101782 DOI: 10.1016/j.sbi.2017.09.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 01/08/2023]
Abstract
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful catalysis, are examples of basic chemical activities that the great majority of polypeptides do not display, and are thought to be the outcome of the natural history of proteins. Function, a concept genuine to Biology, is at the core of evolution and often conflicts with the physical constraints. Locating the frustration between discrepant goals in a recurrent system leads to fundamental insights about the chances and necessities that shape the encoding of biological information.
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Affiliation(s)
- Diego U Ferreiro
- Protein Physiology Lab, FCEyN-Universidad de Buenos Aires, IQUIBICEN/CONICET, Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; Department of Chemistry, Rice University, Houston, TX, USA; Department of Physics, Rice University, Houston, TX, USA; Department of Biosciences, Rice University, Houston, TX, USA
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Sawle L, Huihui J, Ghosh K. All-Atom Simulations Reveal Protein Charge Decoration in the Folded and Unfolded Ensemble Is Key in Thermophilic Adaptation. J Chem Theory Comput 2017; 13:5065-5075. [DOI: 10.1021/acs.jctc.7b00545] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucas Sawle
- Department of Physics and
Astronomy, University of Denver, Denver, Colorado 80208, United States
| | - Jonathan Huihui
- Department of Physics and
Astronomy, University of Denver, Denver, Colorado 80208, United States
| | - Kingshuk Ghosh
- Department of Physics and
Astronomy, University of Denver, Denver, Colorado 80208, United States
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46
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Aina A, Wallin S. Multisequence algorithm for coarse-grained biomolecular simulations: Exploring the sequence-structure relationship of proteins. J Chem Phys 2017; 147:095102. [DOI: 10.1063/1.4986933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- A. Aina
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador A1B 3X7, Canada
| | - S. Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador A1B 3X7, Canada
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Reply to Candel et al.: Evidence for evolutionary conservation of folding kinetics in the thioredoxin protein family. Proc Natl Acad Sci U S A 2017; 114:E4124. [PMID: 28512227 DOI: 10.1073/pnas.1704669114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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48
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Fast folding and slow unfolding of a resurrected Precambrian protein. Proc Natl Acad Sci U S A 2017; 114:E4122-E4123. [PMID: 28512228 DOI: 10.1073/pnas.1703227114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Self-Referential Encoding on Modules of Anticodon Pairs-Roots of the Biological Flow System. Life (Basel) 2017; 7:life7020016. [PMID: 28383509 PMCID: PMC5492138 DOI: 10.3390/life7020016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/24/2017] [Accepted: 03/26/2017] [Indexed: 12/22/2022] Open
Abstract
The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes-structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process-anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are stable and apt to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sink-effective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don't accumulate to saturation, which would trigger inhibition.
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