The Dynamic Energy Budget theory unifies the commonalties between organisms, as prescribed by the implications of energetics, and links different levels of biological organisation (cells, organisms and populations). The theory presents simple mechanistic rules that describe the uptake and use of energy and nutrients and the consequences for physiological organization throughout an organism's life cycle. All living organisms are covered in a single quantitative framework, the predictions of which are tested against a variety of experimental results at a range of levels of organisation. The theory explains many general observations, such as the body size scaling relationships of certain physiological traits, and provides a theoretical underpinning to the method of indirect calorimetry. In each case, the theory is developed in elementary mathematical terms, but a more detailed discussion of the methodological aspects of mathematical modelling is also included.

Dynamic Energy and Mass Budgets in Biological Systems

Protein phosphorylation in regulation of photosynthesis

A comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the International Union of Biochemistry and Molecular Biology. This system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. Almost all of the more than 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters, and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Transport mode and energy coupling prove to be relatively immutable characteristics and therefore provide primary bases for classification. Phylogenetic grouping reflects structure, function, mechanism, and often substrate specificity and therefore provides a reliable secondary basis for classification. Substrate specificity and polarity of transport prove to be more readily altered during evolutionary history and therefore provide a tertiary basis for classification. With very few exceptions, a phylogenetic family of transporters includes members that function by a single transport mode and energy coupling mechanism, although a variety of substrates may be transported, sometimes with either inwardly or outwardly directed polarity. In this review, I provide cross-referencing of well-characterized constituent transporters according to (i) transport mode, (ii) energy coupling mechanism, (iii) phylogenetic grouping, and (iv) substrates transported. The structural features and distribution of recognized family members throughout the living world are also evaluated. The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects.

https://mmbr.asm.org/content/mmbr/64/2/354.full.pdf

A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters

Fluorescence spectroscopy, one of the most informative and sensitive analytical techniques, has played and continues to play key roles in modern research. Indeed, unraveling the inner workings of biomolecules, cells and organisms relied on the development of fluorescence-based tools. As many of the players in these sophisticated interactions and exceedingly complex systems are not inherently emissive, researchers have relied on synthesizing fluorescent analogs of the building blocks found in biological macromolecules. These are the constituents of the cell surface and cell membrane, as well as proteins and nucleic acids. This review article is dedicated to emissive analogs of these relatively small molecules.

For organizational purposes, we have arbitrarily selected to approach these diverse families of biomolecules by imagining “a journey into the center of the cell”. Approaching the exterior of a cell, one first encounters oligosaccharides that decorate the cell surface and are involved in cell recognition and signaling. Next, we arrive at the cell membrane itself. This semi-permeable envelope sets the cell boundaries and regulates its traffic. Several types of building blocks assemble this membrane, most notably among them are the phospholipids. Upon entering the cell, the cytosol reveals a plethora of small and large molecules, including proteins, as well as soluble RNA molecules and RNA-rich ribosomes. Within the cytosol of eukaryotes and prokaryotes lies the nucleus or nucleoid, respectively. This membrane-enclosed control center contains most of the cells’ genetic material. DNA, the cellular blueprint, is permanently found in the nucleus, which also hosts diverse RNA molecules. Accordingly, we first discuss emissive carbohydrate derivatives. We then present fluorescent membrane constituents, followed by emissive amino acids. Our journey ends by focusing on emissive analogs of nucleosides and nucleotides, the building blocks of nucleic acids.

The common biomolecular building blocks, excluding a few amino acids, lack appreciably useful fluorescence properties. This implies that structural modifications are required to impart such photophysical features. Ideally, a designer probe should closely resemble its natural counterpart in size and shape without the loss of the original function (a feature we refer to as “isomorphicity”). This presents a fundamental predicament, as any modification attempting to alter the electronic nature of a molecule, typically by including aromatic residues or extending conjugation, will also alter its steric bulk and therefore the interactions with its surroundings.

Clearly not all biomolecular building blocks can or need to accommodate strict isomorphic design criteria. The heterocycles found in nucleosides already provide a platform that facilitates the extension of π-conjugation, which is also true for some aromatic amino acids. In contrast, employing fluorescence spectroscopy to membrane research requires very creative probe designs. Saccharides can be viewed as the most restrictive in this context, as no chemical modification is conceivable without a major structural disruption and likely loss of function. Such aliphatic biomolecules accommodate labeling only, where an established fluorophore is covalently conjugated to provide an emissive derivative. We therefore reserve the term probe to molecular designs that are expected to furnish useful modified biomolecules capable of reliable reporting. Understandably, fluorescent probes must meet the most stringent isomorphic design principles to ensure a biologically meaningful read-out. The isomorphic design principle is therefore a central theme of this review.

This article focuses on designing fluorescent probes for the four major families of macromolecular building blocks discussed above. Although not necessarily in chronological order, it spans roughly four decades of probe design with emphasis, when justified, on recent contributions. As the reader may imagine, this topic encapsulates a vast research field and cannot be comprehensively reviewed within the space limitation of Chemical Reviews. Nevertheless, we have attempted to summarize the most important and general contributions discussing fluorescent probes that were designed to shed light on biological processes and refer the reader to other resources.1 Although a few examples have found their way into the text, we do not generally address here the development of small molecule fluorophores and sensors that are not part of biomolecular assemblies. We open this article with a brief overview of the key features of fluorescence spectroscopy, where essential theoretical, experimental, and practical elements are discussed.

/pdf/fluorescent-analogs-of-biomolecular-building-blocks-design-11xiwhr1gd.pdf

Fluorescent Analogs of Biomolecular Building Blocks: Design, Properties, and Applications

Foreword to the First Edition.Preface.Acknowledgements.Introduction.1 The Chemical Structures and Properties of Condensed Inorganic Phosphates.1.1 The Structures of Condensed Phosphates.1.1.1 Cyclophosphates.1.1.2 Polyphosphates.1.1.3 Branched Inorganic Phosphates, or 'Ultraphosphates'.1.2 Some Chemical Properties of Condensed Inorganic Polyphosphates.1.3 Physico-Chemical Properties of Condensed Inorganic Polyphosphates.2 Methods of Polyphosphate Assay in Biological Materials.2.1 Methods of Extraction from Biological Materials.2.2 Chromatographic Methods.2.3 Colorimetric and Fluorimetric Methods.2.4 Cytochemical Methods.2.5 X-Ray Energy Dispersive Analysis.2.6 31P Nuclear Magnetic Resonance Spectroscopy.2.7 Other Physical Methods.2.8 Gel Electrophoresis.2.9 Enzymatic Methods.3 The Occurrence of Polyphosphates in Living Organisms.4 The Forms in which Polyphosphates are Present in Cells.4.1 Polyphosphate-Cation Complexes.4.2 Polyphosphate-Ca2+-Polyhydroxybutyrate Complexes.4.3 Complexes of Polyphosphates with Nucleic Acids.4.4 Binding of Polyphosphates with Proteins.5 Localization of Polyphosphates in Cells of Prokaryotes and Eukaryotes.5.1 Prokaryotes.5.2 Eukaryotes.6 Enzymes of Polyphosphate Biosynthesis and Degradation.6.1 Enzymes of Polyphosphate Biosynthesis.6.1.1 Polyphosphate Kinase (Polyphosphate:ADP Phosphotransferase, EC 2.7.4.1).6.1.2 3-Phospho-D-Glyceroyl-Phosphate:Polyphosphate Phosphotransferase (EC 2.7.4.17).6.1.3 Dolichyl-Diphosphate:Polyphosphate Phosphotransferase (EC 2.7.4.20).6.2 Enzymes of Polyphosphate Degradation.6.2.1 Polyphosphate-Glucose Phosphotransferase (EC 2.7.1.63).6.2.2 NAD Kinase (ATP:NAD 2--Phosphotransferase, EC 2.7.1.23).6.2.3 Exopolyphosphatase (Polyphosphate Phosphohydrolase, EC 3.6.1.11).6.2.4 Adenosine-Tetraphosphate Phosphohydrolase (EC 3.6.1.14).6.2.5 Triphosphatase (Tripolyphosphatase, EC 3.6.1.25).6.2.6 Endopolyphosphatase (Polyphosphate Depolymerase, EC 3.6.1.10).6.2.7 PolyP:AMP Phosphotransferase.7 The Functions of Polyphosphates and Polyphosphate-Dependent Enzymes.7.1 Phosphate Reserve.7.1.1 In Prokaryotes.7.1.2 In Eukaryotes.7.2 Energy Source.7.2.1 Polyphosphates in Bioenergetics of Prokaryotes.7.2.2 Polyphosphate in Bioenergetics of Eukaryotes.7.3 Cations Sequestration and Storage.7.3.1 In Prokaryotes.7.3.2 In Eukaryotes.7.4 Participation in Membrane Transport.7.5 Cell Envelope Formation and Function.7.5.1 Polyphosphates in the Cell Envelopes of Prokaryotes.7.5.2 Polyphosphates in the Cell Envelopes of Eukaryotes.7.6 Regulation of Enzyme Activities.7.7 Gene Activity Control, Development and Stress Response.7.7.1 In Prokaryotes.7.7.2 In Lower Eukaryotes.7.8 The Functions of Polyphosphates in Higher Eukaryotes.8 The Peculiarities of Polyphosphate Metabolism in Different Organisms.8.1 Escherichia coli.8.1.1 The Dynamics of Polyphosphates under Culture Growth.8.1.2 The Effects of Pi Limitation and Excess.8.1.3 The Effects of Mutations on Polyphosphate Levels and Polyphosphate-Metabolizing Enzyme Activities.8.1.4 The Effects of Nutrition Deficiency and Environmental Stress.8.2 Pseudomonas aeruginosa.8.3 Acinetobacter.8.4 Aerobacter aerogenes (Klebsiella aerogenes).8.5 Azotobacter.8.6 Cyanobacteria (Blue-Green Algae) and other Photosynthetic Bacteria.8.7 Mycobacteria and Corynebacteria.8.8 Propionibacteria.8.9 Archae.8.10 Yeast.8.10.1 Yeast Cells Possess Different Polyphosphate Fractions.8.10.2 The Dynamics of PolyP Fractions during the Cell Cycle.8.10.3 The Relationship between the Metabolism of Polyphosphates and other Compounds.8.10.4 Polyphosphate Fractions at Growth on a Pi-Sufficient Medium with Glucose.8.10.5 The Effects of Pi Limitation and Excess.8.10.6 The Effects of other Conditions on the Polyphosphate Content in Yeast Cells.8.10.7 The Effects of Inhibitors on the Polyphosphate Content in Yeast Cells.8.10.8 The Effects of Mutations on the Content and Chain Lengths of Polyphosphate in Yeast.8.11 Other Fungi (Mould and Mushrooms).8.12 Algae.8.12.1 Localization and Forms in Cells.8.12.2 The Dynamics of Polyphosphates in the Course of Growth.8.12.3 The Influence of Light and Darkness.8.12.4 The Effects of Pi Limitation and Excess.8.12.5 Changes in Polyphosphate Content under Stress Conditions.8.13 Protozoa.8.14 Higher Plants.8.15 Animals.9 Applied Aspects of Polyphosphate Biochemistry.9.1 Bioremediation of the Environment.9.1.1 Enhanced Biological Phosphate Removal.9.1.2 Removal of Heavy Metals from Waste.9.2 Polyphosphates and Polyphosphate-Metabolizing Enzymes in Assay and Synthesis.9.3 Polyphosphates in Medicine.9.3.1 Antiseptic and Antiviral Agents.9.3.2 Polyphosphate Kinase as a Promising Antimicrobial Target.9.3.3 Polyphosphates as New Biomaterials.9.3.4 Polyphosphates in Bone Therapy and Stomathology.9.4 Polyphosphates in Agriculture.9.5 Polyphosphates in the Food Industry.10 Inorganic Polyphosphates in Chemical and Biological Evolution.10.1 Abiogenic Synthesis of Polyphosphates and Pyrophosphate.10.2 Phosphorus Compounds in Chemical Evolution.10.3 Polyphosphates and Pyrophosphates: Fossil Biochemical Reactions and the Course of Bioenergetic Evolution.10.4 Changes in the Role of Polyphosphates in Organisms at Different Evolutionary Stages.References.Index of Generic Names.Subject Index.

The biochemistry of inorganic polyphosphates

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793%2899%2990617-8

H+ -PPases: a tightly membrane-bound family.

Suggestions by Calvin about a role of inorganic pyrophosphate (PPi) in early photosynthesis and by Lipmann that PPi may have been the original energy-rich phosphate donor in biological energy conversion, were followed in the mid-1960s by experimental results with isolated chromatophore membranes from the purple photosynthetic bacterium Rhodospirillum rubrum PPi was shown to be hydrolysed in an uncoupler stimulated reaction by a membrane-bound inorganic pyrophosphatase (PPase), to be formed at the expense of light energy in photophosphorylation and to be utilized as an energy donor for various energy-requiring reactions, as a first known alternative to ATP This direct link between PPi and photosynthesis led to increasing attention concerning the role of PPi in both early and present biological energy transfer In the 1970s, the PPase was shown to be a proton pump and to be present also in higher plants In the 1990s, sequences of H(+)-PPase genes were obtained from plants, protists, bacteria and archaea and two classes of H(+)-PPases differing in K(+) sensitivity were established Over 200 H(+)-PPase sequences have now been determined Recent biochemical and biophysical results have led to new progress and questions regarding the H(+)-PPase family, as well as the families of soluble PPases and the inorganic polyphosphatases, which hydrolyse inorganic linear high-molecular-weight polyphosphates (HMW-polyP) Here we will focus attention on the H(+)-PPases, their evolution and putative active site motifs, response to monovalent cations, genetic regulation and some very recent results, based on new methods for obtaining large quantities of purified protein, about their tertiary and quaternary structures

https://iubmb.onlinelibrary.wiley.com/doi/pdf/10.1080/15216540701258132

H+-PPases: yesterday, today and tomorrow.

Both inorganic pyrophosphate and ATP may function as biological energy donors in chromatophores from the photosynthetic bacterium Rhodospirillum rubrum, causing energy requiring spectral changes in endogenous cytochrome(s) and carotenoid(s).

Inorganic pyrophosphate and ATP as energy donors in chromatophores from Rhodospirillum rubrum.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793%2899%2900617-1

Margareta Baltscheffsky

Papers

H+ -PPases: a tightly membrane-bound family.

H+-PPases: yesterday, today and tomorrow.

Inorganic pyrophosphate and ATP as energy donors in chromatophores from Rhodospirillum rubrum.

H+-proton-pumping inorganic pyrophosphatase: a tightly membrane-bound family

Energy conversion-linked changes of carotenoid absorbance in Rhodospirillum rubrum chromatophores