Relevance of Lysine Snorkeling in the Outer Transmembrane Domain of Small Viral Potassium Ion Channels

Transmembrane domains (TMDs) are often flanked by Lys or Arg because they keep their aliphatic parts in the bilayer and their charged groups in the polar interface. Here we examine the relevance of this so-called “snorkeling” of a cationic amino acid, which is conserved in the outer TMD of small viral K+ channels. Experimentally, snorkeling activity is not mandatory for KcvPBCV-1 because K29 can be replaced by most of the natural amino acids without any corruption of function. Two similar channels, KcvATCV-1 and KcvMT325, lack a cytosolic N-terminus, and neutralization of their equivalent cationic amino acids inhibits their function. To understand the variable importance of the cationic amino acids, we reanalyzed molecular dynamics simulations of KcvPBCV-1 and N-terminally truncated mutants; the truncated mutants mimic KcvATCV-1 and KcvMT325. Structures were analyzed with respect to membrane positioning in relation to the orientation of K29. The results indicate that the architecture of the protein (including the selectivity filter) is only weakly dependent on TMD length and protonation of K29. The penetration depth of Lys in a given protonation state is independent of the TMD architecture, which leads to a distortion of shorter proteins. The data imply that snorkeling can be important for K+ channels; however, its significance depends on the architecture of the entire TMD. The observation that the most severe N-terminal truncation causes the outer TMD to move toward the cytosolic side suggests that snorkeling becomes more relevant if TMDs are not stabilized in the membrane by other domains

Relevance of Lysine Snorkeling in the Outer Transmembrane Domain of Small Viral Potassium Ion Channels

Transmembrane domains (TMDs) are often flanked by Lys or Arg because they keep their aliphatic parts in the bilayer and their charged groups in the polar interface. Here we examine the relevance of this so-called “snorkeling” of a cationic amino acid, which is conserved in the outer TMD of small viral K+ channels. Experimentally, snorkeling activity is not mandatory for KcvPBCV-1 because K29 can be replaced by most of the natural amino acids without any corruption of function. Two similar channels, KcvATCV-1 and KcvMT325, lack a cytosolic N-terminus, and neutralization of their equivalent cationic amino acids inhibits their function. To understand the variable importance of the cationic amino acids, we reanalyzed molecular dynamics simulations of KcvPBCV-1 and N-terminally truncated mutants; the truncated mutants mimic KcvATCV-1 and KcvMT325. Structures were analyzed with respect to membrane positioning in relation to the orientation of K29. The results indicate that the architecture of the protein (including the selectivity filter) is only weakly dependent on TMD length and protonation of K29. The penetration depth of Lys in a given protonation state is independent of the TMD architecture, which leads to a distortion of shorter proteins. The data imply that snorkeling can be important for K+ channels; however, its significance depends on the architecture of the entire TMD. The observation that the most severe N-terminal truncation causes the outer TMD to move toward the cytosolic side suggests that snorkeling becomes more relevant if TMDs are not stabilized in the membrane by other domains

A comprehensive update on the potential of curcumin to enhance chemosensitivity in colorectal cancer

Colorectal cancer (CRC) is one of the most common cancers and a major cause of cancer-related mortality worldwide. The efficacy of chemotherapy agents in CRC treatment is often limited due to toxic side effects, heterogeneity of cancer cells, and the possibility of chemoresistance which promotes cancer cell survival through several mechanisms. Combining chemotherapy agents with natural compounds like curcumin, a polyphenol compound from the Curcuma longa plant, has been reported to overcome chemoresistance and increase the sensitivity of cancer cells to chemotherapeutics. Curcumin, alone or in combination with chemotherapy agents, has been demonstrated to prevent chemoresistance by modulating various signaling pathways, reducing the expression of drug resistance-related genes. The purpose of this article is to provide a comprehensive update on studies that have investigated the ability of curcumin to enhance the efficacy of chemotherapy agents used in CRC. It is hoped that it can serve as a template for future research on the efficacy of curcumin, or other natural compounds, combined with chemotherapy agents to maximize the effectiveness of therapy and reduce the side effects that occur in CRC or other cancers

Computational study of the Kcv potassium channel

The K+ channel Kcv from Paramecium bursaria chlorella virus is the smallest known functional K+ channel. As a minimal working model, this K+ channel protein can be considered close to being prototypical in order to understand basic channel design principles and to gain insight into fundamental transport mechanisms. The objective of this work was the computational study of the impact of various mutations of the Kcv N-Terminus on the Kcv function. By the mean of molecular dynamics simulations of K+ channel models in explicit membrane and explicit solvent, the structure, dynamics, and thermodynamics of alternate model systems was examined on the atomic level. In addition to the wildtype, a hyperactive point mutant (KcvP13A) and two inactive deletion mutants (KcvDN8 and KcvDN14) were examined. The protonation state of a key amino acid (Lys29) was also exhaustingly studied. As a working hypothesis it was assumed that analog topology results in analog functionality. Hence, Kcv homology models were generated as well as KirBac1.1 X-ray structure models adapted in analogy to Kcv. A new method was developed in order to extract reasonable and symmetric expectation structures from very long trajectories. These structures can be compared to structures determined by structural biological methods and can be used as an input for proceeding with advanced methods, like e.g. the Poisson-Boltzmann theory or the 3D-RISM integral equation theory. Latter method was used in order to determin the ionic distribution around the protein. Most important results from this thesis are: 1. A workflow was developed that allows the creation of plausible K+ channel homology models. The quality of such a model is good enough to exhibit a full ion transition cycle during simulation. 2. The interaction of positively charged amino acids in the N-terminal helix with the C-terminus results in mutant dependent saltbridge patterns. Weakening of this interaction correlates with dysfuntion. 3. The N-terminus can act as a steric barrier for the transition of K+ ions and, thus, may contribute to the gating mechanism. 4. The protonation state of Lys29 is crutial for the transition of K+ ions and, thus, may also contribute to the gating mechanism. 5. Funtional analogy between distantly related K+ channels is apparent. 6. The reason for the hyperactivity of the point mutant P13A was not determined satisfactorily. Further investigations are necessary in order to generate more plausible models

Salt bridges in the miniature viral channel Kcv are important for function.

The viral potassium channel Kcv comprises only 94 amino acids, which represent the pore module of more complex K(+) channels. As for Kir-type channels, Kcv also has a short N-terminal helix exposed to the cytoplasm, upstream of the first transmembrane domain. Here we show that this helix is relevant for Kcv function. The presence of charged amino acids, which form dynamic inter- and intra-subunit salt bridges is crucial. Electrophysiological measurements, yeast rescue experiments and molecular dynamics simulations show that mutants in which the critical salt bridge formation is impaired have no or reduced channel activity. We conclude that these salt bridges destabilise the complexation of K(+) ions by negative charges on the inner transmembrane domain at the entrance into the cavity. This feature facilitates a continuous and coordinated transfer of ions between the cavity and the cytoplasm for channels without the canonical bundle crossing