Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 35
Filtrar
1.
J Mol Evol ; 91(1): 10-23, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-36396786

RESUMEN

Understanding the origin and early evolution of proteins is important for unveiling how the RNA world developed into an RNA-protein world. Because the composition of organic molecules in the Earth's primitive environment was plausibly not as diverse as today, the number of different amino acids used in early protein synthesis is likely to be substantially less than the current 20 proteinogenic residues. In this study, we have explored the thermal stability and RNA binding of ancestral variants of the ribosomal protein uS8 constructed from a reduced-alphabet of amino acids. First, we built a phylogenetic tree based on the amino acid sequences of uS8 from multiple extant organisms and used the tree to infer two plausible amino acid sequences corresponding to the last bacterial common ancestor of uS8. Both ancestral proteins were thermally stable and bound to an RNA fragment. By eliminating individual amino acid letters and monitoring thermal stability and RNA binding in the resulting proteins, we reduced the size of the amino acid set constituting one of the ancestral proteins, eventually finding that convergent sequences consisting of 15- or 14-amino acid alphabets still folded into stable structures that bound to the RNA fragment. Furthermore, a simplified variant reconstructed from a 13-amino-acid alphabet retained affinity for the RNA fragment, although it lost conformational stability. Collectively, RNA-binding activity may be achieved with a subset of the current 20 amino acids, raising the possibility of a simpler composition of RNA-binding proteins in the earliest stage of protein evolution.


Asunto(s)
Aminoácidos , Proteínas Ribosómicas , Aminoácidos/genética , Aminoácidos/química , Proteínas Ribosómicas/genética , Proteínas Ribosómicas/metabolismo , Filogenia , Secuencia de Aminoácidos , ARN , Evolución Molecular
2.
J Mol Evol ; 88(4): 372-381, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32201904

RESUMEN

While extant organisms synthesize proteins using approximately 20 kinds of genetically coded amino acids, the earliest protein synthesis system is likely to have been much simpler, utilizing a reduced set of amino acids. However, which types of building blocks were involved in primordial protein synthesis remains unclear. Herein, we reconstructed three convergent sequences of an ancestral nucleoside diphosphate kinase, each comprising a 10 amino acid "alphabet," and found that two of these variants folded into soluble and stable tertiary structures. Therefore, an alphabet consisting of 10 amino acids contains sufficient information for creating stable proteins. Furthermore, re-incorporation of a few more amino acid types into the active site of the 10 amino acid variants improved the catalytic activity, although the specific activity was not as high as that of extant proteins. Collectively, our results provide experimental support for the idea that robust protein scaffolds can be built with a subset of the current 20 amino acids that might have existed abundantly in the prebiotic environment, while the other amino acids, especially those with functional sidechains, evolved to contribute to efficient enzyme catalysis.


Asunto(s)
Aminoácidos , Proteínas , Catálisis , Biosíntesis de Proteínas , Estabilidad Proteica , Proteínas/genética
3.
Proc Natl Acad Sci U S A ; 114(18): 4619-4624, 2017 05 02.
Artículo en Inglés | MEDLINE | ID: mdl-28416654

RESUMEN

Paleotemperatures inferred from the isotopic compositions (δ18O and δ30Si) of marine cherts suggest that Earth's oceans cooled from 70 ± 15 °C in the Archean to the present ∼15 °C. This interpretation, however, has been subject to question due to uncertainties regarding oceanic isotopic compositions, diagenetic or metamorphic resetting of the isotopic record, and depositional environments. Analyses of the thermostability of reconstructed ancestral enzymes provide an independent method by which to assess the temperature history inferred from the isotopic evidence. Although previous studies have demonstrated extreme thermostability in reconstructed archaeal and bacterial proteins compatible with a hot early Earth, taxa investigated may have inhabited local thermal environments that differed significantly from average surface conditions. We here present thermostability measurements of reconstructed ancestral enzymatically active nucleoside diphosphate kinases (NDKs) derived from light-requiring prokaryotic and eukaryotic phototrophs having widely separated fossil-based divergence ages. The ancestral environmental temperatures thereby determined for these photic-zone organisms--shown in modern taxa to correlate strongly with NDK thermostability--are inferred to reflect ancient surface-environment paleotemperatures. Our results suggest that Earth's surface temperature decreased over geological time from ∼65-80 °C in the Archean, a finding consistent both with previous isotope-based and protein reconstruction-based interpretations. Interdisciplinary studies such as those reported here integrating genomic, geologic, and paleontologic data hold promise for providing new insight into the coevolution of life and environment over Earth history.


Asunto(s)
Archaea , Proteínas Arqueales/genética , Proteínas Bacterianas/genética , Cianobacterias , Evolución Molecular , Nucleósido-Difosfato Quinasa/genética , Proteínas de Plantas/genética , Plantas , Archaea/enzimología , Archaea/genética , Cianobacterias/enzimología , Cianobacterias/genética , Planeta Tierra , Respiraderos Hidrotermales/microbiología , Océanos y Mares , Plantas/enzimología , Plantas/genética , Microbiología del Agua
4.
Biochem Biophys Res Commun ; 495(3): 2209-2213, 2018 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-29269293

RESUMEN

Various physiologically active effects of polymerized polyphenols have been reported. In this study, we synthesized a polymerized polyphenol (mL2a-pCA) by polymerizing caffeic acid using mutant Agaricus brasiliensis laccase and analyzed its physiological activity and mechanism of action. We found that mL2a-pCA induced morphological changes and the production of cytokines and chemokines in C3H/HeN mouse-derived resident peritoneal macrophages in vitro. The mechanisms of action of polymerized polyphenols on in vitro mouse resident peritoneal cells have not been characterized in detail previously. Herein, we report that the mL2a-pCA-induced production of interleukin-6 (IL-6) and monocyte chemotactic protein-1 (MCP-1) in C3H/HeN mouse-derived resident peritoneal cells was inhibited by treatment with the Rac1 inhibitor NSC23766 trihydrochloride. In addition, we found that mL2a-pCA activated the phosphorylation Rac1. Taken together, the results show that mL2a-pCA induced macrophage activation via Rac1 phosphorylation-dependent pathways.


Asunto(s)
Lacasa/química , Activación de Macrófagos/inmunología , Macrófagos/inmunología , Macrófagos/patología , Neuropéptidos/inmunología , Polifenoles/administración & dosificación , Polifenoles/química , Proteína de Unión al GTP rac1/inmunología , Animales , Células Cultivadas , Relación Dosis-Respuesta a Droga , Activación Enzimática , Activación de Macrófagos/efectos de los fármacos , Macrófagos/efectos de los fármacos , Masculino , Ratones , Ratones Endogámicos C3H , Fosforilación/efectos de los fármacos
5.
Biochim Biophys Acta ; 1864(5): 479-87, 2016 May.
Artículo en Inglés | MEDLINE | ID: mdl-26867971

RESUMEN

For de novo design of protein-protein interactions (PPIs), information on the shape and chemical complementarity of their interfaces is generally required. Recent advances in computational PPI design have allowed for de novo design of protein complexes, and several successful examples have been reported. In addition, a simple and easy-to-use approach has also been reported that arranges leucines on a solvent-accessible region of an α-helix and places charged residues around the leucine patch to induce interactions between the two helical peptides. For this study, we adopted this approach to de novo design a new PPI between the helical bundle proteins sulerythrin and LARFH. A non-polar patch was created on an α-helix of LARFH around which arginine residues were introduced to retain its solubility. The strongest interaction found was for the LARFH variant cysLARFH-IV-3L3R and the sulerythrin mutant 6L6D (KD=0.16 µM). This artificial protein complex is maintained by hydrophobic and ionic interactions formed by the inter-molecular helical bundle structure. Therefore, by the simple and easy-to-use approach to create de novo interfaces on the α-helices, we successfully generated an artificial PPI. We also created a second LARFH variant with the non-polar patch surrounded by positively charged residues at each end. Upon mixing this LARFH variant with 6L6D, mesh-like fibrous nanostructures were observed by atomic force microscopy. Our method may, therefore, also be applicable to the de novo design of protein nanostructures.


Asunto(s)
Hemeritrina/química , Represoras Lac/química , Complejos Multiproteicos , Mapas de Interacción de Proteínas , Estructura Secundaria de Proteína/genética , Rubredoxinas/química , Secuencia de Aminoácidos/genética , Sitios de Unión , Disulfuros/química , Escherichia coli/química , Hemeritrina/metabolismo , Interacciones Hidrofóbicas e Hidrofílicas , Represoras Lac/metabolismo , Leucina , Unión Proteica , Ingeniería de Proteínas , Pliegue de Proteína , Rubredoxinas/metabolismo , Solventes/química , Sulfolobus/química , Sulfolobus/metabolismo
6.
Archaea ; 2016: 1802675, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27774041

RESUMEN

Bacteria and Eukarya have cell membranes with sn-glycerol-3-phosphate (G3P), whereas archaeal membranes contain sn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis. Together with the distribution of these protein-encoding genes among archaeal and bacterial groups, our phylogenetic analyses suggested that GlpA/GlpD in the Commonote (the last universal common ancestor of all extant life with a cellular form, Commonote commonote) acquired EgsA (G1PDH) from the archaeal common ancestor (Commonote archaea) and acquired GpsA and GlpK from a bacterial common ancestor (Commonote bacteria). In our scenario based on this study, the Commonote probably possessed a G3P-lipid membrane synthesized enzymatically, after which the archaeal lineage acquired G1PDH followed by the replacement of a G3P-lipid membrane with a G1P-lipid membrane.


Asunto(s)
Archaea/enzimología , Membrana Celular/química , Evolución Molecular , Glicerol Quinasa/genética , Glicerolfosfato Deshidrogenasa/genética , Fosfolípidos/metabolismo , Archaea/genética , Filogenia , Homología de Secuencia de Aminoácido
7.
Proc Natl Acad Sci U S A ; 110(27): 11067-72, 2013 Jul 02.
Artículo en Inglés | MEDLINE | ID: mdl-23776221

RESUMEN

Theoretical studies have focused on the environmental temperature of the universal common ancestor of life with conflicting conclusions. Here we provide experimental support for the existence of a thermophilic universal common ancestor. We present the thermal stabilities and catalytic efficiencies of nucleoside diphosphate kinases (NDK), designed using the information contained in predictive phylogenetic trees, that seem to represent the last common ancestors of Archaea and of Bacteria. These enzymes display extreme thermal stabilities, suggesting thermophilic ancestries for Archaea and Bacteria. The results are robust to the uncertainties associated with the sequence predictions and to the tree topologies used to infer the ancestral sequences. Moreover, mutagenesis experiments suggest that the universal ancestor also possessed a very thermostable NDK. Because, as we show, the stability of an NDK is directly related to the environmental temperature of its host organism, our results indicate that the last common ancestor of extant life was a thermophile that flourished at a very high temperature.


Asunto(s)
Estabilidad de Enzimas/genética , Evolución Molecular , Nucleósido-Difosfato Quinasa/genética , Secuencia de Aminoácidos , Proteínas Arqueales/química , Proteínas Arqueales/clasificación , Proteínas Arqueales/genética , Proteínas Bacterianas/química , Proteínas Bacterianas/clasificación , Proteínas Bacterianas/genética , Secuencia de Consenso , Cristalografía por Rayos X , Modelos Moleculares , Datos de Secuencia Molecular , Nucleósido-Difosfato Quinasa/química , Nucleósido-Difosfato Quinasa/clasificación , Origen de la Vida , Filogenia , Homología de Secuencia de Aminoácido , Temperatura
8.
J Biol Chem ; 289(7): 3888-900, 2014 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-24379400

RESUMEN

Activating transcription factor 5 (ATF5) is a stress-response transcription factor that responds to amino acid limitation and exposure to cadmium chloride (CdCl2) and sodium arsenite (NaAsO2). The N-terminal amino acids contribute to the destabilization of the ATF5 protein in steady-state conditions and serve as a stabilization domain in the stress response after CdCl2 or NaAsO2 exposure. In this study, we show that interleukin 1ß (IL-1ß), a proinflammatory cytokine, increases the expression of ATF5 protein in HepG2 hepatoma cells in part by stabilizing the ATF5 protein. The N-terminal domain rich in hydrophobic amino acids that is predicted to form a hydrophobic network was responsible for destabilization in steady-state conditions and served as an IL-1ß response domain. Furthermore, IL-1ß increased the translational efficiency of ATF5 mRNA via the 5' UTRα and phosphorylation of the eukaryotic translation initiation factor 2α (eIF2α). ATF5 knockdown in HepG2 cells up-regulated the IL-1ß-induced expression of the serum amyloid A 1 (SAA1) and SAA2 genes. Our results show that the N-terminal hydrophobic amino acids play an important role in the regulation of ATF5 protein expression in IL-1ß-mediated immune response and that ATF5 is a negative regulator for IL-1ß-induced expression of SAA1 and SAA2 in HepG2 cells.


Asunto(s)
Factores de Transcripción Activadores/metabolismo , Interleucina-1beta/metabolismo , Biosíntesis de Proteínas/fisiología , Factores de Transcripción Activadores/genética , Arsenitos/farmacología , Cloruro de Cadmio/farmacología , Inhibidores Enzimáticos/farmacología , Células Hep G2 , Humanos , Interacciones Hidrofóbicas e Hidrofílicas/efectos de los fármacos , Interleucina-1beta/genética , Biosíntesis de Proteínas/efectos de los fármacos , Estabilidad Proteica/efectos de los fármacos , Estructura Terciaria de Proteína , Proteína Amiloide A Sérica/biosíntesis , Proteína Amiloide A Sérica/genética , Compuestos de Sodio/farmacología
9.
Biochim Biophys Acta ; 1844(3): 553-60, 2014 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-24373877

RESUMEN

A non-polar patch on the surface of a protein can cause a reduction in the solubility and stability of the protein, and thereby induce aggregation. However, a non-polar patch may be required so that the protein can bind to another molecule. The mutant 6L-derived from the acidic, dimeric α-helical protein sulerythrin and containing six additional leucines arranged to form a non-polar patch on its surface when properly folded-has a substantially reduced solubility in comparison with that of wild-type sulerythrin. This reduced solubility appears to cause 6L to aggregate. To reverse this aggregation, we mutated 6L so that it contained three to six additional glutamates or aspartates that we predicted would surround the non-polar leucine patch on natively folded 6L. Although the introduction of three glutamates or aspartates increased solubility, the mutants still aggregate and have a reduced α-helical content. Conversely, mutants with six additional glutamates or aspartates appear to exist mostly as dimers and to have the same α-helical content as that of wild-type sulerythrin. Notably, the introduction of five lysines or five arginines at the positions held by the glutamates or aspartates did not recover solubility as effectively as did the negatively charged residues. These results demonstrate that negatively charged residues, but not positively charged ones, surrounding a non-polar patch on an acidic protein can completely reverse the decrease in its solubility caused by the patch of non-polar surface residues.


Asunto(s)
Ácidos/química , Proteínas/química , Cromatografía en Gel , Dicroismo Circular , Modelos Moleculares , Conformación Proteica , Pliegue de Proteína , Solubilidad , Espectrometría de Fluorescencia , Espectrofotometría Ultravioleta
10.
Sci Rep ; 14(1): 398, 2024 01 03.
Artículo en Inglés | MEDLINE | ID: mdl-38172176

RESUMEN

To understand the origin and early evolution of life it is crucial to establish characteristics of the primordial environment that facilitated the emergence and evolution of life. One important environmental factor is the pH of the primordial environment. Here, we assessed the pH-dependent thermal stabilities of previously reconstructed ancestral nucleoside diphosphate kinases and ribosomal protein uS8s. The selected proteins were likely to be present in ancient organisms such as the last common ancestor of bacteria and that of archaea. We also assessed the thermal stability of homologous proteins from extant acidophilic, neutralophilic, and alkaliphilic microorganisms as a function of pH. Our results indicate that the reconstructed ancestral proteins are more akin to those of extant alkaliphilic bacteria, which display greater stability under alkaline conditions. These findings suggest that the common ancestors of bacterial and archaeal species thrived in an alkaline environment. Moreover, we demonstrate the reconstruction method employed in this study is a valuable technique for generating alkali-tolerant proteins that can be used in a variety of biotechnological and environmental applications.


Asunto(s)
Evolución Molecular , Proteínas , Filogenia , Proteínas/metabolismo , Bacterias/genética , Bacterias/metabolismo , Archaea/genética , Archaea/metabolismo
11.
Biochemistry ; 50(40): 8583-93, 2011 Oct 11.
Artículo en Inglés | MEDLINE | ID: mdl-21894900

RESUMEN

Although enzymes of thermophilic organisms are often very resistant to thermal denaturation, they are usually less active than their mesophilic or psychrophilic homologues at moderate or low temperatures. To explore the structural features that would improve the activity of a thermophilic enzyme at less than optimal temperatures, we randomly mutated the DNA of single-site mutants of the thermostable Thermus thermophilus 3-isopropylmalate dehydrogenase that already had improved low-temperature activity and selected for additional improved low-temperature activity. A mutant (Ile279 → Val) with improved low-temperature activity contained a residue that directly interacts with the adenine of the coenzyme NAD(+), suggesting that modulation of the coenzyme-binding pocket's volume can enhance low-temperature activity. This idea was further supported by a saturation mutagenesis study of the two codons of two other residues that interact with the adenine. Furthermore, a similar type of amino acid substitution also improved the catalytic efficiency of another thermophilic dehydrogenase, T. thermophilus lactate dehydrogenase. Steady-state kinetic experiments showed that the mutations all favorably affected the catalytic turnover numbers. Thermal stability measurements demonstrated that the mutants remain very resistant to heat. Calculation of the energetic contributions to catalysis indicated that the increased turnover numbers are the result of destabilized enzyme-substrate-coenzyme complexes. Therefore, small changes in the side chain volumes of coenzyme-binding residues improved the catalytic efficiencies of two thermophilic dehydrogenases while preserving their high thermal stabilities and may be a way to improve low-temperature activities of dehydrogenases in general.


Asunto(s)
3-Isopropilmalato Deshidrogenasa/química , 3-Isopropilmalato Deshidrogenasa/genética , Sustitución de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , NAD/metabolismo , Thermus thermophilus/enzimología , 3-Isopropilmalato Deshidrogenasa/metabolismo , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Proteínas Bacterianas/metabolismo , Sitios de Unión , Frío , Estabilidad de Enzimas , Cinética , Datos de Secuencia Molecular , Mutación , Unión Proteica , Thermus thermophilus/genética
12.
Proteins ; 79(1): 221-31, 2011 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-21058300

RESUMEN

The (ß/α)8-barrel is one of the most abundant folds found in enzymes. To identify the independent folding units and the segment(s) that correspond to a minimum core structure within a (ß/α)8-barrel protein, fragmentation experiments were performed with Escherichia coli phosphoribosylanthranilate isomerase, which has a single (ß/α)8-barrel domain. Our previous studies indicated that the central four ß/α segments comprise an independent folding unit; whereas, the role(s) of the first two ß/α segments in folding had not been clarified prior to this report. Herein, we report the design and synthesis of a series of N-terminally deleted fragments starting with (ß/α)(1-5)ß6 as the parent construct. Analytical gel filtration and urea-induced equilibrium unfolding experiments indicated that deletions within the N-terminal region, that is, within the first two ß/α modules, resulted in reduced stability or aggregation of the remaining segments. The (ß/α)(3-5)ß6 segment appeared to fold into a stable structure and deletion of ß6 from (ß/α)(3-5)ß6 yielded (ß/α)(3-5), which did not form native-like secondary structures. However, urea-induced unfolding of (ß/α)(3-5), monitored by reduction of tryptophan fluorescence, indicated that the fragment contained a loosely packed hydrophobic core. Taken together, the results of our previous and present fragmentation experiments suggest the importance of the central (ß/α)(3-4)ß5 module in folding, which is a finding that is compatible with our simulated unfolding study performed previously.


Asunto(s)
Isomerasas Aldosa-Cetosa/química , Proteínas de Escherichia coli/química , Modelos Moleculares , Ingeniería de Proteínas , Pliegue de Proteína , Estructura Terciaria de Proteína , Desplegamiento Proteico , Homología Estructural de Proteína , Urea
13.
Int J Med Mushrooms ; 13(1): 73-82, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-22135906

RESUMEN

The Royal Sun mushroom, the Himematsutake culinary-medicinal mushroom, Agaricus brasiliensis has several polyphenoloxidase activities in a broad sense. Here we report the partial purification of tyrosinase-type polyphenoloxidase (PPO). PPO is purified from A. brasiliensis without browning using a two-phase partitioning with Triton X-114 and ammonium sulfate fractionation. Partially denaturing SDS-PAGE (sodium dodecyl sulfate-polyacrylamide electrophoresis) staining with L-3,4-dihydroxyphenylalanine was performed and the indicated molecular sizes were approximately 70 kDa and 45 kDa. The purified enzyme is in its latent state and can be activated maximally in the presence of 1.6 mM sodium dodecyl sulfate (SDS). This enzyme catalyzes two distinct reactions, monophenolase and diphenolase activity, and the monophenolase activity showed a lag time typical of polyphenoloxidase. The K(m) value for 4-tert-butylcatechol was quite similar in the presence and absence of SDS, but the apparent V(max) value was increased 2.0-fold by SDS. Mimosine was a typical competitive inhibitor with K(i) values of 138.2 microM and 281.0 microM n the presence and absence of SDS, respectively.


Asunto(s)
Agaricus/enzimología , Catecol Oxidasa/metabolismo , Cuerpos Fructíferos de los Hongos/enzimología , Catecol Oxidasa/antagonistas & inhibidores , Catecol Oxidasa/aislamiento & purificación , Electroforesis en Gel de Poliacrilamida , Activación Enzimática/efectos de los fármacos , Proteínas Fúngicas/aislamiento & purificación , Proteínas Fúngicas/metabolismo , Concentración de Iones de Hidrógeno , Cinética , Monofenol Monooxigenasa/aislamiento & purificación , Monofenol Monooxigenasa/metabolismo , Dodecil Sulfato de Sodio/farmacología , Temperatura
14.
PLoS One ; 16(10): e0258821, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34673819

RESUMEN

Further improvement of the thermostability of inherently thermostable proteins is an attractive challenge because more thermostable proteins are industrially more useful and serve as better scaffolds for protein engineering. To establish guidelines that can be applied for the rational design of hyperthermostable proteins, we compared the amino acid sequences of two ancestral nucleoside diphosphate kinases, Arc1 and Bac1, reconstructed in our previous study. Although Bac1 is a thermostable protein whose unfolding temperature is around 100°C, Arc1 is much more thermostable with an unfolding temperature of 114°C. However, only 12 out of 139 amino acids are different between the two sequences. In this study, one or a combination of amino acid(s) in Bac1 was/were substituted by a residue(s) found in Arc1 at the same position(s). The best mutant, which contained three amino acid substitutions (S108D, G116A and L120P substitutions), showed an unfolding temperature more than 10°C higher than that of Bac1. Furthermore, a combination of the other nine amino acid substitutions also led to improved thermostability of Bac1, although the effects of individual substitutions were small. Therefore, not only the sum of the contributions of individual amino acids, but also the synergistic effects of multiple amino acids are deeply involved in the stability of a hyperthermostable protein. Such insights will be helpful for future rational design of hyperthermostable proteins.


Asunto(s)
Aminoácidos/genética , Dictyostelium/enzimología , Mutación , Nucleósido-Difosfato Quinasa/metabolismo , Temperatura , Secuencia de Aminoácidos , Estabilidad de Enzimas , Mutagénesis Sitio-Dirigida , Nucleósido-Difosfato Quinasa/química , Nucleósido-Difosfato Quinasa/genética , Conformación Proteica , Homología de Secuencia
15.
Sci Rep ; 10(1): 15493, 2020 09 23.
Artículo en Inglés | MEDLINE | ID: mdl-32968141

RESUMEN

Enzymes have high catalytic efficiency and low environmental impact, and are therefore potentially useful tools for various industrial processes. Crucially, however, natural enzymes do not always have the properties required for specific processes. It may be necessary, therefore, to design, engineer, and evolve enzymes with properties that are not found in natural enzymes. In particular, the creation of enzymes that are thermally stable and catalytically active at low temperature is desirable for processes involving both high and low temperatures. In the current study, we designed two ancestral sequences of 3-isopropylmalate dehydrogenase by an ancestral sequence reconstruction technique based on a phylogenetic analysis of extant homologous amino acid sequences. Genes encoding the designed sequences were artificially synthesized and expressed in Escherichia coli. The reconstructed enzymes were found to be slightly more thermally stable than the extant thermophilic homologue from Thermus thermophilus. Moreover, they had considerably higher low-temperature catalytic activity as compared with the T. thermophilus enzyme. Detailed analyses of their temperature-dependent specific activities and kinetic properties showed that the reconstructed enzymes have catalytic properties similar to those of mesophilic homologues. Collectively, our study demonstrates that ancestral sequence reconstruction can produce a thermally stable enzyme with catalytic properties adapted to low-temperature reactions.


Asunto(s)
Secuencia de Aminoácidos , Catálisis , Enzimas/metabolismo , 3-Isopropilmalato Deshidrogenasa/genética , 3-Isopropilmalato Deshidrogenasa/metabolismo , Secuencia de Aminoácidos/genética , Secuencia de Aminoácidos/fisiología , Frío , Estabilidad de Enzimas/genética , Enzimas/genética , Cinética , Filogenia , Alineación de Secuencia , Temperatura , Thermus thermophilus/enzimología , Thermus thermophilus/genética
16.
Sci Rep ; 9(1): 9346, 2019 06 27.
Artículo en Inglés | MEDLINE | ID: mdl-31249343

RESUMEN

Thermophilic enzymes are generally more thermally stable but are less active at moderate temperatures than are their mesophilic counterparts. Thermophilic enzymes with improved low-temperature activity that retain their high stability would serve as useful tools for industrial processes especially when robust biocatalysts are required. Here we show an effective way to explore amino acid substitutions that enhance the low-temperature catalytic activity of a thermophilic enzyme, based on a pairwise sequence comparison of thermophilic/mesophilic enzymes. One or a combination of amino acid(s) in 3-isopropylmalate dehydrogenase from the extreme thermophile Thermus thermophilus was/were substituted by a residue(s) found in the Escherichia coli enzyme at the same position(s). The best mutant, which contained three amino acid substitutions, showed a 17-fold higher specific activity at 25 °C compared to the original wild-type enzyme while retaining high thermal stability. The kinetic and thermodynamic parameters of the mutant showed similar patterns along the reaction coordinate to those of the mesophilic enzyme. We also analyzed the residues at the substitution sites from a structural and phylogenetic point of view.


Asunto(s)
Enzimas/química , Ingeniería de Proteínas , Temperatura , Sustitución de Aminoácidos , Catálisis , Dominio Catalítico , Activación Enzimática , Estabilidad de Enzimas , Enzimas/clasificación , Enzimas/genética , Cinética , Mutagénesis , Filogenia , Termodinámica
17.
Anal Biochem ; 380(1): 51-8, 2008 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-18559251

RESUMEN

We developed a method to measure the rupture forces between antibody and antigen by atomic force microscopy (AFM). Previous studies have reported that in the measurement of antibody-antigen interaction using AFM, the specific intermolecular forces are often obscured by nonspecific adhesive binding forces between antibody immobilized cantilever and substrate surfaces on which antigen or nonantigen are fixed. Here, we examined whether detergent and nonreactive protein, which have been widely used to reduce nonspecific background signals in ordinary immunoassay and immunoblotting, could reduce the nonspecific forces in the AFM measurement. The results showed that, in the presence of both nonreactive protein and detergent, the rupture forces between anti-ferritin antibodies immobilized on a tip of cantilever and ferritin (antigen) on the substrate could be successfully measured, distinguishing from nonspecific adhesive forces. In addition, we found that approach/retraction velocity of the AFM cantilever was also important in the reduction of nonspecific adhesion. These insights will contribute to the detection of specific molecules at nanometer scale region and the investigation of intermolecular interaction by the use of AFM.


Asunto(s)
Anticuerpos/inmunología , Anticuerpos/metabolismo , Ferritinas/inmunología , Ferritinas/metabolismo , Inmunoensayo/métodos , Microscopía de Fuerza Atómica/métodos , Animales , Bovinos , Detergentes/farmacología , Humanos , Unión Proteica/efectos de los fármacos , Especificidad por Sustrato , Compuestos de Sulfhidrilo/metabolismo , Propiedades de Superficie
18.
Biophys Rev ; 10(2): 411-420, 2018 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-29214605

RESUMEN

Designing novel protein-protein interactions (PPIs) with high affinity is a challenging task. Directed evolution, a combination of randomization of the gene for the protein of interest and selection using a display technique, is one of the most powerful tools for producing a protein binder. However, the selected proteins often bind to the target protein at an undesired surface. More problematically, some selected proteins bind to their targets even though they are unfolded. Current state-of-the-art computational design methods have successfully created novel protein binders. These computational methods have optimized the non-covalent interactions at interfaces and thus produced artificial protein complexes. However, to date there are only a limited number of successful examples of computationally designed de novo PPIs. De novo design of coiled-coil proteins has been extensively performed and, therefore, a large amount of knowledge of the sequence-structure relationship of coiled-coil proteins has been accumulated. Taking advantage of this knowledge, de novo design of inter-helical interactions has been used to produce artificial PPIs. Here, we review recent progress in the in silico design and rational design of de novo PPIs and the use of α-helices as interfaces.

19.
Sci Rep ; 8(1): 1227, 2018 01 19.
Artículo en Inglés | MEDLINE | ID: mdl-29352156

RESUMEN

Modern organisms commonly use the same set of 20 genetically coded amino acids for protein synthesis with very few exceptions. However, earlier protein synthesis was plausibly much simpler than modern one and utilized only a limited set of amino acids. Nevertheless, few experimental tests of this issue with arbitrarily chosen amino acid sets had been reported prior to this report. Herein we comprehensively and systematically reduced the size of the amino acid set constituting an ancestral nucleoside kinase that was reconstructed in our previous study. We eventually found that two convergent sequences, each comprised of a 13-amino acid alphabet, folded into soluble, stable and catalytically active structures, even though their stabilities and activities were not as high as those of the parent protein. Notably, many but not all of the reduced-set amino acids coincide with those plausibly abundant in primitive Earth. The inconsistent amino acids appeared to be important for catalytic activity but not for stability. Therefore, our findings suggest that the prebiotically abundant amino acids were used for creating stable protein structures and other amino acids with functional side chains were recruited to achieve efficient catalysis.


Asunto(s)
Proteínas Bacterianas/química , Evolución Molecular , Nucleósido-Difosfato Quinasa/química , Aminoácidos/análisis , Proteínas Bacterianas/genética , Estabilidad de Enzimas/genética , Nucleósido-Difosfato Quinasa/genética
20.
J Biosci Bioeng ; 125(2): 192-198, 2018 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-29050803

RESUMEN

Protein-metal hybrids are functional materials with various industrial applications. For example, a redox enzyme immobilized on a platinum electrode is a key component of some biofuel cells and biosensors. To create these hybrid materials, protein molecules are bound to metal surfaces. Here, we report the selection of a novel platinum-binding sequence in a loop of a four-helix bundle protein, the Lac repressor four-helix protein (LARFH), an artificial protein in which four identical α-helices are connected via three identical loops. We created a genetic library in which the Ser-Gly-Gln-Gly-Gly-Ser sequence within the first inter-helical loop of LARFH was semi-randomly mutated. The library was then subjected to selection for platinum-binding affinity by using the T7 phage display method. The majority of the selected variants contained the Tyr-Lys-Arg-Gly-Tyr-Lys (YKRGYK) sequence in their randomized segment. We characterized the platinum-binding properties of mutant LARFH by using quartz crystal microbalance analysis. Mutant LARFH seemed to interact with platinum through its loop containing the YKRGYK sequence, as judged by the estimated exclusive area occupied by a single molecule. Furthermore, a 10-residue peptide containing the YKRGYK sequence bound to platinum with reasonably high affinity and basic side chains in the peptide were crucial in mediating this interaction. In conclusion, we have identified an amino acid sequence, YKRGYK, in the loop of a helix-loop-helix motif that shows high platinum-binding affinity. This sequence could be grafted into loops of other polypeptides as an approach to immobilize proteins on platinum electrodes for use as biosensors among other applications.


Asunto(s)
Péptidos/química , Platino (Metal)/química , Secuencia de Aminoácidos , Técnicas Biosensibles , Electrodos , Biblioteca de Péptidos , Estructura Secundaria de Proteína
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA