Potassium channels: structures, models, simulations

Intrinsic Opening of BK Channels Derives from Inherent Leakage in Hydrophobic Gating

The big potassium (BK) channels remain open with a small limiting probability of P o ~ 10-7 at minimal Ca2+ and negative voltages < -100 mV. The molecular origin and functional significance of such "intrinsic opening" are not understood. Here we combine atomistic simulations and electrophysiological experiments to show that the intrinsic opening of BK channels is an inherent property of the vapor barrier, generated by hydrophobic dewetting of the BK inner pore in the deactivated state. The vapor barrier only gives rise to a finite free energy barrier, of ~ 8 kcal/mol, and cannot completely shut down K+ flow even when the voltage sensor domains are fully deactivated. This results in the leaking currents that can be measured at negative voltages as the indication of intrinsic opening. The shallow limiting slope of P o at negative voltages results primarily from the electric field effects on the permeating ion through the vapor barrier. We further demonstrate that the vapor barrier can be perturbed by inner pore mutations and truncation of the cytosolic domains, leading to predicable changes in limiting slope measurements. Therefore, the intrinsic opening in BK channels, and possibly in other ion channels, opens up an opportunity to experimentally study hydrophobic gating. Our results further suggest that intrinsic opening in BK channels is the fundamental basis for the allosteric mechanism of activation by both voltage and Ca2+.

Transmembrane Ion Channels: From Natural to Artificial Systems

Natural channel proteins allow the selective permeation of ions, water or other nutritious entities across bilayer membranes, facilitating various essential physiological functions in living systems. Inspired by nature, chemists endeavor to simulate the structural features and transport behaviors of channel proteins through biomimetic strategies. In this review, we start from introducing the inherent traits of channel proteins such as their crystal structures, functions and mechanisms. Subsequently, different kind of synthetic ion channels including their design principles, dynamic regulations and therapeutic applications were carefully reviewed. Finally, the potential challenges and opportunities in this research field were also carefully discussed. It is anticipated that this review could provide some inspiring ideas and future directions towards the construction of novel bionic ion channels with higher-level structures, properties, functions and practical applications.

PUFA stabilizes a conductive state of the selectivity filter in IKs channels

In cardiomyocytes, the KCNQ1/KCNE1 channel complex mediates the slow delayed-rectifier current (IKs), pivotal during the repolarization phase of the ventricular action potential. Mutations in IKs cause long QT syndrome (LQTS), a syndrome with a prolonged QT interval on the ECG, which increases the risk of ventricular arrhythmia and sudden cardiac death. One potential therapeutical intervention for LQTS is based on targeting IKs channels to restore channel function and/or the physiological QT interval. Polyunsaturated fatty acids (PUFAs) are potent activators of KCNQ1 channels and activate IKs channels by binding to two different sites, one in the voltage sensor domain - which shifts the voltage dependence to more negative voltages - and the other in the pore domain - which increases the maximal conductance of the channels (Gmax). However, the mechanism by which PUFAs increase the Gmax of the IKs channels is still poorly understood. In addition, it is unclear why IKs channels have a very small single-channel conductance and a low open probability or whether PUFAs affect any of these properties of IKs channels. Our results suggest that the selectivity filter in KCNQ1 is normally unstable, contributing to the low open probability, and that the PUFA-induced increase in Gmax is caused by a stabilization of the selectivity filter in an open-conductive state.

Kv1.3-induced hyperpolarization is required for efficient Kaposi's sarcoma-associated herpesvirus lytic replication

Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic herpesvirus that is linked directly to the development of Kaposi's sarcoma. KSHV establishes a latent infection in B cells, which can be reactivated to initiate lytic replication, producing infectious virions. Using pharmacological and genetic silencing approaches, we showed that the voltage-gated K+ channel Kv1.3 in B cells enhanced KSHV lytic replication. The KSHV replication and transcription activator (RTA) protein increased the abundance of Kv1.3 and led to enhanced K+ channel activity and hyperpolarization of the B cell membrane. Enhanced Kv1.3 activity promoted intracellular Ca2+ influx, leading to the Ca2+-driven nuclear localization of KSHV RTA and host nuclear factor of activated T cells (NFAT) proteins and subsequently increased the expression of NFAT1 target genes. KSHV lytic replication and infectious virion production were inhibited by Kv1.3 blockers or silencing. These findings highlight Kv1.3 as a druggable host factor that is key to the successful completion of KSHV lytic replication.

Bioinspired 2D nanofluidic membranes for energy applications

Bioinspired two-dimensional (2D) nanofluidic membranes have been explored for the creation of high-performance ion transport systems that can mimic the delicate transport functions of living organisms. Advanced energy devices made from these membranes show excellent energy storage and conversion capabilities. Further research and development in this area are essential to unlock the full potential of energy devices and facilitate the development of high-performance equipment toward real-world applications and a sustainable future. However, there has been minimal review and summarization of 2D nanofluidic membranes in recent years. Thus, it is necessary to carry out an extensive review to provide a survey library for researchers in related fields. In this review, the classification and the raw materials that are used to construct 2D nanofluidic membranes are first presented. Second, the top-down and bottom-up methods for constructing 2D membranes are introduced. Next, the applications of bioinspired 2D membranes in osmotic energy, hydraulic energy, mechanical energy, photoelectric conversion, lithium batteries, and flow batteries are discussed in detail. Finally, the opportunities and challenges that 2D nanofluidic membranes are likely to face in the future are envisioned. This review aims to provide a broad knowledge base for constructing high-performance bioinspired 2D nanofluidic membranes for advanced energy applications.

Experimental and Theoretical Brownian Dynamics Analysis of Ion Transport During Cellular Electroporation of E. coli Bacteria

Escherichia coli bacterium is a rod-shaped organism composed of a complex double membrane structure. Knowledge of electric field driven ion transport through both membranes and the evolution of their induced permeabilization has important applications in biomedical engineering, delivery of genes and antibacterial agents. However, few studies have been conducted on Gram-negative bacteria in this regard considering the contribution of all ion types. To address this gap in knowledge, we have developed a deterministic and stochastic Brownian dynamics model to simulate in 3D space the motion of ions through pores formed in the plasma membranes of E. coli cells during electroporation. The diffusion coefficient, mobility, and translation time of Ca2+, Mg2+, Na+, K+, and Cl- ions within the pore region are estimated from the numerical model. Calculations of pore's conductance have been validated with experiments conducted at Gustave Roussy. From the simulations, it was found that the main driving force of ionic uptake during the pulse is the one due to the externally applied electric field. The results from this work provide a better understanding of ion transport during electroporation, aiding in the design of electrical pulses for maximizing ion throughput, primarily for application in cancer treatment.

Membrane Targeted Azobenzene Drives Optical Modulation of Bacterial Membrane Potential

Recent studies have shown that bacterial membrane potential is dynamic and plays signaling roles. Yet, little is still known about the mechanisms of membrane potential dynamics regulation-owing to a scarcity of appropriate research tools. Optical modulation of bacterial membrane potential could fill this gap and provide a new approach for studying and controlling bacterial physiology and electrical signaling. Here, the authors show that a membrane-targeted azobenzene (Ziapin2) can be used to photo-modulate the membrane potential in cells of the Gram-positive bacterium Bacillus subtilis. It is found that upon exposure to blue-green light (λ = 470 nm), isomerization of Ziapin2 in the bacteria membrane induces hyperpolarization of the potential. To investigate the origin of this phenomenon, ion-channel-deletion strains and ion channel blockers are examined. The authors found that in presence of the chloride channel blocker idanyloxyacetic acid-94 (IAA-94) or in absence of KtrAB potassium transporter, the hyperpolarization response is attenuated. These results reveal that the Ziapin2 isomerization can induce ion channel opening in the bacterial membrane and suggest that Ziapin2 can be used for studying and controlling bacterial electrical signaling. This new optical tool could contribute to better understand various microbial phenomena, such as biofilm electric signaling and antimicrobial resistance.

The Optimized Conformation Dynamics of the KcsA Filter as a Probe for Lateral Membrane Effects: A First Principle Based Femto-Sec Resolution MD Study

We provide a high resolution, all-atom, femto-second molecular dynamics (MD) simulation of the passage of K⁺ ions and H₂O molecules through the selectivity filter of the KcsA potassium ion channel, based on first principle physical methods. Our results show that a change in the length of the selectivity filter of as little as 3%, regardless of whether the filter is made longer or shorter, will reduce the K⁺ ion current by around 50%. In addition, further squeezing or stretching by about 9% can effectively stop the current. Our results demonstrate optimized conformational dynamics that associate an increased mobility of parts in the filter linings with a standard configuration, leading to maximized conduction rates that are highly sensitive to geometrical distortions. We discuss this latter aspect in relation to lateral membrane effects on the filter region of ion channels and the 'force from lipids' hypothesis.

Molecular mechanisms of centipede toxin SsTx-4 inhibition of inwardly rectifying potassium channels

Inwardly rectifying potassium channels (Kirs) are important drug targets, with antagonists for the Kir1.1, Kir4.1, and pancreatic Kir6.2/SUR1 channels being potential drug candidates for treating hypertension, depression, and diabetes, respectively. However, few peptide toxins acting on Kirs are identified and their interacting mechanisms remain largely elusive yet. Herein, we showed that the centipede toxin SsTx-4 potently inhibited the Kir1.1, Kir4.1, and Kir6.2/SUR1 channels with nanomolar to submicromolar affinities and intensively studied the molecular bases for toxin–channel interactions using patch-clamp analysis and site-directed mutations. Other Kirs including Kir2.1 to 2.4, Kir4.2, and Kir7.1 were resistant to SsTx-4 treatment. Moreover, SsTx-4 inhibited the inward and outward currents of Kirs with different potencies, possibly caused by a K⁺ “knock-off” effect, suggesting the toxin functions as an out pore blocker physically occluding the K⁺-conducting pathway. This conclusion was further supported by a mutation analysis showing that M137 located in the outer vestibule of the Kir6.2/ΔC26 channel was the key residue mediating interaction with SsTx-4. On the other hand, the molecular determinants within SsTx-4 for binding these Kir channels only partially overlapped, with K13 and F44 being the common key residues. Most importantly, K11A, P15A, and Y16A mutant toxins showed improved affinity and/or selectivity toward Kir6.2, while R12A mutant toxin had increased affinity for Kir4.1. To our knowledge, SsTx-4 is the first characterized peptide toxin with Kir4.1 inhibitory activity. This study provides useful insights for engineering a Kir6.2/SUR1 channel–specific antagonist based on the SsTx-4 template molecule and may be useful in developing new antidiabetic drugs.

Roles of Key Ion Channels and Transport Proteins in Age-Related Hearing Loss

The auditory system is a fascinating sensory organ that overall, converts sound signals to electrical signals of the nervous system. Initially, sound energy is converted to mechanical energy via amplification processes in the middle ear, followed by transduction of mechanical movements of the oval window into electrochemical signals in the cochlear hair cells, and finally, neural signals travel to the central auditory system, via the auditory division of the 8th cranial nerve. The majority of people above 60 years have some form of age-related hearing loss, also known as presbycusis. However, the biological mechanisms of presbycusis are complex and not yet fully delineated. In the present article, we highlight ion channels and transport proteins, which are integral for the proper functioning of the auditory system, facilitating the diffusion of various ions across auditory structures for signal transduction and processing. Like most other physiological systems, hearing abilities decline with age, hence, it is imperative to fully understand inner ear aging changes, so ion channel functions should be further investigated in the aging cochlea. In this review article, we discuss key various ion channels in the auditory system and how their functions change with age. Understanding the roles of ion channels in auditory processing could enhance the development of potential biotherapies for age-related hearing loss.

Unraveling of a Strongly Correlated Dynamical Network of Residues Controlling the Permeation of Potassium in KcsA Ion Channel

The complicated patterns of the single-channel currents in potassium ion channel KcsA are governed by the structural variability of the selectivity filter. A comparative analysis of the dynamics of the wild type KcsA channel and several of its mutants showing different conducting patterns was performed. A strongly correlated dynamical network of interacting residues is found to play a key role in regulating the state of the wild type channel. The network is centered on the aspartate D80 which plays the role of a hub by strong interacting via hydrogen bonds with residues E71, R64, R89, and W67. Residue D80 also affects the selectivity filter via its backbones. This network further compromises ions and water molecules located inside the channel that results in the mutual influence: the permeation depends on the configuration of residues in the network, and the dynamics of network's residues depends on locations of ions and water molecules inside the selectivity filter. Some features of the network provide a further understanding of experimental results describing the KcsA activity. In particular, the necessity of anionic lipids to be present for functioning the channel is explained by the interaction between the lipids and the arginine residues R64 and R89 that prevents destabilizing the structure of the selectivity filter.

Quantum-confined superfluid reactions

A helium atom superfluid was originally discovered by Kapitsa and Allen. Biological channels in such a fluid allow ultrafast molecule and ion transport, defined as a quantum-confined superfluid (QSF). In the process of enzymatic biosynthesis, unique performances can be achieved with high flux, 100% selectivity and low reaction activation energy at room temperature, under atmospheric pressure in an aqueous environment. Such reactions are considered as QSF reactions. In this perspective, we introduce the concept of QSF reactions in artificial systems. Through designing the channel size at the van der Waals equilibrium distance (r₀) for molecules or the Debye length (λ_D) for ions, and arranging the reactants orderly in the channel to satisfy symmetry-matching principles, QSF reactions in artificial systems can be realized with high flux, 100% selectivity and low reaction activation energy. Several types of QSF-like molecular reactions are summarized, including quantum-confined polymerizations, quasi-superfluid-based reactions and superfluid-based molecular reactions, followed by the discussion of QSF ion redox reactions. We envision in the future that chemical engineering, based on multi-step QSF reactions, and a tubular reactor with continuous nanochannel membranes taking advantage of high flux, high selectivity and low energy consumption, will replace the traditional tower reactor, and bring revolutionary technology to both chemistry and chemical engineering.

The concept of quantum-confined superfluid reactions is introduced into artificial systems, which is expected to be useful in future chemical engineering.

Quantum Mechanical Coherence of K+ Ion Wave Packets Increases Conduction in the KcsA Ion Channel

We simulate the transmission of K+ ions through the KcsA potassium ion channel filter region at physiological temperatures, employing classical molecular dynamics (MD) at the atomic scale together with a quantum mechanical version of MD simulation (QMD), treating single ions as quantum wave packets. We provide a direct comparison between both concepts, embedding the simulations into identical force fields and thermal fluctuations. The quantum simulations permit the estimation of coherence times and wave packet dispersions of a K+ ion over a range of 0.5 nm (a range that covers almost 50% of the filter domains longitudinal extension). We find that this observed extension of particle delocalization changes the mean orientation of the coordinating carbonyl oxygen atoms significantly, transiently suppressing their ‘caging action’ responsible for selective ion coordination. Compared to classical MD simulations, this particular quantum effect allows the K+ ions to ‘escape’ more easily from temporary binding sites provided by the surrounding filter atoms. To further elucidate the role of this observation for ion conduction rates, we compare the temporal pattern of single conduction events between classical MD and quantum QMD simulations at a femto-sec time scale. A finding from both approaches is that ion permeation follows a very irregular time pattern, involving flushes of permeation interrupted by non-conductive time intervals. However, as compared with classical behavior, the QMD simulation shortens non-conductive time by more than a half. As a consequence, and given the same force-fields, the QMD-simulated ion current appears to be considerably stronger as compared with the classical current. To bring this result in line with experimentally observed ion currents and the predictions based on Nernst–Planck theories, the conclusion is that a transient short time quantum behavior of permeating ions can successfully compromise high conduction rates with ion selectivity in the filter of channel proteins.

Medicinal Chemistry of Potassium Channel Modulators: An Update of Recent Progress (2011-2017)

BACKGROUND

Potassium (K+) channels participate in many physiological processes, cardiac function, cell proliferation, neuronal signaling, muscle contractility, immune function, hormone secretion, osmotic pressure, changes in gene expression, and are involved in critical biological functions, and in a variety of diseases. Potassium channels represent a large family of tetrameric membrane proteins. Potassium channels activation reduces excitability, whereas channel inhibition increases excitability.

OBJECTIVE

Small molecule K+ channel activators and inhibitors interact with voltage-gated, inward rectifying, and two-pore tandem potassium channels. Due to their involvement in biological functions, and in a variety of diseases, small molecules as potassium channel modulators have received great scientific attention.

METHODS

In this review, we have compiled the literature, patents and patent applications (2011 to 2017) related to different chemical classes of potassium channel openers and blockers as therapeutic agents for the treatment of various diseases. Many different chemical classes of selective small molecule have emerged as potassium channel modulators over the past years.

CONCLUSION

This review discussed the current understanding of medicinal chemistry research in the field of potassium channel modulators to update the key advances in this field.

Inactivation in the potassium channel KcsA

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C-type inactivation in potassium channels is a nearly universal regulatory mechanism.

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A major hypothesis states that C-type inactivation involves ion loss at the selectivity filter as an allosteric response to activation.

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NMR is used to probe protein conformational changes in response to pH and [K⁺], demonstrating that H⁺ and K⁺ binding are allosterically coupled in KcsA.

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The lipids are integrated parts of potassium channels in terms of structure, energetics and function.

Inactivation, the slow cessation of transmission after activation, is a general feature of potassium channels. It is essential for their function, and malfunctions in inactivation leads to numerous pathologies. The detailed mechanism for the C-type inactivation, distinct from the N-type inactivation, remains an active area of investigation. Crystallography, computational simulations, and NMR have greatly enriched our understanding of the process. Here we review the major hypotheses regarding C-type inactivation, particularly focusing on the key role played by NMR studies of the prokaryotic potassium channel KcsA, which serves as a good model for voltage gated mammalian channels.

Biochemical and physiological properties of K+ channel-associated AKR6A (Kvβ) proteins

Voltage-gated potassium (Kv) channels play an essential role in the regulation of membrane excitability and thereby control physiological processes such as cardiac excitability, neural communication, muscle contraction, and hormone secretion. Members of the Kv1 and Kv4 families are known to associate with auxiliary intracellular Kvβ subunits, which belong to the aldo-keto reductase superfamily. Electrophysiological studies have shown that these proteins regulate the gating properties of Kv channels. Although the three gene products encoding Kvβ proteins are functional enzymes in that they catalyze the nicotinamide adenine dinucleotide phosphate (NAD[P]H)-dependent reduction of a wide range of aldehyde and ketone substrates, the physiological role for these proteins and how each subtype may perform unique roles in coupling membrane excitability with cellular metabolic processes remains unclear. Here, we discuss current knowledge of the enzymatic properties of Kvβ proteins from biochemical studies with their described and purported physiological and pathophysiological influences.

Wettability and Applications of Nanochannels

Wettability in nanochannels is of great importance for understanding many challenging problems in interface chemistry and fluid mechanics, and presents versatile applications including mass transport, catalysis, chemical reaction, nanofabrication, batteries, and separation. Recently, both molecular dynamic simulations and experimental measurements have been employed to study wettability in nanochannels. Here, wettability in three types of nanochannels comprising 1D nanochannels, 2D nanochannels, and 3D nanochannels is summarized both theoretically and experimentally. The proposed concept of "quantum-confined superfluid" for ultrafast mass transport in nanochannels is first introduced, and the mostly studied 1D nanochannels are reviewed from molecular simulation to water wettability, followed by reversible switching of water wettability via external stimuli (temperature and voltage). Liquid transport and two confinement strategies in nanochannels of melt wetting and liquid wetting are also included. Then, molecular simulation, water wettability, liquid transport, and confinement in nanochannels are introduced for 2D nanochannels and 3D nanochannels, respectively. Based on the wettability in nanochannels, broad applications of various nanochannels are presented. Finally, the perspective for future challenges in the wettability and applications of nanochannels is discussed.

Hydrophobic gating in BK channels

The gating mechanism of transmembrane ion channels is crucial for understanding how these proteins control ion flow across membranes in various physiological processes. Big potassium (BK) channels are particularly interesting with large single-channel conductance and dual regulation by membrane voltage and intracellular Ca²⁺. Recent atomistic structures of BK channels failed to identify structural features that could physically block the ion flow in the closed state. Here, we show that gating of BK channels does not seem to require a physical gate. Instead, changes in the pore shape and surface hydrophobicity in the Ca²⁺-free state allow the channel to readily undergo hydrophobic dewetting transitions, giving rise to a large free energy barrier for K⁺ permeation. Importantly, the dry pore remains physically open and is readily accessible to quaternary ammonium channel blockers. The hydrophobic gating mechanism is also consistent with scanning mutagenesis studies showing that modulation of pore hydrophobicity is correlated with activation properties.

BK channels are regulated by membrane voltage and intracellular Ca2+ but the structural features that block the ion flow in the closed state remain unknown. Here authors use molecular dynamics simulation and show that a physical gate is not required; instead ion flow is regulated by hydrophobic dewetting due to changes in pore shape and surface hydrophobicity.

Modeling squid axon K+ channel by a nucleation and growth kinetic mechanism

A kinetic model accounting for all salient features of the K⁺ channel of the squid giant axon, including the rising phase of the ON gating charge and the Cole-Moore effect, is provided. Upon accounting for a significant feature distinguishing K⁺, Na⁺ and Ca²⁺ channels from channel-forming peptides modeled in our previous 2016 BBA paper, the nucleation-and-growth kinetic model developed therein is extended to simulate ON ionic and gating currents of the K⁺ channel of the squid giant axon at different depolarization potentials by the use of only two free parameters. K⁺ channel opening is considered to proceed by progressive aggregation of single subunits, while they are moving their gating charge outward under depolarizing conditions within their tetrameric structure; K⁺ channel closing proceeds in the opposite direction, by repolarization-induced disaggregation of subunits, accompanied by inward movement of their gating charge.

Molecular Dynamics Simulations of the Host Defense Peptide Temporin L and Its Q3K Derivative: An Atomic Level View from Aggregation in Water to Bilayer Perturbation

Temporin L (TempL) is a 13 residue Host Defense Peptide (HDP) isolated from the skin of frogs. It has a strong affinity for lipopolysaccharides (LPS), which is related to its high activity against Gram-negative bacteria and also to its strong tendency to neutralize the pro-inflammatory response caused by LPS release from inactivated bacteria. A designed analog with the Q3K substitution shows an enhancement in both these activities. In the present paper, Molecular Dynamics (MD) simulations have been used to investigate the origin of these improved properties. To this end, we have studied the behavior of the peptides both in water solution and in the presence of LPS lipid-A bilayers, demonstrating that the main effect through which the Q3K substitution improves the peptide activities is the destabilization of peptide aggregates in water.

Impact of geometry changes in the channel pore by the gating movements on the channel's conductance

Kv 1.2 are voltage-dependent potassium channels of great biological importance. Despite the existence of many reports considering structure - function relations of the Kv 1.2 channel's quantitative domains, some details of the voltage gating remain ambiguous, or even unknown. One of the examples is the range of the S4-S6 domains motions involved in channel activation and gating. Another important question is to what extent the channel geometry influences the observable channel conductance at different voltages, and what mechanism stands behind. Does the narrowing of the pore reduce the conductance by ohmic resistance growth? The answer is surprisingly negative. But it can be explained in an alternative way by considering the fluctuations. To address these problems, we formulate geometric models that mimic the generic features of voltage sensor movement and trigger the movement of the other domains involved in gating. We carry out a complete simulation of S4-S6 domains translations and tilts. The obtained pore profiles allow to estimate the (ohmic) conductance dependency on the voltage. From a family of analysed models, we choose the one most concurring with the experimental data. The results allow to suggest the most probable scenario of S4-S6 domains movement during channel activation by membrane depolarization.

Trk2 Potassium Transport System in Streptococcus mutans and Its Role in Potassium Homeostasis, Biofilm Formation, and Stress Tolerance

Potassium (K(+)) is the most abundant cation in the fluids of dental biofilm. The biochemical and biophysical functions of K(+) and a variety of K(+) transport systems have been studied for most pathogenic bacteria but not for oral pathogens. In this study, we establish the modes of K(+) acquisition in Streptococcus mutans and the importance of K(+) homeostasis for its virulence attributes. The S. mutans genome harbors four putative K(+) transport systems that included two Trk-like transporters (designated Trk1 and Trk2), one glutamate/K(+) cotransporter (GlnQHMP), and a channel-like K(+) transport system (Kch). Mutants lacking Trk2 had significantly impaired growth, acidogenicity, aciduricity, and biofilm formation. [K(+)] less than 5 mM eliminated biofilm formation in S. mutans. The functionality of the Trk2 system was confirmed by complementing an Escherichia coli TK2420 mutant strain, which resulted in significant K(+) accumulation, improved growth, and survival under stress. Taken together, these results suggest that Trk2 is the main facet of the K(+)-dependent cellular response of S. mutans to environment stresses.

IMPORTANCE

Biofilm formation and stress tolerance are important virulence properties of caries-causing Streptococcus mutans. To limit these properties of this bacterium, it is imperative to understand its survival mechanisms. Potassium is the most abundant cation in dental plaque, the natural environment of S. mutans. K(+) is known to function in stress tolerance, and bacteria have specialized mechanisms for its uptake. However, there are no reports to identify or characterize specific K(+) transporters in S. mutans. We identified the most important system for K(+) homeostasis and its role in the biofilm formation, stress tolerance, and growth. We also show the requirement of environmental K(+) for the activity of biofilm-forming enzymes, which explains why such high levels of K(+) would favor biofilm formation.

Electrochemical behavior of a membrane based on zirconium(iv) phosphoborate nanocomposite and its application in dye removal

A new hybrid ion-exchange membrane was prepared from a novel composite obtained by dispersion of polyaniline into an inorganic matrix of zirconium(iv) phosphoborate employing a sol–gel method.

Scorpion toxins prefer salt solutions

There is a wide variety of ion channel types with various types of blockers, making research in this field very complicated. To reduce this complexity, it is essential to study ion channels and their blockers independently. Scorpion toxins, a major class of blockers, are charged short peptides with high affinities for potassium channels. Their high selectivity and inhibitory properties make them an important pharmacological tool for treating autoimmune or nervous system disorders. Scorpion toxins typically have highly charged surfaces and-like other proteins-an intrinsic ability to bind ions (Friedman J Phys Chem B 115(29):9213-9223, 1996; Baldwin Biophys J 71(4):2056-2063, 1996; Vrbka et al. Proc Natl Acad Sci USA 103(42):15440-15444, 2006a; Vrbka et al. J Phys Chem B 110(13):7036-43, 2006b). Thus, their effects on potassium channels are usually investigated in various ionic solutions. In this work, computer simulations of protein structures were performed to analyze the structural properties of the key residues (i.e., those that are presumably involved in contact with the surfaces of the ion channels) of 12 scorpion toxins. The presence of the two most physiologically abundant cations, Na(+) and K(+), was considered. The results indicated that the ion-binding properties of the toxin residues vary. Overall, all of the investigated toxins had more stable structures in ionic solutions than in water. We found that both the number and length of elements in the secondary structure varied depending on the ionic solution used (i.e., in the presence of NaCl or KCl). This study revealed that the ionic solution should be chosen carefully before performing experiments on these toxins. Similarly, the influence of these ions should be taken into consideration in the design of toxin-based pharmaceuticals.

Focus on Kir7.1: physiology and channelopathy

Genetic studies have linked alterations in Kir7.1 channel to diverse pathologies. We summarize functional relevance of Kir7.1 channel in retinal pigment epithelium (RPE), regulation of channel function by various cytoplasmic metabolites, and mutations that cause channelopathies. At the apical membrane of RPE, K(+) channels contribute to subretinal K(+) homeostasis and support Na(+)/K(+) pump and Na(+)-K(+)-2Cl(-) cotransporter function by providing a pathway for K(+) secretion. Electrophysiological studies have established that barium- and cesium-sensitive inwardly rectifying K(+) (Kir) channels make up a major component of the RPE apical membrane K(+) conductance. Native human RPE expresses transcripts for Kir1.1, Kir2.1, Kir2.2, Kir3.1, Kir3.4, Kir4.2, and Kir6.1, albeit at levels at least 50-fold lower than Kir7.1. Kir7.1 is structurally similar to other Kir channels, consisting of 2 trans-membrane domains, a pore-forming loop that contains the selectivity filter, and 2 cytoplasmic polar tails. Within the cytoplasmic structure, clusters of amino acid sequences form regulatory domains that interact with cellular metabolites and control the opening and closing of the channel. Recent evidence indicated that intrinsic sequence motifs present in Kir7.1 control surface expression. Mutant Kir7.1 channels are associated with inherited eye pathologies such as Snowflake Vitreoretinal Degeneration (SVD) and Lebers Congenital Amaurosis (LCA16). Based on the current evidence, mutations implicated in channelopathies have the potential to be used for genetic testing to diagnose blindness due to Kir7.1.

Structure of potassium channels

Potassium channels ubiquitously exist in nearly all kingdoms of life and perform diverse but important functions. Since the first atomic structure of a prokaryotic potassium channel (KcsA, a channel from Streptomyces lividans) was determined, tremendous progress has been made in understanding the mechanism of potassium channels and channels conducting other ions. In this review, we discuss the structure of various kinds of potassium channels, including the potassium channel with the pore-forming domain only (KcsA), voltage-gated, inwardly rectifying, tandem pore domain, and ligand-gated ones. The general properties shared by all potassium channels are introduced first, followed by specific features in each class. Our purpose is to help readers to grasp the basic concepts, to be familiar with the property of the different domains, and to understand the structure and function of the potassium channels better.

A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation

Electrophysiological studies have established that the permeation of Ba(2+) ions through the KcsA K(+)-channel is impeded by the presence of K(+) ions in the external solution, while no effect is observed for external Na(+) ions. This Ba(2+) "lock-in" effect suggests that at least one of the external binding sites of the KcsA channel is thermodynamically selective for K(+). We used molecular dynamics simulations to interpret these lock-in experiments in the context of the crystallographic structure of KcsA. Assuming that the Ba(2+) is bound in site S(2) in the dominant blocked state, we examine the conditions that could impede its translocation and cause the observed "lock-in" effect. Although the binding of a K(+) ion to site S(1) when site S(2) is occupied by Ba(2+) is prohibitively high in energy (>10 kcal/mol), binding to site S0 appears to be more plausible (ΔG > 4 kcal/mol). The 2D potential of mean force (PMF) for the simultaneous translocation of Ba(2+) from site S(2) to site S(1) and of a K(+) ion on the extracellular side shows a barrier that is consistent with the concept of external lock-in. The barrier opposing the movement of Ba(2+) is very high when a cation is in site S(0), and considerably smaller when the site is unoccupied. Furthermore, free energy perturbation calculations show that site S(0) is selective for K(+) by 1.8 kcal/mol when S(2) is occupied by Ba(2+). However, the same site S(0) is nonselective when site S(2) is occupied by K(+), which shows that the presence of Ba(2+) affects the selectivity of the pore. A theoretical framework within classical rate theory is presented to incorporate the concentration dependence of the external ions on the lock-in effect.

Evolution of the genetic code by incorporation of amino acids that improved or changed protein function

Fifty years have passed since the genetic code was deciphered, but how the genetic code came into being has not been satisfactorily addressed. It is now widely accepted that the earliest genetic code did not encode all 20 amino acids found in the universal genetic code as some amino acids have complex biosynthetic pathways and likely were not available from the environment. Therefore, the genetic code evolved as pathways for synthesis of new amino acids became available. One hypothesis proposes that early in the evolution of the genetic code four amino acids-valine, alanine, aspartic acid, and glycine-were coded by GNC codons (N = any base) with the remaining codons being nonsense codons. The other sixteen amino acids were subsequently added to the genetic code by changing nonsense codons into sense codons for these amino acids. Improvement in protein function is presumed to be the driving force behind the evolution of the code, but how improved function was achieved by adding amino acids has not been examined. Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used. The improved or altered protein function afforded by the changes in amino acid function provided the selective advantage underlying the expansion of the genetic code. Analysis of amino acid properties and functions explains why amino acids are found in their respective positions in the genetic code.

Relation between sequence and structure in membrane proteins

MOTIVATION

Integral polytopic membrane proteins contain only two types of folds in their transmembrane domains: α-helix bundles and β-barrels. The increasing number of available crystal structures of these proteins permits an initial estimation of how sequence variability affects the structure conservation in their transmembrane domains. We, thus, aim to determine the pairwise sequence identity necessary to maintain the transmembrane molecular architectures compatible with the hydrophobic nature of the lipid bilayer.

RESULTS

Root-mean-square deviation (rmsd) and sequence identity were calculated from the structural alignments of pairs of homologous polytopic membrane proteins sharing the same fold. Analysis of these data reveals that transmembrane segment pairs with sequence identity in the so-called 'twilight zone' (20-35%) display high-structural similarity (rmsd < 1.5 Å). Moreover, a large group of β-barrel pairs with low-sequence identity (<20%) still maintain a close structural similarity (rmsd < 2.5 Å). Thus, we conclude that fold preservation in transmembrane regions requires less sequence conservation than for globular proteins. These findings have direct implications in homology modeling of evolutionary-related membrane proteins.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Stimulatory effect of xenobiotics on oxidative electron transport of chemolithotrophic nitrifying bacteria used as biosensing element

Electron transport chain (ETCh) of ammonium (AOB) and nitrite oxidizing bacteria (NOB) participates in oxidation of ammonium to nitrate (nitrification). Operation of ETCh may be perturbed by a range of water-soluble xenobiotics. Therefore, consortia of nitrifying bacteria may be used as a biosensor to detect water contamination. A surprising feature of this system is an increase of oxygen consumption, detected in the presence of certain inhibitors of ETCh. Thus, to shed light on the mechanism of this effect (and other differences between inhibitors) we monitored separately respiration of the bacteria of the first (AOB - Nitrosomonas) and second (NOB -Nitrobacter) stages of nitrification. Furthermore, we measured plasma membrane potential and the level of reduction of NAD(P)H. We propose a novel model of ETCh in NOB to explain the role of reverse electron transport in the stimulation of oxygen consumption (previously attributed to hormesis).

Multiscale molecular dynamics simulations of membrane proteins

The time and length scales accessible by biomolecular simulations continue to increase. This is in part due to improvements in algorithms and computing performance, but is also the result of the emergence of coarse-grained (CG) potentials, which complement and extend the information obtainable from fully detailed models. CG methods have already proven successful for a range of applications that benefit from the ability to rapidly simulate spontaneous self-assembly within a lipid membrane environment, including the insertion and/or oligomerization of a range of "toy models," transmembrane peptides, and single- and multi-domain proteins. While these simplified approaches sacrifice atomistic level detail, it is now straightforward to "reverse map" from CG to atomistic descriptions, providing a strategy to assemble membrane proteins within a lipid environment, prior to all-atom simulation. Moreover, recent developments have been made in "dual resolution" techniques, allowing different molecules in the system to be modeled with atomistic or CG resolution simultaneously.

Identification of blocker binding site in mouse TRESK by molecular modeling and mutational studies

TWIK (tandem-pore domain weak inward rectifying K(+))-related spinal cord K(+) channel, TRESK, a member of the tandem-pore domain K(+) channel family, is the most recently cloned K(2P) channel. TRESK is highly expressed in dorsal root ganglion neuron, a pain sensing neuron, which is a target for analgesics. In this study, a reliable 3D structure for transmembrane (TM) region of mouse TRESK (mTRESK) was constructed, and then the reasonable blocker binding mode of the protein was investigated. The 3D structure of the mTRESK built by homology modeling method was validated with recommend value of stereochemical quality. Based on the validated structure, K(+) channel blocker-bound conformation was obtained by molecular docking and 5ns MD simulation with DPPC lipid bilayer. Our docking study provides the plausible binding mode of known blockers with key interacting residues, especially, F156 and F364. Finally, these modeling results were verified by experimental study with mutation from phenylalanine to alanine (F156A, F364A and F156A/F364A) at the TM2 and TM4. This is the first modeling study for TRESK that can provide structural information of the protein including ligand binding information. These results can be useful in structure based drug design for finding new blockers of the TRESK as potential therapeutic target of pain treatment.

Mechanism of function of viral channel proteins and implications for drug development

Viral channel-forming proteins comprise a class of viral proteins which, similar to their host companions, are made to alter electrochemical or substrate gradients across lipid membranes. These proteins are active during all stages of the cellular life cycle of viruses. An increasing number of proteins are identified as channel proteins, but the precise role in the viral life cycle is yet unknown for the majority of them. This review presents an overview about these proteins with an emphasis on those with available structural information. A concept is introduced which aligns the transmembrane domains of viral channel proteins with those of host channels and toxins to give insights into the mechanism of function of the viral proteins from potential sequence identities. A summary of to date investigations on drugs targeting these proteins is given and discussed in respect of their mode of action in vivo.

The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke "design creationism" to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane's hydrophobic/philic nature; a selective "pore" for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the "jackprot," which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation http://faculty.rwu.edu/cbai/JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the "jackprot," or highest-fitness complete-peptide sequence, required cumulative smaller "wins" (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons ("jackdons" that led to "jackacids" that led to the "jackprot"). The "jackprot" is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide "edition" and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists.

Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures

Atomic positions obtained by X-ray crystallography are time and space averages over many molecules in the crystal. Importantly, interatomic distances, calculated between such average positions and frequently used in structural and mechanistic analyses, can be substantially different from the more appropriate time-average and ensemble-average interatomic distances. Using crystallographic B-factors, one can deduce corrections, which have so far been applied exclusively to small molecules, to obtain correct average distances as a function of the type of atomic motion. Here, using 4774 high-quality protein X-ray structures, we study the significance of such corrections for different types of atomic motion. Importantly, we show that for distances shorter than 5 Å, corrections greater than 0.5 Å may apply, especially for noncorrelated or anticorrelated motion. For example, 14% of the studied structures have at least one pair of atoms with a correction of ≥0.5 Å in the case of noncorrelated motion. Using molecular dynamics simulations of villin headpiece, ubiquitin, and SH3 domain unit cells, we demonstrate that the majority of average interatomic distances in these proteins agree with noncorrelated corrections, suggesting that such deviations may be truly relevant. Importantly, we demonstrate that the corrections do not significantly affect stereochemistry and the overall quality of final refined X-ray structures, but can provide marked improvements in starting unrefined models obtained from low-resolution X-ray data. Finally, we illustrate the potential mechanistic and biological significance of the calculated corrections for KcsA ion channel and show that they provide indirect evidence that motions in its selectivity filter are highly correlated.

Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides

Since their initial discovery, 30 years ago, antimicrobial peptides (AMPs) have been intensely investigated as a possible solution to the increasing problem of drug-resistant bacteria. The interaction of antimicrobial peptides with the cellular membrane of bacteria is the key step of their mechanism of action. Fluorescence spectroscopy can provide several structural details on peptide-membrane systems, such as partition free energy, aggregation state, peptide position and orientation in the bilayer, and the effects of the peptides on the membrane order. However, these "low-resolution" structural data are hardly sufficient to define the structural requirements for the pore formation process. Molecular dynamics simulations, on the other hand, provide atomic-level information on the structure and dynamics of the peptide-membrane system, but they need to be validated experimentally. In this review we summarize the information that can be obtained by both approaches, highlighting their versatility and complementarity, suggesting that their synergistic application could lead to a new level of insight into the mechanism of membrane destabilization by AMPs.

Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels

Biological ion channels rely on a multi-ion transport mechanism for fast yet selective permeation of ions. The crystal structure of the KcsA potassium channel provided the first microscopic picture of this process. A similar mechanism is assumed to operate in all potassium channels, but the validity of this assumption has not been well investigated. Here, we examine the energetics of ion permeation in Shaker Kv1.2 and KcsA channels, which exemplify the six-transmembrane voltage-gated and two-transmembrane inward-rectifier channels. We study the feasibility of binding a third ion to the filter and the concerted motion of ions in the channel by constructing the potential of mean force for K(+) ions in various configurations. For both channels, we find that a pair of K(+) ions can move almost freely within the filter, but a relatively large free-energy barrier hinders the K(+) ion from stepping outside the filter. We discuss the effect of the CMAP dihedral energy correction that was recently incorporated into the CHARMM force field on ion permeation dynamics.

Chronic deficit in the expression of voltage-gated potassium channel Kv3.4 subunit in the hippocampus of pilocarpine-treated epileptic rats

Voltage gated K(+) channels (Kv) are a highly diverse group of channels critical in determining neuronal excitability. Deficits of Kv channel subunit expression and function have been implicated in the pathogenesis of epilepsy. In this study, we investigate whether the expression of the specific subunit Kv3.4 is affected during epileptogenesis following pilocarpine-induced status epilepticus. For this purpose, we used immunohistochemistry, Western blotting assays and comparative analysis of gene expression using TaqMan-based probes and delta-delta cycle threshold (ΔΔCT) method of quantitative real-time polymerase chain reaction (qPCR) technique in samples obtained from age-matched control and epileptic rats. A marked down-regulation of Kv3.4 immunoreactivity was detected in the stratum lucidum and hilus of dentate gyrus in areas corresponding to the mossy fiber system of chronically epileptic rats. Correspondingly, a 20% reduction of Kv3.4 protein levels was detected in the hippocampus of chronic epileptic rats. Real-time quantitative PCR analysis of gene expression revealed that a significant 33% reduction of transcripts for Kv3.4 (gene Kcnc4) occurred after 1 month of pilocarpine-induced status epilepticus and persisted during the chronic phase of the model. These data indicate a reduced expression of Kv3.4 channels at protein and transcript levels in the epileptic hippocampus. Down-regulation of Kv3.4 in mossy fibers may contribute to enhanced presynaptic excitability leading to recurrent seizures in the pilocarpine model of temporal lobe epilepsy.

Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes

Potassium (K(+)) channels are specialized membrane proteins that are able to facilitate and regulate the conduction of K(+) through cell membranes. Comprising five specific cation binding sites (S(0)-S(4)) formed by the backbone carbonyl groups of conserved residues common to all K(+) channels, the narrow selectivity filter allows fast conduction of K(+) while being highly selective for K(+) over Na(+). To extend our knowledge of the microscopic mechanism underlying selectivity in K(+) channels, we characterize the free energy landscapes governing the entry and translocation of a Na(+) or a K(+) from the extracellular side into the selectivity filter of KcsA. The entry process of an extracellular ion is examined in the presence of two additional K(+) in the pore, and the three-ion potential of mean force is computed using extensive all-atom umbrella sampling molecular dynamics simulations. A comparison of the potentials of mean force yields a number of important results. First, the free energy minima corresponding to configurations with extracellular K(+) or Na(+) in binding site S(0) or S(1) are similar in depth, suggesting that the thermodynamic selectivity governed by the free energy minima for those two binding sites is insignificant. Second, the free energy barriers between stable multi-ion configurations are generally higher for Na(+) than for K(+), implying that the kinetics of ion conduction is slower when a Na(+) enters the pore. Third, the region corresponding to binding site S(2) near the center of the narrow pore emerges as the most selective for K(+) over Na(+). In particular, while there is a stable minimum for K(+) in site S(2), Na(+) faces a steep free energy increase with no local free energy well in this region. Lastly, analysis shows that selectivity is not correlated with the overall coordination number of the ion entering the pore, but is predominantly affected by changes in the type of coordinating ligands (carbonyls versus water molecules). These results further highlight the importance of the central region near binding site S(2) in the selectivity filter of K(+) channels.

Retigabine: bending potassium channels to our will

The New Anticonvulsant Retigabine Favors Voltage-dependent Opening of the Kv7.2 (KCNQ2) Channel by Binding to Its Activation Gate

Wuttke TV, Seebohm G, Bail S, Maljevic S, Lerche H

Mol Pharmacol 2005;67:1009–1017

Retigabine (RTG) is an anticonvulsant drug with a novel mechanism of action. It activates neuronal KCNQ-type K+ channels by inducing a large hyperpolarizing shift of steady-state activation. To identify the structural determinants of KCNQ channel activation by RTG, we constructed a set of chimeras by using the neuronal KV7.2 ( KCNQ2) channel, which is activated by RTG, and the cardiac KV7.1 ( KCNQ1) channel, which is not affected by this drug. Substitution of either the S5 or the S6 segment in KV7.2 by the respective parts of KV7.1 led to a complete loss of activation by RTG. Trp236 in the cytoplasmic part of S5 and the conserved Gly301 in S6 (KV7.2), considered as the gating hinge (Ala336 in KV7.1), were found to be crucial for the RTG effect: mutation of these residues could either knock out the effect in KV7.2 or restore it partially in KV7.1/KV7.2 chimeras. We propose that RTG binds to a hydrophobic pocket formed upon channel opening between the cytoplasmic parts of S5 and S6 involving Trp236 and the channel's gate, which could well explain the strong shift in voltage-dependent activation.

Prestin forms oligomer with four mechanically independent subunits

Prestin is the motor protein of cochlear outer hair cells (OHCs) with the unique capability of performing direct, rapid, and reciprocal electromechanical conversion. Prestin consists of 744 amino acids with a molecular mass of approximately 81.4 kDa. The predicted membrane topology and molecular mass of a single prestin molecule appear inadequate to account for the size of intramembrane particles (IMPs) expressed in the OHC membrane. Although recent biochemical evidence suggests that prestin forms homo-oligomers, most likely as a tetramer, the oligomeric structure of prestin in OHCs remains unclear. We obtained the charge density of prestin in the gerbil OHCs by measuring their nonlinear capacitance (NLC). The average charge density (22,608 microm(-2) measured was four times the average IMP density (5686 microm(-2) reported in the freeze-fracture study. This suggests that each IMP contains four prestin molecules, based on the general notion that each prestin transfers a single elementary charge. We subsequently compared the voltage dependency and the values of slope factor of NLC and somatic motility simultaneously measured from the same OHCs to determine whether NLC and motility are fully coupled and how prestin subunits function within the tetramer. We showed that the voltage dependency and slope factors of NLC and motility were not statistically different, suggesting that NLC and motility are fully coupled. The fact that the slope factor is the same between NLC and motility suggests that each prestin monomer in the tetramer is in parallel, each interacting independently with cytoplasmic or other partners to facilitate the mechanical response.

Threonine at position 306 of the KAT1 potassium channel is essential for channel activity and is a target site for ABA-activated SnRK2/OST1/SnRK2.6 protein kinase

The Arabidopsis thaliana K+ channel KAT1 has been suggested to have a key role in mediating the aperture of stomata pores on the surface of plant leaves. Although the activity of KAT1 is thought to be regulated by phosphorylation, the endogenous pathway and the primary target site for this modification remained unknown. In the present study, we have demonstrated that the C-terminal region of KAT1 acts as a phosphorylation target for the Arabidopsis calcium-independent ABA (abscisic acid)-activated protein kinase SnRK2.6 (Snf1-related protein kinase 2.6). This was confirmed by LC-MS/MS (liquid chromatography tandem MS) analysis, which showed that Thr306 and Thr308 of KAT1 were modified by phosphorylation. The role of these specific residues was examined by single point mutations and measurement of KAT1 channel activities in Xenopus oocyte and yeast systems. Modification of Thr308 had minimal effect on KAT1 activity. On the other hand, modification of Thr306 reduced the K+ transport uptake activity of KAT1 in both systems, indicating that Thr306 is responsible for the functional regulation of KAT1. These results suggest that negative regulation of KAT1 activity, required for stomatal closure, probably occurs by phosphorylation of KAT1 Thr306 by the stress-activated endogenous SnRK2.6 protein kinase.