Structural Plasticity Is a Feature of Rheostat Positions in the Human Na+/Taurocholate Cotransporting Polypeptide (NTCP)

In the Na⁺/taurocholate cotransporting polypeptide (NTCP), the clinically relevant S267F polymorphism occurs at a “rheostat position”. That is, amino acid substitutions at this position (“S267X”) lead to a wide range of functional outcomes. This result was particularly striking because molecular models predicted the S267X side chains are buried, and thus, usually expected to be less tolerant of substitutions. To assess whether structural tolerance to buried substitutions is widespread in NTCP, here we used Rosetta to model all 19 potential substitutions at another 13 buried positions. Again, only subtle changes in the calculated stabilities and structures were predicted. Calculations were experimentally validated for 19 variants at codon 271 (“N271X”). Results showed near wildtype expression and rheostatic modulation of substrate transport, implicating N271 as a rheostat position. Notably, each N271X substitution showed a similar effect on the transport of three different substrates and thus did not alter substrate specificity. This differs from S267X, which altered both transport kinetics and specificity. As both transport and specificity may change during protein evolution, the recognition of such rheostat positions may be important for evolutionary studies. We further propose that the presence of rheostat positions is facilitated by local plasticity within the protein structure. Finally, we note that identifying rheostat positions may advance efforts to predict new biomedically relevant missense variants in NTCP and other membrane transport proteins.     

A 2.7-V 900-MHz CMOS LNA and mixer

A CMOS low-noise amplifier (LNA) and a mixer for RF front-end applications are described. A current reuse technique is described that increases amplifier transconductance for the LNA and mixer without increasing power dissipation, compared to standard topologies. At 900 MHz, the LNA minimum noise figure (NF) is 1.9 dB, input third-order intercept point (IIP3) is -3.2 dBm and forward gain is 15.6 dB. With a 1-GHz local oscillator (LO) and a 900-MHz RF input, the mixer minimum double sideband noise figure (DSB NF) is 5.8 dB, IIP3 is -4.1 dBm, and power conversion gain is 8.8 dB. The LNA and mixer, respectively, consume 20 mW and 7 mW from a 2.7 V power supply. The active areas of the LNA and mixer are 0.7 mm×0.4 mm and 0.7 mm×0.2 mm, respectively. The prototypes were fabricated in a 0.5-μm CMOS process     

A high-frequency fully differential BiCMOS operational amplifier

A high-frequency fully differential BiCMOS operational amplifier design for use in switched-capacitor circuits is presented. The operational amplifier is integrated in a 3.0-GHz, 2-μm BiCMOS process with an active die area of 1.0 mm×1.2 mm. This BiCMOS op amp offers an infinite input resistance, a DC gain of 100 dB, a unity-gain frequency of 90 MHz with 45° phase margin, and a slew rate of 150 V/μs. The differential output range is 12 V. The circuit is operated from a ±5-V power supply and dissipates 125 mW. The op amp is unity-gain stable with 7 pF of capacitive loading at each output. The op amp is a two-stage, pole-split frequency compensated design that uses a PMOS input stage for infinite input resistance and an n-p-n bipolar second stage for high gain and high bandwidth. The frequency compensation network serves both the differential- and common-mode amplifiers so the differential- and common-mode amplifier dynamics are similar. A dynamic switched-capacitor common-mode feedback scheme is used to set the output common-mode level of the first and second stages     

A 15-b 1-Msample/s digitally self-calibrated pipeline ADC

A 15-b 1-Msample/s digitally self-calibrated pipeline analog-to-digital converter (ADC) is presented. A radix 1.93, 1 b per stage design is employed. The digital self-calibration accounts for capacitor mismatch, comparator offset, charge injection, finite op-amp gain, and capacitor nonlinearity contributing to DNL. A THD of -90 dB was measured with a 9.8756-kHz sine-wave input. The DNL was measured to be within ±0.25 LSB at 15 b, and the INL was measured to be within ±1.25 LSB at 15 b. The die area is 9.3 mm×8.3 mm and operates on ±4-V power supply with 1.8-W power dissipation. The ADC is fabricated in an 11-V, 4-GHz, 2.4-μm BiCMOS process     

A 2.7-V 300-MS/s track-and-hold amplifier

A fully differential bipolar track-and-hold amplifier (THA) employs an open-loop linearization technique compatible with low supply voltage. A feedthrough reduction method utilizes the junction capacitance of a replica switch to provide a close match to the junction capacitance of the main switch. The differential full-scale (FS) input range is 0.5 V. In the track mode, with f_in=10 MHz, FS sinewave input, the measured total harmonic distortion (THD) is less than -72 dB. With f_s=300 MS/s and f_in=10-50 MHz, FS sinewave input, the measured THD is less than -65 dB. This THD measurement reflects the held values as well as the tracking components of the output waveform. With f_s<10 MS/s and f_in=10-50 MHz, FS sinewave input, the measured feedthrough is less than -60 dB. The hold capacitance is 2.5 pF and the differential droop rate is 16 mV/μs. The THA consumes 32 mW from a 2.7-V power supply and is fabricated in a 0.5-μm, 18-GHz BiCMOS process     

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology

We describe the Multiscale Modeling Tools for Structural Biology (MMTSB) Tool Set (https://mmtsb.scripps.edu/software/mmtsbToolSet.html), which is a novel set of utilities and programming libraries that provide new enhanced sampling and multiscale modeling techniques for the simulation of proteins and nucleic acids. The tool set interfaces with the existing molecular modeling packages CHARMM and Amber for classical all-atom simulations, and with MONSSTER for lattice-based low-resolution conformational sampling. In addition, it adds new functionality for the integration and translation between both levels of detail. The replica exchange method is implemented to allow enhanced sampling of both the all-atom and low-resolution models. The tool set aims at applications in structural biology that involve protein or nucleic acid structure prediction, refinement, and/or extended conformational sampling. With structure prediction applications in mind, the tool set also implements a facility that allows the control and application of modeling tasks on a large set of conformations in what we have termed ensemble computing. Ensemble computing encompasses loosely coupled, parallel computation on high-end parallel computers, clustered computational grids and desktop grid environments. This paper describes the design and implementation of the MMTSB Tool Set and illustrates its utility with three typical examples--scoring of a set of predicted protein conformations in order to identify the most native-like structures, ab initio folding of peptides in implicit solvent with the replica exchange method, and the prediction of a missing fragment in a larger protein structure.     

Using soft computing to define standards of care in glaucoma monitoring

A fuzzy knowledge base encapsulating core expert rules for glaucoma follow up is developed and subsequently refined into a standard of care by reconciling several expert opinions. The Learning from Examples (LFE) [1] technique is used in addition to expert interviews to generate fuzzy rules from numerical data, and soft competition defines a fuzzy consensus metrics for the expert opinions. Web-based extension of this system into a comprehensive set of e-Health services for the glaucoma community enables, besides wide accessibility of the expert knowledge, continuous improvement of the core rule set (standard of care) with the perspectives of several experts.This work is funded under Collaborative Health Research Project Grant by the National Science and Engineering Research Council (NSERC) of Canada. We gratefully acknowledge the contributions of TransferTech GmbH Germany(www.Transfertech.de) with their soft computing software suite as well as their valuable insights in solving the implementation challenges we are faced with constantly.