scholarly journals A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family

2021 ◽  
Vol 118 (17) ◽  
pp. e2019571118
Author(s):  
Rohit Jain ◽  
Khaja Muneeruddin ◽  
Jeremy Anderson ◽  
Michael J. Harms ◽  
Scott A. Shaffer ◽  
...  
Keyword(s):  
Free Energy ◽  
Dynamic Equilibrium ◽  
High Energy ◽  
Amino Acid Sequences ◽  
Intact Protein ◽  
Free Energy Surface ◽  
Conserved Sequence ◽  
Evolutionary Forces ◽  
Tim Barrel ◽  
Hdx Ms

The amino acid sequences of proteins have evolved over billions of years, preserving their structures and functions while responding to evolutionary forces. Are there conserved sequence and structural elements that preserve the protein folding mechanisms? The functionally diverse and ancient (βα)1–8 TIM barrel motif may answer this question. We mapped the complex six-state folding free energy surface of a ∼3.6 billion y old, bacterial indole-3-glycerol phosphate synthase (IGPS) TIM barrel enzyme by equilibrium and kinetic hydrogen–deuterium exchange mass spectrometry (HDX-MS). HDX-MS on the intact protein reported exchange in the native basin and the presence of two thermodynamically distinct on- and off-pathway intermediates in slow but dynamic equilibrium with each other. Proteolysis revealed protection in a small (α1β2) and a large cluster (β5α5β6α6β7) and that these clusters form cores of stability in Ia and Ibp. The strongest protection in both states resides in β4α4 with the highest density of branched aliphatic side chain contacts in the folded structure. Similar correlations were observed previously for an evolutionarily distinct archaeal IGPS, emphasizing a key role for hydrophobicity in stabilizing common high-energy folding intermediates. A bioinformatics analysis of IGPS sequences from the three superkingdoms revealed an exceedingly high hydrophobicity and surprising α-helix propensity for β4, preceded by a highly conserved βα-hairpin clamp that links β3 and β4. The conservation of the folding mechanisms for archaeal and bacterial IGPS proteins reflects the conservation of key elements of sequence and structure that first appeared in the last universal common ancestor of these ancient proteins.

scholarly journals Amylolytic enzymes - focus on the alpha-amylases from Archae and plants

2021 ◽  
Vol 9 (1) ◽  
pp. 5-26
Author(s):  
Štefan Janeček
Keyword(s):  
Three Dimensional ◽  
Structural Features ◽  
Catalytic Triad ◽  
Amino Acid Sequences ◽  
Glycoside Hydrolases ◽  
Amylolytic Enzymes ◽  
Conserved Sequence ◽  
Glycosidic Bonds ◽  
Evolutionary Relatedness ◽  
Tim Barrel

Amylolytic enzymes represent a group of starch hydrolases and related enzymes that are active towards the α-glycosidic bonds in starch and related poly- and oligosaccharides. The three best known amylolytic enzymes are α-amylase, β-amylase and glucoamylase that, however, differ from each other by their amino acid sequences, three-dimensional structures, reaction mechanisms and catalytic machineries. In the sequence-based classification of all glycoside hydrolases (GHs) they have therefore been classified into the three independent families: GH13 (α-amylases), GH14 (β-amylases) and GH15 (glucoamylases). Some amylolytic enzymes have been placed to the families GH31 and GH57. The family GH13 together with the families GH70 and GH77 constitutes the clan GH-H, well-known as the α-amylase family. It contains more than 6,000 sequences and covers 30 various enzyme specificities sharing the conserved sequence regions, catalytic TIM-barrel fold, retaining reaction mechanism and catalytic triad. Among the GH13 α-amylases, those produced by plants and archaebacteria exhibit common sequence similarities that distinguish them from the α-amylases of the remaining taxonomic sources. Despite the close evolutionary relatedness between the plant and archaeal α-amylases, there are also specific differences that discriminate them from each other. These specific differences could be used in an effort to reveal the sequence-structural features responsible for the high thermostability of the α-amylases from Archaea.

scholarly journals Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein

2019 ◽  
Vol 116 (14) ◽  
pp. 6806-6811 ◽  
Author(s):  
Sujit Basak ◽  
R. Paul Nobrega ◽  
Davide Tavella ◽  
Laura M. Deveau ◽  
Nobuyasu Koga ◽  
...  
Keyword(s):  
Energy Surface ◽  
De Novo ◽  
Mutational Analysis ◽  
Hydrophobic Interactions ◽  
Guanidine Hydrochloride ◽  
High Energy ◽  
Amino Acid Sequences ◽  
Time Range ◽  
Free Energy Surface ◽  
Energy States

The successful de novo design of proteins can provide insights into the physical chemical basis of stability, the role of evolution in constraining amino acid sequences, and the production of customizable platforms for engineering applications. Previous guanidine hydrochloride (GdnHCl; an ionic denaturant) experiments of a designed, naturally occurring βα fold, Di-III_14, revealed a cooperative, two-state unfolding transition and a modest stability. Continuous-flow mixing experiments in our laboratory revealed a simple two-state reaction in the microsecond to millisecond time range and consistent with the thermodynamic results. In striking contrast, the protein remains folded up to 9.25 M in urea, a neutral denaturant, and hydrogen exchange (HDX) NMR analysis in water revealed the presence of numerous high-energy states that interconvert on a time scale greater than seconds. The complex protection pattern for HDX corresponds closely with a pair of electrostatic networks on the surface and an extensive network of hydrophobic side chains in the interior of the protein. Mutational analysis showed that electrostatic and hydrophobic networks contribute to the resistance to urea denaturation for the WT protein; remarkably, single charge reversals on the protein surface restore the expected urea sensitivity. The roughness of the energy surface reflects the densely packed hydrophobic core; the removal of only two methyl groups eliminates the high-energy states and creates a smooth surface. The design of a very stable βα fold containing electrostatic and hydrophobic networks has created a complex energy surface rarely observed in natural proteins.

scholarly journals Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be6B11− Fluxional Cluster

Materials ◽  
2020 ◽  
Vol 14 (1) ◽  
pp. 112
Author(s):  
Carlos Emiliano Buelna-Garcia ◽  
José Luis Cabellos ◽  
Jesus Manuel Quiroz-Castillo ◽  
Gerardo Martinez-Guajardo ◽  
Cesar Castillo-Quevedo ◽  
...  
Keyword(s):  
Free Energy ◽  
Infrared Spectrum ◽  
Infrared Spectra ◽  
Thermal Effects ◽  
Global Minimum ◽  
Energy Surface ◽  
Weighted Sums ◽  
Free Energy Surface ◽  
Temperature Dependent ◽  
Relative Population

The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be6B11− clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be6B11− clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations’ temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer’s infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the spectra of the lowest-energy structure and its isomers located at higher energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra.

scholarly journals The Influence of Starch Origin on the Properties of Starch Films: Packaging Performance

Materials ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 1146
Author(s):  
Zuzanna Żołek-Tryznowska ◽  
Alicja Kałuża
Keyword(s):  
Tensile Strength ◽  
Free Energy ◽  
Surface Free Energy ◽  
Food Packaging ◽  
Energy Surface ◽  
Free Energy Surface ◽  
Casting Method ◽  
Starch Solution ◽  
Film Properties ◽  
Starch Films

Starch films can be used as materials for food packaging purposes. The goal of this study is to compare how the starch origin influence the selected starch film properties. The films were made from various starches such as that from maize, potato, oat, rice, and tapioca using 50%w of glycerine as a plasticizer. The obtained starch-based films were made using the well-known casting method from a starch solution in water. The properties of the films that were evaluated were tensile strength, water vapour transition rate, moisture content, wettability, and their surface free energy. Surface free energy (SFE) and its polar and dispersive components were calculated using the Owens-Wendt-Rabel-Kaelbe approach. The values of SFE in the range of 51.64 to 70.81 mJ∙m−2 for the oat starch-based film and the maize starch-based film. The films revealed worse mechanical properties than those of conventional plastics for packaging purposes. The results indicated that the poorest tensile strength was exhibited by the starch-based films made from oat (0.36 MPa) and tapioca (0.78 MPa) and the greatest tensile strength (1.49 MPa) from potato.

Characterization of Textured Aluminum Lines and Modelling of Stress Voiding

1994 ◽  
Vol 343 ◽  
Author(s):  
S.C. Wardle ◽  
B.L. Adams ◽  
C.S. Nichols ◽  
D.A. Smith
Keyword(s):  
Free Energy ◽  
Excess Free Energy ◽  
Mean Field ◽  
High Energy ◽  
Polycrystalline Structure ◽  
Field Approach ◽  
Bamboo Structure ◽  
Automated Technique ◽  
Theory And Modeling

ABSTRACTIt is well known from studies of individual interfaces that grain boundaries exhibit a spectrum of properties because their structure is misorientation dependent. Usually this variability is neglected and properties are modeled using a mean field approach. The limitations inherent in this approach can be overcome, in principle, using a combination of experimental techniques, theory and modeling. The bamboo structure of an interconnect is a particularly simple polycrystalline structure that can now be readily characterized experimentally and modeled in the computer. The grain misorientations in a [111] textured aluminum line have been measured using the new automated technique of orientational imaging microscopy. By relating boundary angle to diffusivity the expected stress voiding failure processes can be predicted through the link between misorientation angle, grain boundary excess free energy and diffusivity. Consequently it can be shown that the high energy boundaries are the favored failure sites thermodynamically and kinetically.

Efficient approach to include molecular polarizations using charge and atom dipole response kernels to calculate free energy gradients in the QM/MM scheme

2015 ◽  
Vol 17 (40) ◽  
pp. 26955-26968 ◽  
Author(s):  
Toshio Asada ◽  
Kanta Ando ◽  
Koji Sakurai ◽  
Shiro Koseki ◽  
Masataka Nagaoka
Keyword(s):  
Free Energy ◽  
Energy Surface ◽  
Free Energy Surface ◽  
Efficient Approach ◽  
Reaction Processes ◽  
Dipole Response

An efficient approach to evaluate free energy gradients within the QM/MM framework has been proposed to clarify reaction processes on the free energy surface.

Metabolic and energy correlates of intracellular pH in progressive fatigue of squid (L. brevis) mantle muscle

1996 ◽  
Vol 271 (5) ◽  
pp. R1403-R1414 ◽  
Author(s):  
H. O. Portner ◽  
E. Finke ◽  
P. G. Lee
Keyword(s):  
Free Energy ◽  
Critical Velocity ◽  
Energy Levels ◽  
High Energy ◽  
Swimming Velocity ◽  
High Energy Phosphates ◽  
Energy Status ◽  
Intracellular Acidosis ◽  
Model Calculations

Squid (Lolliguncula brevis) were exercised at increasing swimming speeds to allow us to analyze the correlated changes in intracellular metabolic, acid-base, and energy status of the mantle musculature. Beyond a critical swimming velocity of 1.5 mantle lengths/s, an intracellular acidosis developed that was caused by an initial base loss from the cells, the onset of respiratory acidification, and, predominantly, octopine formation. The acidosis was correlated with decreasing levels of phospho-L-arginine and, thus, supported ATP buffering at the expense of the phosphagen. Monohydrogenphosphate, the actual substrate of glycogen phosphorylase accumulated, enabling glycogen degradation, despite progressive acidosis. In addition to octopine, succinate, and glycerophosphate accumulation, the onset of acidosis characterizes the critical velocity and indicates the transition to a non-steady-state time-limited situation. Accordingly, swimming above the critical velocity caused cellular energy levels (in vivo Gibbs free energy change of ATP hydrolysis) to fall. A minimal value was reached at about -45 kJ/mol. Model calculations demonstrate that changes in free Mg2+ levels only minimally affect ATP free energy, but minimum levels are relevant in maintaining functional concentrations of Mg(2+)-complexed adenylates. Model calculations also reveal that phosphagen breakdown enabled L. brevis to reach swimming speeds about three times higher than the critical velocity. Comparison of two offshore squid species (Loligo pealei and Illex illecebrosus) with the estuarine squid L.brevis indicates that the latter uses a strategy to delay the exploitation of high-energy phosphates and protect energy levels at higher than the minimum levels (-42 kJ/mol) characterizing fatigue in the other species. A more economical use of anaerobic resources and an early reduction in performance may enable L. brevis to tolerate more extreme environmental conditions in shallow estuarine waters and even hypoxic environments and to prevent a fatal depletion of energy stores.

Experimental evidence for the need of thermodynamic considerations in modelling of anaerobic environmental bioprocesses

1997 ◽  
Vol 36 (10) ◽  
pp. 109-115 ◽  
Author(s):  
Choon-Yee Hoh ◽  
Ralf Cord-Ruwisch
Keyword(s):  
Free Energy ◽  
Experimental Evidence ◽  
Positive Reaction ◽  
Rate Equation ◽  
Dynamic Equilibrium ◽  
Reaction Rates ◽  
Product Inhibition ◽  
Experimental Results ◽  
Biological Processes ◽  
Laws Of Thermodynamics

For modeling of biological processes that operate close to the dynamic equilibrium (eg. anaerobic processes), it is critical to prevent the prediction of positive reaction rates when the reaction has already reached dynamic equilibrium. Traditional Michaelis-Menten based models were found to violate the laws of thermodynamics as they predicted positive reaction rates for reactions that were endergonic due to high endproduct concentrations. The inclusion of empirical “product inhibition factors” as suggested by previous work could not prevent this problem. This paper compares the predictions of the Michaelis-Menten Model (with and without product inhibition factors) and the Equilibrium Based Model (which has a thermodynamic term introduced into its rate equation) with experimental results of reactions in anaerobic bacterial environments. In contrast to the Michaelis-Menten based models that used traditional inhibition factors, the Equilibrium Based Model correctly predicted the nature and the degree of inhibition due to endproduct accumulation. Moreover, this model also correctly predicted when reaction rates must be zero due to the free energy change of the conversion reaction being zero. With these added advantages, the Equilibrium Based Model thus seemed to provide a scientifically correct and more realistic basis for a variety of models that describe anaerobic biosystems.

Sign in / Sign up

Export Citation Format

Share Document