1
|
Ruiz-Cruz S, Erazo Garzon A, Cambillau C, Ortiz Charneco G, Lugli GA, Ventura M, Mahony J, van Sinderen D. The tal gene of lactococcal bacteriophage TP901-1 is involved in DNA release following host adsorption. Appl Environ Microbiol 2024; 90:e0069424. [PMID: 39132999 PMCID: PMC11409707 DOI: 10.1128/aem.00694-24] [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: 04/11/2024] [Accepted: 07/10/2024] [Indexed: 08/13/2024] Open
Abstract
Temperate P335 phage TP901-1 represents one of the best-characterized Gram-positive phages regarding its structure and host interactions. Following its reversible adsorption to the polysaccharidic side-chain of the cell wall polysaccharide of its host Lactococcus cremoris 3107, TP901-1 requires a glucosylated cell envelope moiety to trigger its genome delivery into the host cytoplasm. Here, we demonstrate that three distinct single amino acid substitutions in the Tal protein of TP901-1 baseplate are sufficient to overcome the TP901-1 resistance of three L. cremoris 3107 derivatives, whose resistance is due to impaired DNA release of the phage. All of these Tal alterations are located in the N-terminally located gp27-like domain of the protein, conserved in many tailed phages. AlphaFold2 predictions of the Tal mutant proteins suggest that these mutations favor conformational changes necessary to reposition the Tal fiber and thus facilitate release of the tape measure protein from the tail tube and subsequent DNA ejection in the absence of the trigger otherwise required for phage genome release. IMPORTANCE Understanding the molecular mechanisms involved in phage-host interactions is essential to develop phage-based applications in the food and probiotic industries, yet also to reduce the risk of phage infections in fermentations. Lactococcus, extensively used in dairy fermentations, has been widely employed to unravel such interactions. Phage infection commences with the recognition of a suitable host followed by the release of its DNA into the bacterial cytoplasm. Details on this latter, irreversible step are still very scarce in lactococci and other Gram-positive bacteria. We demonstrate that a component of the baseplate of the lactococcal phage TP901-1, the tail-associated lysin (Tal), is involved in the DNA delivery into its host, L. cremoris 3107. Specifically, we have found that three amino acid changes in Tal appear to facilitate structural rearrangements in the baseplate necessary for the DNA release process, even in the absence of an otherwise required host trigger.
Collapse
Affiliation(s)
- Sofía Ruiz-Cruz
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Andrea Erazo Garzon
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Christian Cambillau
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université—CNRS, Marseille, France
| | | | - Gabriele Andrea Lugli
- Department of Chemistry, Life Sciences, and Environmental Sustainability, Laboratory of Probiogenomics, University of Parma, Parma, Italy
| | - Marco Ventura
- Department of Chemistry, Life Sciences, and Environmental Sustainability, Laboratory of Probiogenomics, University of Parma, Parma, Italy
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| |
Collapse
|
2
|
Rege NK, Liu M, Dhayalan B, Chen YS, Smith NA, Rahimi L, Sun J, Guo H, Yang Y, Haataja L, Phillips NFB, Whittaker J, Smith BJ, Arvan P, Ismail-Beigi F, Weiss MA. "Register-shift" insulin analogs uncover constraints of proteotoxicity in protein evolution. J Biol Chem 2020; 295:3080-3098. [PMID: 32005662 DOI: 10.1074/jbc.ra119.011389] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
Globular protein sequences encode not only functional structures (the native state) but also protein foldability, i.e. a conformational search that is both efficient and robustly minimizes misfolding. Studies of mutations associated with toxic misfolding have yielded insights into molecular determinants of protein foldability. Of particular interest are residues that are conserved yet dispensable in the native state. Here, we exploited the mutant proinsulin syndrome (a major cause of permanent neonatal-onset diabetes mellitus) to investigate whether toxic misfolding poses an evolutionary constraint. Our experiments focused on an invariant aromatic motif (PheB24-PheB25-TyrB26) with complementary roles in native self-assembly and receptor binding. A novel class of mutations provided evidence that insulin can bind to the insulin receptor (IR) in two different modes, distinguished by a "register shift" in this motif, as visualized by molecular dynamics (MD) simulations. Register-shift variants are active but defective in cellular foldability and exquisitely susceptible to fibrillation in vitro Indeed, expression of the corresponding proinsulin variant induced endoplasmic reticulum stress, a general feature of the mutant proinsulin syndrome. Although not present among vertebrate insulin and insulin-like sequences, a prototypical variant ([GlyB24]insulin) was as potent as WT insulin in a rat model of diabetes. Although in MD simulations the shifted register of receptor engagement is compatible with the structure and allosteric reorganization of the IR-signaling complex, our results suggest that this binding mode is associated with toxic misfolding and so is disallowed in evolution. The implicit threat of proteotoxicity limits sequence variation among vertebrate insulins and insulin-like growth factors.
Collapse
Affiliation(s)
- Nischay K Rege
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Ming Liu
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan 48105, Australia; Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, Heping District, 300052 China
| | - Balamurugan Dhayalan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Yen-Shan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Nicholas A Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Leili Rahimi
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106; Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Jinhong Sun
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan 48105, Australia
| | - Huan Guo
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan 48105, Australia
| | - Yanwu Yang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Leena Haataja
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan 48105, Australia
| | - Nelson F B Phillips
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Jonathan Whittaker
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Brian J Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Peter Arvan
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, Michigan 48105, Australia
| | - Faramarz Ismail-Beigi
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106; Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Michael A Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202.
| |
Collapse
|
3
|
de Marco A, Ferrer-Miralles N, Garcia-Fruitós E, Mitraki A, Peternel S, Rinas U, Trujillo-Roldán MA, Valdez-Cruz NA, Vázquez E, Villaverde A. Bacterial inclusion bodies are industrially exploitable amyloids. FEMS Microbiol Rev 2019; 43:53-72. [PMID: 30357330 DOI: 10.1093/femsre/fuy038] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
Understanding the structure, functionalities and biology of functional amyloids is an issue of emerging interest. Inclusion bodies, namely protein clusters formed in recombinant bacteria during protein production processes, have emerged as unanticipated, highly tunable models for the scrutiny of the physiology and architecture of functional amyloids. Based on an amyloidal skeleton combined with varying amounts of native or native-like protein forms, bacterial inclusion bodies exhibit an unusual arrangement that confers mechanical stability, biological activity and conditional protein release, being thus exploitable as versatile biomaterials. The applicability of inclusion bodies in biotechnology as enriched sources of protein and reusable catalysts, and in biomedicine as biocompatible topographies, nanopills or mimetics of endocrine secretory granules has been largely validated. Beyond these uses, the dissection of how recombinant bacteria manage the aggregation of functional protein species into structures of highly variable complexity offers insights about unsuspected connections between protein quality (conformational status compatible with functionality) and cell physiology.
Collapse
Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000 Nova Gorica, Slovenia
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Vassilika Vouton, 70013 Heraklion, Crete, Greece.,Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology Hellas (FORTH), N. Plastira 100, Vassilika Vouton, 70013 Heraklion, Crete, Greece
| | | | - Ursula Rinas
- Leibniz University of Hannover, Technical Chemistry and Life Science, 30167 Hannover, Germany.,Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| |
Collapse
|
4
|
Structural constraints-based evaluation of immunogenic avirulent toxins from Clostridium botulinum C2 and C3 toxins as subunit vaccines. INFECTION GENETICS AND EVOLUTION 2016; 44:17-27. [PMID: 27320793 DOI: 10.1016/j.meegid.2016.06.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 05/26/2016] [Accepted: 06/13/2016] [Indexed: 12/11/2022]
Abstract
Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 and C3 toxins in addition to botulinum neurotoxins in avian and mammalian cells. C2 and C3 toxins are members of bacterial ADP-ribosyltransferase superfamily, which modify the eukaryotic cell surface proteins by ADP-ribosylation reaction. Herein, the mutant proteins with lack of catalytic and pore forming function derived from C2 (C2I and C2II) and C3 toxins were computationally evaluated to understand their structure-function integrity. We have chosen many structural constraints including local structural environment, folding process, backbone conformation, conformational dynamic sub-space, NAD-binding specificity and antigenic determinants for screening of suitable avirulent toxins. A total of 20 avirulent mutants were identified out of 23 mutants, which were experimentally produced by site-directed mutagenesis. No changes in secondary structural elements in particular to α-helices and β-sheets and also in fold rate of all-β classes. Structural stability was maintained by reordered hydrophobic and hydrogen bonding patterns. Molecular dynamic studies suggested that coupled mutations may restrain the binding affinity to NAD(+) or protein substrate upon structural destabilization. Avirulent toxins of this study have stable energetic backbone conformation with a common blue print of folding process. Molecular docking studies revealed that avirulent mutants formed more favorable hydrogen bonding with the side-chain of amino acids near to conserved NAD-binding core, despite of restraining NAD-binding specificity. Thus, structural constraints in the avirulent toxins would determine their immunogenic nature for the prioritization of protein-based subunit vaccine/immunogens to avian and veterinary animals infected with C. botulinum.
Collapse
|
5
|
Parker MS, Sah R, Balasubramaniam A, Sallee FR, Zerbe O, Parker SL. Non-specific binding and general cross-reactivity of Y receptor agonists are correlated and should importantly depend on their acidic sectors. Peptides 2011; 32:258-65. [PMID: 21126552 PMCID: PMC3025077 DOI: 10.1016/j.peptides.2010.11.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Revised: 11/12/2010] [Accepted: 11/12/2010] [Indexed: 10/18/2022]
Abstract
Non-specific binding of Y receptor agonists to intact CHO cells, and to CHO cell or rat brain particulates, is much greater for human neuropeptide Y (hNPY) compared to porcine peptide Y (pPYY), and especially relative to human pancreatic polypeptide (hPP). This binding of hNPY is reduced by alkali cations in preference to non-ionic chaotrope urea, while the much lower non-specific binding of pPYY is more sensitive to urea. The difference could mainly be due to the 10-16 stretch in 36-residue Y agonists (residues 8-14 in N-terminally clipped 34-peptides), located in the sector that contains all acidic residues of physiological Y agonists. Anionic pairs containing aspartate in the 10-16 zone could be principally responsible for non-specific attachments, but may also aid the receptor site binding. Two such pairs are found in hNPY, one in pPYY, and none in hPP. The hydroxyl amino acid residue at position 13 in mammalian PYY and PP molecules could lower conformational plasticity and the non-selective binding via intrachain hydrogen bonding. The acidity of this tract could also be important in agonist selectivity of the Y receptor subtypes. The differences point to an evolutionary reduction of promiscuous protein binding from NPY to PP, and should also be important for Y agonist selectivity within NPY receptor group, and correlate with partial agonism and out-of group cross-reactivity with other receptors.
Collapse
Affiliation(s)
- M. S. Parker
- Department. of Molecular Cell Sciences, Univ. of Memphis, Memphis, TN 38152, USA
| | - R. Sah
- Department of Surgery, Univ. of Cincinnati, Cincinnati, OH 45267, USA
| | - A. Balasubramaniam
- Department of Psychiatry, Univ. of Cincinnati, Cincinnati, OH 45267, USA
| | - F. R. Sallee
- Department of Surgery, Univ. of Cincinnati, Cincinnati, OH 45267, USA
| | - O. Zerbe
- Department of Organic Chemistry, Univ. of Basel, Basel, CH-8057, Switzerland
| | - S. L. Parker
- Department of Pharmacology, Univ. of Tennessee Health Science Center, Memphis, TN 38163, USA
- Corresponding author at: Department of Pharmacology, UTHSC Memphis, Memphis TN 38163, USA,
| |
Collapse
|
6
|
Mitraki A. Protein aggregation from inclusion bodies to amyloid and biomaterials. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 79:89-125. [PMID: 20621282 DOI: 10.1016/s1876-1623(10)79003-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inclusion bodies and amyloid are two different outcomes of the same fundamental biological process: protein aggregation. They share two important features that suggest sequence-specific aggregation: oligomeric intermediates as precursors to the aggregated sate and sensitivity to site-specific point mutations. For a long time, the physical state of inclusion bodies was refractory to the use of protein structural characterization techniques that were developed for soluble proteins. Recent high-resolution studies reveal that the apparently amorphous state of these dense protein agglomerates consists of amyloid-type structures adopted by short segments that initiate aggregation. Under certain circumstances it is possible for the aggregation-prone segments to "recruit" a globular counterpart within the inclusion body, with the latter being able to fold into an active conformation. In this chapter we will discuss these recent structural insights in relation with the also recent, high-resolution structures for amyloid "spines" and their ability to accommodate globular or "swapped" domains in their periphery. Finally, unexpected natural roles for amyloid structures such as protection, adhesion, and storage materials gradually emerge. We will discuss how these properties in combination with biochemical and structural insights can inspire "biomimetic" approaches for the rational design of novel nanobiomaterials.
Collapse
Affiliation(s)
- Anna Mitraki
- Department of Materials Science and Technology, University of Crete and Institute for Electronic Structure and Laser, Foundation for Research and Technology-Hellas (IESL-FORTH), Vassilika Vouton, Heraklion, Crete, Greece
| |
Collapse
|
7
|
Kurochkina LP, Vishnevskiy AY, Mesyanzhinov VV. Role of the C-terminus in folding and oligomerization of bacteriophage T4 gene product 9. BIOCHEMISTRY. BIOKHIMIIA 2008; 73:995-999. [PMID: 18976216 DOI: 10.1134/s000629790809006x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Bacteriophage T4 gene product 9 (gp9) is a structural protein of baseplate that plays a key role at the beginning of the infection process. Biologically active gp9 is a trimer that consists of three domains. It is a convenient model to study folding and oligomerization mechanisms of complex multidomain proteins. The influence of deletions and mutations of several amino acid residues in the C-terminal part of molecule on protein folding, oligomerization, and functional activity has been studied. It was determined that gp9 trimerization occurs post-translationally. It was shown that Gln282 and Ile284 are essential for gp9 trimer stabilization. The disruption of hydrogen bonds formed by Gln282 with Leu203 and Thr205 of neighboring chain has effect not only on interaction between monomers within trimer but also on folding of the polypeptide chain. Tsf (temperature sensitive for folding) and su (suppressor) mutations in the C-terminal region of the polypeptide chain affecting protein folding have been found.
Collapse
Affiliation(s)
- L P Kurochkina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | | | | |
Collapse
|
8
|
Betts S, Haase-Pettingell C, Cook K, King J. Buried hydrophobic side-chains essential for the folding of the parallel beta-helix domains of the P22 tailspike. Protein Sci 2005; 13:2291-303. [PMID: 15322277 PMCID: PMC2280027 DOI: 10.1110/ps.04676704] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The processive beta-strands and turns of a polypeptide parallel beta-helix represent one of the topologically simplest beta-sheet folds. The three subunits of the tailspike adhesin of phage P22 each contain 13 rungs of a parallel beta-helix followed by an interdigitated section of triple-stranded beta-helix. Long stacks of hydrophobic residues dominate the elongated buried core of these two beta-helix domains and extend into the core of the contiguous triple beta-prism domain. To test whether these side-chain stacks represent essential residues for driving the chain into the correct fold, each of three stacked phenylalanine residues within the buried core were substituted with less bulky amino acids. The mutant chains with alanine in place of phenylalanine were defective in intracellular folding. The chains accumulated exclusively in the aggregated inclusion body state regardless of temperature of folding. These severe folding defects indicate that the stacked phenylalanine residues are essential for correct parallel beta-helix folding. Replacement of the same phenylalanine residues with valine or leucine also impaired folding in vivo, but with less severity. Mutants were also constructed in a second buried stack that extends into the intertwined triple-stranded beta-helix and contiguous beta-prism regions of the protein. These mutants exhibited severe defects in later stages of chain folding or assembly, accumulating as misfolded but soluble multimeric species. The results indicate that the formation of the buried hydrophobic stacks is critical for the correct folding of the parallel beta-helix, triple-stranded beta-helix, and beta-prism domains in the tailspike protein.
Collapse
Affiliation(s)
- Scott Betts
- Department of Biology 68-330, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | | | | | | |
Collapse
|
9
|
Mesyanzhinov VV, Leiman PG, Kostyuchenko VA, Kurochkina LP, Miroshnikov KA, Sykilinda NN, Shneider MM. Molecular architecture of bacteriophage T4. BIOCHEMISTRY (MOSCOW) 2005; 69:1190-202. [PMID: 15627372 DOI: 10.1007/s10541-005-0064-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In studying bacteriophage T4--one of the basic models of molecular biology for several decades--there has come a Renaissance, and this virus is now actively used as object of structural biology. The structures of six proteins of the phage particle have recently been determined at atomic resolution by X-ray crystallography. Three-dimensional reconstruction of the infection device--one of the most complex multiprotein components--has been developed on the basis of cryo-electron microscopy images. The further study of bacteriophage T4 structure will allow a better understanding of the regulation of protein folding, assembly of biological structures, and also mechanisms of functioning of the complex biological molecular machines.
Collapse
Affiliation(s)
- V V Mesyanzhinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
| | | | | | | | | | | | | |
Collapse
|
10
|
Mesyanzhinov VV, Leiman PG, Kostyuchenko VA, Kurochkina LP, Miroshnikov KA, Sykilinda NN, Shneider MM. Molecular architecture of bacteriophage T4. BIOCHEMISTRY (MOSCOW) 2004. [DOI: 10.1007/pl00021751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
11
|
Compiani M, Capriotti E, Casadio R. Dynamics of the minimally frustrated helices determine the hierarchical folding of small helical proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 69:051905. [PMID: 15244845 DOI: 10.1103/physreve.69.051905] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2003] [Revised: 12/09/2003] [Indexed: 05/24/2023]
Abstract
In this paper we aim at determining the key residues of small helical proteins in order to build up reduced models of the folding dynamics. We start by arguing that the folding process can be dissected into concurrent fast and slow dynamics. The fast events are the quasiautonomous coil-to-helix transitions occurring in the minimally frustrated initiation sites of folding in the early stages of the process. The slow processes consist in the docking of the fluctuating helices formed in these critical sites. We show that a neural network devised to predict native secondary structures from sequence can be used to estimate the probabilities of formation of these helical traits as they are embedded in the protein. The resulting probabilities are shown to correlate well with the experimental helicities measured in the same isolated peptides. The relevance of this finding to the hierarchical character of folding is confirmed within the framework of a diffusion-collision-like mechanism. We demonstrate that thermodynamic and topological features of these critical helices allow accurate estimation of the folding times of five proteins that have been kinetically studied. This suggests that these critical helices determine the fundamental events of the whole folding process. A remarkable feature of our model is that not all of the native helices are eligible as critical helices, whereas the whole set of the native helices has been used so far in other reconstructions of the folding mechanism. This stresses that the minimally frustrated helices of these helical proteins comprise the minimal set of determinants of the folding process.
Collapse
Affiliation(s)
- M Compiani
- Department of Chemical Sciences, University of Camerino, Camerino, Italy
| | | | | |
Collapse
|
12
|
Mesyanzhinov VV. Bacteriophage T4: Structure, Assembly, and Initiation Infection Studied in Three Dimensions. Adv Virus Res 2004; 63:287-352. [PMID: 15530564 DOI: 10.1016/s0065-3527(04)63005-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Vadim V Mesyanzhinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya S., 117997 Moscow, Russia
| |
Collapse
|
13
|
Boudko SP, Londer YY, Letarov AV, Sernova NV, Engel J, Mesyanzhinov VV. Domain organization, folding and stability of bacteriophage T4 fibritin, a segmented coiled-coil protein. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:833-41. [PMID: 11846809 DOI: 10.1046/j.1432-1033.2002.02734.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fibritin is a segmented coiled-coil homotrimer of the 486-residue product of phage T4 gene wac. This protein attaches to a phage particle by the N-terminal region and forms fibrous whiskers of 530 A, which perform a chaperone function during virus assembly. The short C-terminal region has a beta-annulus-like structure. We engineered a set of fibritin deletion mutants sequentially truncated from the N-termini, and the mutants were studied by differential scanning calorimetry (DSC) and CD measurements. The analysis of DSC curves indicates that full-length fibritin exhibits three thermal-heat-absorption peaks centred at 321 K (Delta H=1390 kJ x mol trimer(-1)), at 336 K (Delta H=7600 kJ x mol trimer(-1)), and at 345 K (Delta H=515 kJ x mol trimer(-1)). These transitions were assigned to the N-terminal, segmented coiled-coil, and C-terminal functional domains, respectively. The coiled-coil region, containing 13 segments, melts co-operatively as a single domain with a mean enthalpy Delta Hres=21 kJ x mol residue(-1). The ratio of Delta HVH/Delta Hcal for the coiled-coil part of the 120-, 182-, 258- and 281-residue per monomer mutants, truncated from the N-termini, and for full-length fibritin are 0.91, 0.88, 0.42, 0.39, and 0.13, respectively. This gives an indication of the decrease of the 'all-or-none' character of the transition with increasing protein size. The deletion of the 12-residue-long loop in the 120-residue fibritin increases the thermal stability of the coiled-coil region. According to CD data, full-length fibritin and all the mutants truncated from the N-termini refold properly after heat denaturation. In contrast, fibritin XN, which is deleted for the C-terminal domain, forms aggregates inside the cell. The XN protein can be partially refolded by dilution from urea and does not refold after heat denaturation. These results confirm that the C-terminal domain is essential for correct fibritin assembly both in vivo and in vitro and acts as a foldon.
Collapse
Affiliation(s)
- Sergei P Boudko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | | | | | | |
Collapse
|
14
|
Salmon KA, Freedman O, Ritchings BW, DuBow MS. Characterization of the lysogenic repressor (c) gene of the Pseudomonas aeruginosa transposable bacteriophage D3112. Virology 2000; 272:85-97. [PMID: 10873751 DOI: 10.1006/viro.2000.0341] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacteriophage D3112 is a Mu-like temperate transposable phage of Pseudomonas aeruginosa. Genetic mapping and DNA sequence analysis have identified the left end of the phage genome as encoding the transposase enzyme (A) and the lysogenic (c) repressor. The c open reading frame (ORF), located at the leftmost end of the phage genome and transcribed from right to left, has four possible GTG initiation codons. Using site-directed mutagenesis, each of the four GTG codons was modified to GTA, which cannot serve as an initiation codon. Plasmids were constructed expressing either the wild-type repressor ORF or the ORFs containing the mutated GTA codons. When introduced into Pseudomonas aeruginosa, no immunity to superinfection by D3112 was observed when the second GTG had been mutated. Northern blotting analysis demonstrated that the D3112 c repressor is transcribed as a 900-nt mRNA. The promoter region was defined by transcriptional lacZ fusions and primer extension analyses to bp 972-940 from the left end of the phage genome. When the D3112 c repressor was overexpressed and purified as a fusion protein with a C-terminal six-histidine extension (cts15-His6), it showed high affinity for a 261-bp PvuII fragment localized directly upstream of the c repressor ORF. Our results indicate that although D3112 c shows higher amino acid similarity to the lambda family of repressors than it does to those of Mu and D108, it appears that its structure and function more accurately reflect an evolutionary ancestry with those from transposable coliphages Mu and D108.
Collapse
MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- Codon, Initiator/genetics
- DNA Transposable Elements/genetics
- DNA, Viral/genetics
- DNA, Viral/metabolism
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/isolation & purification
- DNA-Binding Proteins/metabolism
- Genes, Reporter/genetics
- Genes, Viral/genetics
- Lysogeny/genetics
- Lysogeny/immunology
- Molecular Sequence Data
- Mutation/genetics
- Open Reading Frames/genetics
- Operator Regions, Genetic/genetics
- Promoter Regions, Genetic/genetics
- Pseudomonas Phages/genetics
- Pseudomonas Phages/physiology
- Pseudomonas aeruginosa/virology
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Viral/analysis
- RNA, Viral/genetics
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/isolation & purification
- Recombinant Fusion Proteins/metabolism
- Repressor Proteins/chemistry
- Repressor Proteins/genetics
- Repressor Proteins/isolation & purification
- Repressor Proteins/metabolism
- Sequence Alignment
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/isolation & purification
- Viral Proteins/metabolism
Collapse
Affiliation(s)
- K A Salmon
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | | | | | | |
Collapse
|
15
|
Schuler B, F�rst F, Osterroth F, Steinbacher S, Huber R, Seckler R. Plasticity and steric strain in a parallel ?-helix: Rational mutations in the P22 tailspike protein. Proteins 2000. [DOI: 10.1002/(sici)1097-0134(20000401)39:1<89::aid-prot10>3.0.co;2-q] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
16
|
Casadio R, Compiani M, Fariselli P, Jacoboni I, Martelli PL. Neural networks predict protein folding and structure: artificial intelligence faces biomolecular complexity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2000; 11:149-182. [PMID: 10877475 DOI: 10.1080/10629360008039120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In the genomic era DNA sequencing is increasing our knowledge of the molecular structure of genetic codes from bacteria to man at a hyperbolic rate. Billions of nucleotides and millions of aminoacids are already filling the electronic files of the data bases presently available, which contain a tremendous amount of information on the most biologically relevant macromolecules, such as DNA, RNA and proteins. The most urgent problem originates from the need to single out the relevant information amidst a wealth of general features. Intelligent tools are therefore needed to optimise the search. Data mining for sequence analysis in biotechnology has been substantially aided by the development of new powerful methods borrowed from the machine learning approach. In this paper we discuss the application of artificial feedforward neural networks to deal with some fundamental problems tied with the folding process and the structure-function relationship in proteins.
Collapse
Affiliation(s)
- R Casadio
- Laboratory of Biocomputing, Centro Interdipartimentale per le Ricerche Biotecnologiche (CIRB), University of Bologna, Italy.
| | | | | | | | | |
Collapse
|
17
|
Baxa U, Steinbacher S, Weintraub A, Huber R, Seckler R. Mutations improving the folding of phage P22 tailspike protein affect its receptor binding activity. J Mol Biol 1999; 293:693-701. [PMID: 10543960 DOI: 10.1006/jmbi.1999.3165] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Four previously isolated mutations in Salmonella phage P22 tailspike protein were used to study the relationship between protein stability, folding, and function. Tailspike protein binds and hydrolyzes the repetitive O-antigen structure in Salmonella lipopolysaccharide. Four mutations (V331G, V331A, A334V, A334I) are known to increase the folding efficiency, and two of them (at position 331) also increase the thermal stability of the protein. Octasaccharides comprising two repeating units of the O-antigens from two different Salmonella strains were employed to analyze the receptor binding function of the mutant proteins. Their endorhamnosidase enzymatic activity was assayed with the aid of a fluorescence-labeled dodecasaccharide. Both V331A and V331G were found to strongly affect O-antigen binding. Octasaccharide binding affinities of the mutant proteins are reduced tenfold and 200-fold, corresponding to a loss of 17% and 36% of the standard free energy of binding, respectively. Both mutations at position 334 affected O-antigen binding only slightly (DeltaDeltaG(0)B approximately 1 kJ/mol), but these mutations reduce the thermal stability of the protein. The observed effects on the endoglycosidase activity are fully explained by the changes in substrate binding, suggesting that neither of the mutations affect the catalytic rate. Crystal structures of all four mutants were determined to a resolution of 2.0 A. Except for the partly or completely missing side-chain, no significant changes compared to the wild-type protein structure were found for the mutants at position 331, whereas a small but significant backbone displacement around the mutation site in A334V and A334I may explain the observed thermal destabilization.
Collapse
Affiliation(s)
- U Baxa
- Physikalische Biochemie, Universität Potsdam, Im Biotechnologiepark, Luckenwalde, D-14943, Germany
| | | | | | | | | |
Collapse
|
18
|
Schuler B, Rachel R, Seckler R. Formation of fibrous aggregates from a non-native intermediate: the isolated P22 tailspike beta-helix domain. J Biol Chem 1999; 274:18589-96. [PMID: 10373469 DOI: 10.1074/jbc.274.26.18589] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the assembly pathway of the trimeric P22 tailspike protein, the protein conformation critical for the partitioning between productive folding and off-pathway aggregation is a monomeric folding intermediate. The central domain of tailspike, a large right-handed parallel beta-helix, is essentially structured in this species. We used the isolated beta-helix domain (Bhx), expressed with a hexahistidine tag, to investigate the mechanism of aggregation without the two terminal domains present in the complete protein. Although Bhx has been shown to fold reversibly at low ionic strength conditions, increased ionic strength induced aggregation with a maximum at urea concentrations corresponding to the midpoint of urea-induced folding transitions. According to size exclusion chromatography, aggregation appeared to proceed via a linear polymerization mechanism. Circular dichroism indicated a secondary structure content of the aggregates similar to that of the native state, but at the same time their tryptophan fluorescence was largely quenched. Microscopic analysis of the aggregates revealed a variety of morphologies; among others, fibrils with fine structure were observed that exhibited bright green birefringence if viewed under cross-polarized light after staining with Congo red. These observations, together with the effects of folding mutations on the aggregation process, indicate the involvement of a partially structured intermediate distinct from both unfolded and native Bhx.
Collapse
Affiliation(s)
- B Schuler
- Institut für Biophysik und Physikalische Biochemie, Genetik und Mikrobiologie, Universität Regensburg, 93040 Regensburg, Germany.
| | | | | |
Collapse
|
19
|
Miller S, Schuler B, Seckler R. Phage P22 tailspike protein: removal of head-binding domain unmasks effects of folding mutations on native-state thermal stability. Protein Sci 1998; 7:2223-32. [PMID: 9792111 PMCID: PMC2143837 DOI: 10.1002/pro.5560071021] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A shortened, recombinant protein comprising residues 109-666 of the tailspike endorhamnosidase of Salmonella phage P22 was purified from Escherichia coli and crystallized. Like the full-length tailspike, the protein lacking the amino-terminal head-binding domain is an SDS-resistant, thermostable trimer. Its fluorescence and circular dichroism spectra indicate native structure. Oligosaccharide binding and endoglycosidase activities of both proteins are identical. A number of tailspike folding mutants have been obtained previously in a genetic approach to protein folding. Two temperature-sensitive-folding (tsf) mutations and the four known global second-site suppressor (su) mutations were introduced into the shortened protein and found to reduce or increase folding yields at high temperature. The mutational effects on folding yields and subunit folding kinetics parallel those observed with the full-length protein. They mirror the in vivo phenotypes and are consistent with the substitutions altering the stability of thermolabile folding intermediates. Because full-length and shortened tailspikes aggregate upon thermal denaturation, and their denaturant-induced unfolding displays hysteresis, kinetics of thermal unfolding were measured to assess the stability of the native proteins. Unfolding of the shortened wild-type protein in the presence of 2% SDS at 71 degrees C occurs at a rate of 9.2 x 10(-4) s(-1). It reflects the second kinetic phase of unfolding of the full-length protein. All six mutations were found to affect the thermal stability of the native protein. Both tsf mutations accelerate thermal unfolding about 10-fold. Two of the su mutations retard thermal unfolding up to 5-fold, while the remaining two mutations accelerate unfolding up to 5-fold. The mutational effects can be rationalized on the background of the recently determined crystal structure of the protein.
Collapse
Affiliation(s)
- S Miller
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Germany
| | | | | |
Collapse
|
20
|
Schuler B, Seckler R. P22 tailspike folding mutants revisited: effects on the thermodynamic stability of the isolated beta-helix domain. J Mol Biol 1998; 281:227-34. [PMID: 9698543 DOI: 10.1006/jmbi.1998.1944] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The folding of the trimeric phage P22 tailspike protein is influenced by amino acid substitutions of two types, virtually all of which affect residues in the central domain, a large parallel beta-helix. Temperature sensitive folding (tsf) mutations lead to drastically decreased folding yields at elevated temperature. Their phenotype can be alleviated by global suppressor (su) mutations. Both types of mutations appeared to have no influence on the stability of the native protein at the time of their first isolation and were thus suggested to carry information needed for the folding pathway exclusively. The monomeric beta-helix of tailspike, expressed as an isolated domain, exhibits freely reversible unfolding and refolding transitions, allowing us to analyse the effects of two well-characterised tsf and all four known su mutations on its thermodynamic stability. We find a marked decrease in stability for the tsf mutants and a striking increase in stability for all su mutants. This leads to the conception that the isolated beta-helix domain, although active in receptor-binding and native-like in its spectroscopic properties, is close in conformation to a crucial monomeric folding intermediate whose thermolability is responsible for the kinetic partitioning between productive folding and irreversible aggregation during the maturation process of P22 tailspike protein.
Collapse
Affiliation(s)
- B Schuler
- Physikalische Biochemie, Universität Regensburg, Universitätsstrasse 31, 93040 Regensburg, Germany
| | | |
Collapse
|
21
|
Schnappinger D, Schubert P, Pfleiderer K, Hillen W. Determinants of protein-protein recognition by four helix bundles: changing the dimerization specificity of Tet repressor. EMBO J 1998; 17:535-43. [PMID: 9430644 PMCID: PMC1170403 DOI: 10.1093/emboj/17.2.535] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Homo- and heterodimerization is essential for the activity of many proteins, particularly transcription factors. One widely distributed structural motif for protein recognition is the four helix bundle. To understand the molecular details determining specificity of subunit recognition in a dimer formed by a four helix bundle, we investigated Tet repressor (TetR) sequence variants TetR(B) and TetR(D), which do not form heterodimers. We used molecular modeling to identify residues with the potential to determine recognition of subunits. Directed mutagenesis of these residues in TetR(B) by the TetR(D) sequence resulted in chimeric TetR(B/D) repressors with new subunit recognition specificities. The single LS192 exchange in TetR(B/D)192 in the center of the helix bundle leads to a relaxed specificity since this variant dimerizes with TetR(B) and (D). To construct a variant with a new specificity it was not sufficient to mutate the contacting residue, F197, in the other subunit. Instead, it was necessary to exchange two more residues in the vicinity of F197 and S192. The resulting TetR(B/D)188, 192,193,197 forms dimers with TetR(D) but not with TetR(B), indicating that four amino acid exchanges are sufficient to change subunit recognition. These results establish that targeted alterations in the structural complementarity of protein-protein interaction surfaces can be used to construct new recognition specificities. However, it is not sufficient to adjust the complementary residues since the surrounding amino acids contribute essentially to protein-protein recognition.
Collapse
Affiliation(s)
- D Schnappinger
- Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie, Biochemie und Genetik der Friedrich-Alexander Universität Erlangen-Nürnberg, Germany
| | | | | | | |
Collapse
|
22
|
Lee SC, Yu MH. Side-chain specificity at three temperature-sensitive folding mutation sites of P22 tailspike protein. Biochem Biophys Res Commun 1997; 233:857-62. [PMID: 9168948 DOI: 10.1006/bbrc.1997.6566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The phage P22 tailspike protein is one of the few proteins for which both in vivo and in vitro folding pathways have been thoroughly characterized. Many temperature-sensitive folding (tsf) mutations that cause the mutant tailspike polypeptides not to be folded at high restrictive temperatures have been identified. One-third of the tsf mutation sites are located in one domain called the dorsal fin domain (residues 197-259), which protrudes on the solvent-exposed side of the main beta helix. In the present study, we introduced various amino acid substitutions at three tsf mutation sites (residue numbers 235, 238, and 244) in this domain to elucidate the mechanism of these tsf mutations in detail. The side-chain specificity at these tsf sites, together with structural examination in the tertiary fold, strongly suggests that destabilization of folding intermediates by loss of specific interactions is likely to be the major cause of the tsf defect in the dorsal fin domain.
Collapse
Affiliation(s)
- S C Lee
- Division of Protein Engineering, Korea Research Institute of Bioscience and Biotechnology, KIST, Yusong, Taejon, Korea
| | | |
Collapse
|
23
|
Haase-Pettingell C, King J. Prevalence of temperature sensitive folding mutations in the parallel beta coil domain of the phage P22 tailspike endorhamnosidase. J Mol Biol 1997; 267:88-102. [PMID: 9096209 DOI: 10.1006/jmbi.1996.0841] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Temperature sensitive mutations fall into two general classes: tl mutations, which render the mature protein thermolabile, and tsf (temperature sensitive folding) mutations, which destabilize an intermediate in the folding pathway without altering the functions of the folded state. The molecular defects caused by tsf mutations have been intensively studied for the elongated tailspike endorhamnosidase of Salmonella phage P22. The tailspike, responsible for host cell recognition and attachment, contains a 13 strand parallel beta coil domain. A set of tsf mutants located in the beta coil domain have been shown to cause folding defects in the in vivo folding pathway for the tailspike. We report here additional data on 17 other temperature sensitive mutants which are in the beta coil domain. Using mutant proteins formed at low temperature, the essential functions of assembling on the phage head, and binding to the O-antigen lipopolysaccharide (LPS) receptor of Salmonella were examined at high temperatures. All of the mutant proteins once folded at permissive temperature, were functional at restrictive temperatures. When synthesized at restrictive temperature the mutant chains formed an early folding intermediate, but failed to reach the mature conformation, accumulating instead in the aggregated inclusion body state. Thus this set of mutants all have the temperature sensitive folding phenotype. The prevalence of tsf mutants in the parallel beta coil domain presumably reflects properties of its folding intermediates. The key property may be the tendency of the intermediate to associate off pathway to the kinetically trapped inclusion body state.
Collapse
|
24
|
Abstract
The crystal structure of bacteriophage P22 tailspike protein reveals a striking fold with a distinctive, fish-like appearance, and helps explain many of the properties of this unusual molecule and its folding pathway.
Collapse
Affiliation(s)
- D P Goldenberg
- Department of Biology, University of Utah, Salt Lake City 84112
| | | |
Collapse
|
25
|
Villafane R, Fleming A, Haase-Pettingell C. Isolation of suppressors of temperature-sensitive folding mutations. J Bacteriol 1994; 176:137-42. [PMID: 8282689 PMCID: PMC205024 DOI: 10.1128/jb.176.1.137-142.1994] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Mutations in the tailspike gene (gene 9) of Salmonella typhimurium phage P22 have been used to identify amino acid interactions during the folding of a polypeptide chain. Since temperature-sensitive folding (tsf) mutations cause folding defects in the P22 tailspike polypeptide chain, it is likely that mutants derived from these and correcting the original tsf defects (second-site intragenic suppressors) identify interactions during the folding pathway. We report the isolation and identification of second-site revertants to tsf mutants.
Collapse
Affiliation(s)
- R Villafane
- Department of Microbiology, University of Tennessee, Knoxville 37996
| | | | | |
Collapse
|
26
|
Abstract
Temperature-sensitive folding (tsf) and global-tsf-suppressor (su) point mutations affect the folding yields of the trimeric, thermostable phage P22 tailspike endorhamnosidase at elevated temperature, both in vivo and in vitro, but they have little effect on function and stability of the native folded protein. To delineate the mechanism by which these mutations modify the partitioning between productive folding and off-pathway aggregation, the kinetics of refolding after dilution from acid-urea solutions and the thermal stability of folding intermediates were analyzed. The study included five tsf mutations of varying severity, the two known su mutations, and four tsf/su double mutants. At low temperature (10 degrees C), subunit-folding rates, measured as an increase in fluorescence, were similar for wild-type and mutants. At 25 degrees C, however, tsf mutations reduced the rate of subunit folding. The su mutations increased this rate, when present in the tsf-mutant background, but had no effect in the wild-type background. Conversely, tsf mutations accelerated, and su mutations retarded the irreversible off-pathway reaction, as revealed by temperature down-shifts after varied times during refolding at high temperature (40 degrees C). The kinetic results are consistent with tsf mutations destabilizing and su mutations stabilizing an essential subunit folding intermediate. In accordance with this interpretation, tsf mutations decreased, and su mutations increased the temperature resistance of folding intermediates, as disclosed by temperature up-shifts during refolding at 25 degrees C. The stabilizing and destabilizing effects were most pronounced early during refolding. However, they were not limited to subunit-folding intermediates and were also observable during thermal unfolding of the native protein.
Collapse
Affiliation(s)
- M Danner
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Germany
| | | |
Collapse
|
27
|
Mitraki A, Danner M, King J, Seckler R. Temperature-sensitive mutations and second-site suppressor substitutions affect folding of the P22 tailspike protein in vitro. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(20)80695-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
28
|
Abstract
How does a protein find its native state without a globally exhaustive search? We propose the "HZ" (hydrophobic zipper) hypothesis: hydrophobic contacts act as constraints that bring other contacts into spatial proximity, which then further constrain and zip up the next contacts, etc. In contrast to helix-coil cooperativity, HZ-heteropolymer collapse cooperativity is driven by nonlocal interactions, causes sheet and irregular conformations in addition to helices, leads to secondary structures concurrently with early hydrophobic core formation, is much more sequence dependent than helix-coil processes, and involves compact intermediate states that have much secondary--but little tertiary--structure. Hydrophobic contacts in the 1992 Protein Data Bank have the type of "topological localness" predicted by the hypothesis. The HZ paths for amino acid sequences that mimic crambin and bovine pancreatic trypsin inhibitor are quickly found by computer; the best configurations thus reached have single hydrophobic cores that are within about 3 kcal/mol of the global minimum. This hypothesis shows how proteins could find globally optimal states without exhaustive search.
Collapse
Affiliation(s)
- K A Dill
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204
| | | | | |
Collapse
|
29
|
Abstract
Though an increasing variety of chaperonins are emerging as important factors in directing polypeptide chain folding off the ribosome, the primary amino acid sequence remains the major determinant of final conformation. The ability to identify cytoplasmic folding intermediates in the formation of the tailspike endorhamnosidase of phage P22 has made it possible to isolate two classes of mutations influencing folding intermediates-temperature-sensitive folding mutations and global suppressors of tsf mutants. These and related amino acid substitutions in eukaryotic proteins are discussed in the context of inclusion body formation and problems in the recovery of correctly folded proteins.
Collapse
Affiliation(s)
- A Mitraki
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
| | | |
Collapse
|
30
|
Lee S, Koh H, Yu M. Molecular properties of global suppressors of temperature-sensitive folding mutations in P22 tailspike endorhamnosidase. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54482-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
31
|
Vogel JL, Li ZJ, Howe MM, Toussaint A, Higgins NP. Temperature-sensitive mutations in the bacteriophage Mu c repressor locate a 63-amino-acid DNA-binding domain. J Bacteriol 1991; 173:6568-77. [PMID: 1833382 PMCID: PMC208994 DOI: 10.1128/jb.173.20.6568-6577.1991] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Phage Mu's c gene product is a cooperative regulatory protein that binds to a large, complex, tripartite 184-bp operator. To probe the mechanism of repressor action, we isolated and characterized 13 phage mutants that cause Mu to undergo lytic development when cells are shifted from 30 to 42 degrees C. This collection contained only four mutations in the repressor gene, and all were clustered near the N terminus. The cts62 substitution of R47----Q caused weakened specific DNA recognition and altered cooperativity in vitro. A functional repressor with only 63 amino acids of Mu repressor fused to a C-terminal fragment of beta-galactosidase was constructed. This chimeric protein was an efficient repressor, as it bound specifically to Mu operator DNA in vitro and its expression conferred Mu immunity in vivo. A DNA looping model is proposed to explain regulation of the tripartite operator site and the highly cooperative nature of repressor binding.
Collapse
Affiliation(s)
- J L Vogel
- Department of Biochemistry, University of Alabama, Birmingham 35294
| | | | | | | | | |
Collapse
|
32
|
Mitraki A, Fane B, Haase-Pettingell C, Sturtevant J, King J. Global suppression of protein folding defects and inclusion body formation. Science 1991; 253:54-8. [PMID: 1648264 DOI: 10.1126/science.1648264] [Citation(s) in RCA: 155] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Amino acid substitutions at a site in the center of the bacteriophage protein P22 tailspike polypeptide chain suppress temperature-sensitive folding mutations at many sites throughout the chain. Characterization of the intracellular folding and chain assembly process reveals that the suppressors act in the folding pathway, inhibiting the aggregation of an early folding intermediate into the kinetically trapped inclusion body state. The suppressors alone increase the folding efficiency of the otherwise wild-type polypeptide chain without altering the stability or activity of the native state. These amino acid substitutions identify an unexpected aspect of the protein folding grammar--sequences within the chain that carry information inhibiting unproductive off-pathway conformations. Such mutations may serve to increase the recovery of protein products of cloned genes.
Collapse
Affiliation(s)
- A Mitraki
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
| | | | | | | | | |
Collapse
|
33
|
Chen B, King J. Thermal unfolding pathway for the thermostable P22 tailspike endorhamnosidase. Biochemistry 1991; 30:6260-9. [PMID: 2059632 DOI: 10.1021/bi00239a026] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The conditions in which protein stability is biologically or industrially relevant frequently differ from those in which reversible denaturation is studied. The trimeric tailspike endorhamnosidase of phage P22 is a viral structural protein which exhibits high stability to heat, proteases, and detergents under a range of environmental conditions. Its intracellular folding pathway includes monomeric and trimeric folding intermediates and has been the subject of detailed genetic analysis. To understand the basis of tailspike thermostability, we have examined the kinetics of thermal and detergent unfolding. During thermal unfolding of the tailspike, a metastable unfolding intermediate accumulates which can be trapped in the cold or in the presence of SDS. This species is still trimeric, but has lost the ability to bind to virus capsids and, unlike the native trimer, is partially susceptible to protease digestion. Its N-terminal regions, containing about 110 residues, are unfolded whereas the central regions and the C-termini of the polypeptide chains are still in the folded state. Thus, the initiation step in thermal denaturation is the unfolding of the N-termini, but melting of the intermediate represents a second kinetic barrier in the denaturation process. This two-step unfolding is unusually slow at elevated temperature; for instance, in 2% SDS at 65 degrees C, the unfolding rate constant is 1.1 x 10(-3) s-1 for the transition from the native to the unfolding intermediate and 4.0 x 10(-5) s-1 for the transition from the intermediate to the unfolded chains. The sequential unfolding pathway explains the insensitivity of the apparent Tm to the presence of temperature-sensitive folding mutations [Sturtevant, J. M., Yu, M.-H., Haase-Pettingell, C., & King, J. (1989) J. Biol. Chem. 264, 10693-10698] which are located in the central region of the chain. The metastable unfolding intermediate has not been detected in the forward folding pathway occurring at lower temperatures. The early stage of the high-temperature thermal unfolding pathway is not the reverse of the late stage of the low-temperature folding pathway.
Collapse
Affiliation(s)
- B Chen
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
| | | |
Collapse
|
34
|
Identification of global suppressors for temperature-sensitive folding mutations of the P22 tailspike protein. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)99005-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
35
|
Abstract
Within the amino acid sequences of polypeptide chains little is known of the distribution of sites and sequences critical for directing chain folding and assembly. Temperature-sensitive folding (tsf) mutations identifying such sites have been previously isolated and characterized in gene 9 of phage P22 encoding the tailspike endorhamnosidase. We report here the isolation of a set of second-site conformational suppressors which alleviate the defect in such folding mutants. The suppressors were selected for their ability to correct the defects of missense tailspike polypeptide chains, generated by growth of gene 9 amber mutants on Salmonella host strains inserting either tyrosine, serine, glutamine or leucine at the nonsense codons. Second-site suppressors were recovered for 13 of 22 starting sites. The suppressors of defects at six sites mapped within gene 9. (Suppressors for seven other sites were extragenic and distant from gene 9.) The missense polypeptide chains generated from all six suppressible sites displayed ts phenotypes. Temperature-sensitive alleles were isolated at these amber sites by pseudoreversion. The intragenic suppressors restored growth at the restrictive temperature of these presumptive tsf alleles. Characterization of protein maturation in cells infected with mutant phages carrying the intragenic suppressors indicates that the suppression is acting at the level of polypeptide chain folding and assembly.
Collapse
Affiliation(s)
- B Fane
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
| | | |
Collapse
|
36
|
Lee SC, Choi YC, Yu MH. Effect of the N-terminal hydrophobic sequence of hepatitis B virus surface antigen on the folding and assembly of hybrid beta-galactosidase in Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 187:417-24. [PMID: 2105218 DOI: 10.1111/j.1432-1033.1990.tb15320.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To investigate the mechanism of inclusion body formation and the effect of a hydrophobic sequence on the in vivo polypeptide folding, the aggregation caused by recombinant fusion beta-galactosidase in Escherichia coli was examined. Two plasmids were constructed: pTBG(H-) carried only the preS2 sequence of the hepatitis B virus surface antigen (HBsAg) in front of the beta-galactosidase gene (lacZ) while pTBG(H+) carried an additional sequence encoding the amino-terminal hydrophobic sequence of the S region of HBsAg between preS2 and lacZ. Unlike cells expressing the fusion protein not containing the hydrophobic sequence, E. coli JM109/pTBG(H+) exhibited temperature-sensitive production of beta-galactosidase. As the culture temperature increased the activity decreased dramatically. This decrease in activity was not due to a decrease in fusion polypeptide production, but rather the fusion polypeptides containing the hydrophobic sequence aggregated within the cells at high temperature. However once the fusion polypeptides folded into proper conformation at low temperature, they maintained the activity even at high temperature. The results indicate that aggregation is a consequence of incorrect folding and assembly of the polypeptides, and is not derived from the native structure. The aggregates of the pTBG(H+)-encoded fusion polypeptides did not revert to active form when the culture temperature was lowered.
Collapse
Affiliation(s)
- S C Lee
- Genetic Engineering Center, Korea Institute of Science and Technology, Seoul
| | | | | |
Collapse
|
37
|
|
38
|
Garvey EP, Matthews CR. Site-directed mutagenesis and its application to protein folding. BIOTECHNOLOGY (READING, MASS.) 1990; 14:37-63. [PMID: 2183900 DOI: 10.1016/b978-0-409-90116-0.50011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
39
|
Van Dyk TK, Gatenby AA, LaRossa RA. Demonstration by genetic suppression of interaction of GroE products with many proteins. Nature 1989; 342:451-3. [PMID: 2573840 DOI: 10.1038/342451a0] [Citation(s) in RCA: 169] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The way in which proteins attain and maintain their final form is of fundamental importance. Recent work has focused on the role of a set of ubiquitous proteins, termed chaperonins, in the assembly of phage and multisubunit proteins. The range of chaperonin action is unknown; they could interact with most cellular polypeptides or have a limited subset of protein partners. Included in the chaperonin family is the essential heat-shock regulated Escherichia coli groEL gene product. Over-expression of the groE operon in E. coli causes enhanced assembly of heterologously expressed ribulose bisphosphate carboxylase subunits and suppresses the heat-sensitive mutant phenotype of several dnaA alleles. It has been inferred that suppression of heat-sensitive mutations is confined to dnaA alleles and that this confinement could reflect an interaction between the groE operon products and a dnaA protein aggregate at the replication origin. We now report that multiple copies of the groE operon suppress mutations in genes encoding several diverse proteins. Our data indicate a general role for the groE operon products, the GroEL and GroES proteins, in the folding-assembly pathways of many proteins.
Collapse
Affiliation(s)
- T K Van Dyk
- Central Research and Development Department, E.I. du Pont de Nemours and Company, Wilmington, Delaware 19880-0328
| | | | | |
Collapse
|
40
|
Reconstitution of the thermostable trimeric phage P22 tailspike protein from denatured chains in vitro. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)80129-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
41
|
|
42
|
Lee JA, Püttner IB, Kaback HR. Effect of distance and orientation between arginine-302, histidine-322, and glutamate-325 on the activity of lac permease from Escherichia coli. Biochemistry 1989; 28:2540-4. [PMID: 2567182 DOI: 10.1021/bi00432a029] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
lac permease of Escherichia coli was modified by site-directed mutagenesis in order to investigate the effects of polarity, distance, and orientation between the components of a putative H+ relay system (Arg302/His322/Glu325) postulated to be involved in lactose-coupled H+ translocation. The importance of polarity between His322 and Glu325 was studied by interchanging the residues, and the modified permease--H322E/E325H--is inactive in all modes of translocation. The effect of distance and/or orientation between His322 and Glu325 was investigated by interchanging Glu325 with Val326, thereby moving the carboxylate one residue around putative helix X. The resulting permease molecule--E325V/V326E--is also completely inactive; control mutations, E325V [Carrasco, N., Püttner, I. B., Antes, L. M., Lee, J. A., Larigan, J. D., Lolkema, J. S., Roepe, P. D., & Kaback, H. R. (1989) Biochemistry (second paper of three in this issue)], and E325A/V326E, indicate that a Glu residue at position 326 inactivates the permease. The wild-type orientation between His and Glu was then restored by further mutation of E325V/V326E to introduce a His residue into position 323 or by interchanging Met323 with His322. The resulting permease molecules--M323H/E325V/V326E and H322M/M323H/E325V/V326E--contain the wild-type His/Glu orientation, but the His/Glu ion pair is rotated about the helical axis by 100 degrees relative to Arg302 in putative helix IX. Both mutants are inactive with respect to all modes of translocation. The results provide strong support for the contention that the polarity between His322 and Glu325 and the geometric relationship between Arg302, His322, and Glu325 are critical for permease activity.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- J A Lee
- Roche Institute of Molecular Biology, Roche Research Center, Nutley, New Jersey 07110
| | | | | |
Collapse
|
43
|
Berget PB, Chidambaram M. Fine structure genetic and physical map of the phage P22 tail protein gene. Genetics 1989; 121:13-28. [PMID: 2537251 PMCID: PMC1203596 DOI: 10.1093/genetics/121.1.13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacteriophage P22 which are incapable of making functional tail protein can be propagated by the addition of purified mature tail protein trimers to either liquid or solidified medium. This unique in vitro complementation condition has allowed us to isolate 74 absolute lethal tail protein mutants of P22 after hydroxylamine mutagenesis. These phage mutants have an absolute requirement for purified P22 tail protein to be present in a soft agar overlay in order to form plaques and do not grow on any nonsense suppressing strains of Salmonella typhimurium. In order to genetically map and physically locate these mutations we have constructed two complementary sets of fine structure deletion mapping strains using a collection of Tn1 insertions in gene 9, the structural gene for the tail protein. Fourteen bacteriophage P22 strains carrying unique Tn1 transposon insertions (Ap phage) in gene 9 have been crossed with Ap phage carrying Tn1 insertions in gene 20. Phage carrying deletions that arose from homologous recombination between the Tn1 elements were isolated as P22 lysogens. The deletion prophage were shown to be missing all genetic information bracketed by the parental Tn1 elements and thus form a set of deletions into gene 9 from the 5' end of the gene. From the frequency of production of these deletion phage the orientation of the Tn1 insertions in gene 9 could be deduced. The genetic end points of the deletions in gene 9 and thus the order of Tn1 insertions were determined by marker rescue experiments using the original Ap phage. The genetic end points of the deletions in gene 20 were determined in similar experiments using nonsense mutations in gene 20. To locate the physical end points of these deletions in gene 9, DNA containing the Tn1 element has been cloned from each of the original Ap phage into plasmids. The precise point of insertion of Tn1 into gene 9 was determined by restriction enzyme mapping and DNA sequencing of the relevant portions of each of these plasmids. In vitro deletion of different 3' gene 9 sequences in the plasmid clones was accomplished through the use of unique restriction endonuclease sites in Tn1. The resulting plasmids form a set of deletions extending into the 3' end of the gene which are complementary compared to the deletion lysogens.(ABSTRACT TRUNCATED AT 400 WORDS)
Collapse
Affiliation(s)
- P B Berget
- Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas
| | | |
Collapse
|
44
|
Gharakhanian E, Takahashi J, Clever J, Kasamatsu H. In vitro assay for protein-protein interaction: carboxyl-terminal 40 residues of simian virus 40 structural protein VP3 contain a determinant for interaction with VP1. Proc Natl Acad Sci U S A 1988; 85:6607-11. [PMID: 2842781 PMCID: PMC282026 DOI: 10.1073/pnas.85.18.6607] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Intermolecular interactions between polypeptide chains play essential roles in the functioning of proteins. We describe here an in vitro assay system for identifying and characterizing such interactions. Such interactions are difficult to study in vivo. We have translated synthetic, nonmethyl-capped RNAs in a cell-free protein-synthesizing system. The translation products were allowed to interact posttranslationally to form protein-protein complexes. The chemical nature of the protein interaction(s) was determined by coimmunoprecipitation of associating proteins, sedimentation through sucrose gradients, followed by NaDodSO4/polyacrylamide gel electrophoresis or by nonreducing NaDodSO4/polyacrylamide gel electrophoresis. The system has been utilized to show the self-assembly of monomeric VP1, the major structural protein of simian virus 40, into disulfide-linked pentamers and to show the noncovalent interaction of another structural protein, VP3, with VP1 at low monomer concentrations. Additionally, we show that the carboxyl-terminal 40 amino acids of VP3 are essential and sufficient for its interaction with VP1 in vitro. The in vitro assay system described here provides a method for identifying the domains involved in, and the molecular nature of, protein-protein interactions, which play an important role in such biological phenomena as replication, transcription, translation, transport, ligand binding, and assembly.
Collapse
Affiliation(s)
- E Gharakhanian
- Department of Biology, University of California, Los Angeles 90024-1606
| | | | | | | |
Collapse
|
45
|
Kolchanov NA, Shindyalov IN. Single amino acid substitutions producing instability of globular proteins. Calculation of their frequencies in the entire mutational spectra of the alpha- and beta-subunits of human hemoglobin. J Mol Evol 1988; 27:154-62. [PMID: 3137354 DOI: 10.1007/bf02138376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The frequencies of substitutions resulting in protein instability were calculated by a method estimating changes in stability produced by amino acid substitutions. The method takes into account the accessibility of an amino acid position to a solvent and changes in the specificity of amino acid interactions. When tested on human mutant hemoglobins, the method yielded predictions with a preciseness of 80%. The consideration of the evolutionary homologous proteins in the analysis allowed us to estimate the evolutionary constraints imposed on stability of their spatial structure. With these limitations, approximately 50% of amino acid substitutions in the entire mutational spectra of the alpha- and beta-subunits of human hemoglobin were found to damage the spatial structure of the globular proteins.
Collapse
Affiliation(s)
- N A Kolchanov
- Laboratory of Populational Genetics, USSR Academy of Sciences, Novosibirsk
| | | |
Collapse
|
46
|
Machamer CE, Rose JK. Vesicular stomatitis virus G proteins with altered glycosylation sites display temperature-sensitive intracellular transport and are subject to aberrant intermolecular disulfide bonding. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)60659-3] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
47
|
Haase-Pettingell CA, King J. Formation of aggregates from a thermolabile in vivo folding intermediate in P22 tailspike maturation. A model for inclusion body formation. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68883-0] [Citation(s) in RCA: 153] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
48
|
Surface amino acids as sites of temperature-sensitive folding mutations in the P22 tailspike protein. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)57320-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
49
|
Fane B, King J. Identification of sites influencing the folding and subunit assembly of the P22 tailspike polypeptide chain using nonsense mutations. Genetics 1987; 117:157-71. [PMID: 2822533 PMCID: PMC1203193 DOI: 10.1093/genetics/117.2.157] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Amber mutations have been isolated and mapped to more than 60 sites in gene 9 of P22 encoding the thermostable phage tailspike protein. Gene 9 is the locus of over 30 sites of temperature sensitive folding (tsf) mutations, which affect intermediates in the chain folding and subunit association pathway. The phenotypes of the amber missense proteins produced on tRNA suppressor hosts inserting serine, glutamine, tryosine and leucine have been determined at different temperatures. Thirty-three of the sites are tolerant, producing functional proteins with any of the four amino acids inserted at the sites, independent of temperature. Tolerant sites are concentrated at the N-terminal end of the protein indicating that this region is not critical for conformation or function. Sixteen of the sites yield temperature sensitive missense proteins on at least one nonsense suppressing host. Most of the sites with ts phenotypes map to the central region of the gene which is also the region where most of the tsf mutations map. Mutations at 15 of the sites have a lethal phenotype on at least one tRNA suppressor host. For nine out of ten sites tested with at least one lethal phenotype, the primary defect was in the folding or subunit association of the missense polypeptide chain. This analysis of the tailspike missense proteins distinguishes three classes of amino acid sites in the polypeptide chain; residues whose side chains contribute little to folding, subunit assembly or function; residues critical for maintaining the folding and subunit assembly pathway at the high end of the temperature range of phage growth; and residues critical over the entire temperature range of growth.
Collapse
Affiliation(s)
- B Fane
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
| | | |
Collapse
|
50
|
Milton DL, Napier ML, Myers RM, Hardman JK. In vitro mutagenesis and overexpression of the Escherichia coli trpA gene and the partial characterization of the resultant tryptophan synthase mutant alpha-subunits. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)66610-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|