Chemically accurate protein structures: Validation of protein NMR structures by comparison of measured and predicted pK a values

A new method is presented for evaluating the quality of protein structures obtained by NMR. This method exploits the dependence between measurable chemical properties of a protein, namely pK _a values of acidic residues, and protein structure. The accurate and fast empirical computational method employed by the PROPKA program () allows the user to test the ability of a given structure to reproduce known pK _a values, which in turn can be used as a criterion for the selection of more accurate structures. We demonstrate the feasibility of this novel idea for a series of proteins for which both␣NMR and X-ray structures, as well as pK _a values of all ionizable residues, have been determined. For the 17 NMR ensembles used in this study, this criterion is shown effective in the elimination of a large number of NMR structure ensemble members.     

Resistance training vs. static stretching: effects on flexibility and strength

Morton, SK, Whitehead, JR, Brinkert, RH, and Caine, DJ. Resistance training vs. static stretching: Effects on flexibility and strength. J Strength Cond Res 25(12): 3391-3398, 2011-The purpose of this study was to determine how full-range resistance training (RT) affected flexibility and strength compared to static stretching (SS) of the same muscle-joint complexes in untrained adults. Volunteers (n = 25) were randomized to an RT or SS training group. A group of inactive volunteers (n = 12) served as a convenience control group (CON). After pretesting hamstring extension, hip flexion and extension, shoulder extension flexibility, and peak torque of quadriceps and hamstring muscles, subjects completed 5-week SS or RT treatments in which the aim was to stretch or to strength train the same muscle-joint complexes over similar movements and ranges. Posttests of flexibility and strength were then conducted. There was no difference in hamstring flexibility, hip flexion, and hip extension improvement between RT and SS, but both were superior to CON values. There were no differences between groups on shoulder extension flexibility. The RT group was superior to the CON in knee extension peak torque, but there were no differences between groups on knee flexion peak torque. The results of this preliminary study suggest that carefully constructed full-range RT regimens can improve flexibility as well as the typical SS regimens employed in conditioning programs. Because of the potential practical significance of these results to strength and conditioning programs, further studies using true experimental designs, larger sample sizes, and longer training durations should be conducted with the aim of confirming or disproving these results.     

Dry-land strength training vs. electrical stimulation in sprint swimming performance

This study was undertaken to compare the effects of dry-land strength training vs. an electrical stimulation program on swimmers. Twenty-four national-level swimmers were randomly assigned to 3 groups: the dry-land strength training program (S), the electrical stimulation training program (ES), and the control (C) group. The training program lasted 4 weeks. The subjects were evaluated before the training, at the end of the training program, and 4 weeks later. The outcome values ascertained were peak torque during arm extension at different velocities (from -60 to 180°·s(-1)) using an isokinetic dynamometer and performance, stroke rate, and stroke length during a 50-m front crawl. A significant increase in swimming velocity and peak torque was observed for both S and ES at the end of the training and 4 weeks later. Stroke length increased in the S group but not in the ES group. However, no significant differences in swimming velocity between S and ES groups were observed. No significant changes occurred in the C group. Programs combining swimming training with dry-land strength or electrical stimulation programs led to a similar gain in sprint performance and were more efficient than swimming alone.     

Muscle morphological and strength adaptations to endurance vs. resistance training

Fascicle angle (FA) is suggested to increase as a result of fiber hypertrophy and furthermore to serve as the explanatory link in the discrepancy in the relative adaptations in the anatomical cross-sectional area (CSA) and fiber CSA after resistance training (RT). In contrast to RT, the effects of endurance training on FA are unclear. The purpose of this study was therefore to investigate and compare the longitudinal effects of either progressive endurance training (END, n = 7) or RT (n = 7) in young untrained men on FA, anatomical CSA, and fiber CSA. Muscle morphological measures included the assessment of vastus lateralis FA obtained by ultrasonography and anatomical CSA by magnetic resonance imaging of the thigh and fiber CSA deduced from histochemical analyses of biopsy samples from m. vastus lateralis. Functional performance measures included VO2max and maximal voluntary contraction (MVC). The RT produced increases in FA by 23 ± 8% (p < 0.01), anatomical CSA of the knee extensor muscles by 9 ± 3% (p = 0.001), and fiber CSA by 19 ± 7% (p < 0.05). RT increased knee extensor MVC by 20 ± 5% (p < 0.001). END increased VO2max by 10 ± 2% but did not evoke changes in FA, anatomical CSA, or in fiber CSA. In conclusion, the morphological changes induced by 10 weeks of RT support that FA does indeed serve as the explanatory link in the observed discrepancy between the changes in anatomical and fiber CSA. Contrarily, 10 weeks of endurance training did not induce changes in FA, but the lack of morphological changes from END indirectly support the fact that fiber hypertrophy and FA are interrelated.     

A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison.

This article describes the latest version of an RNA folding algorithm that predicts both optimal and suboptimal solutions based on free energy minimization. A number of RNA's with known structures deduced from comparative sequence analysis are folded to test program performance. The group of solutions obtained for each molecule is analysed to determine how many of the known helixes occur in the optimal solution and in the best suboptimal solution. In most cases, a structure about 80% correct is found with a free energy within 2% of the predicted lowest free energy structure.     

Different effects on human skeletal myosin heavy chain isoform expression: strength vs. combination training.

Myosin heavy chain (MHC) isoform expression changes with physical training. This may be one of the mechanisms for muscular adaptation to exercise. We aimed to investigate the effects of different strength-training protocols on MHC isoform expression, bearing in mind that alpha- MHC(slow) (newly identified MHC isoform) mRNA may be upregulated in response to training. Twelve volunteers performed a 6-wk strength training with maximum contractions (Max group), and another 12 of similar age performed combination training of maximum contractions and ballistic and stretch-shortening movements (Combi group). Muscle samples were taken from triceps brachii before and after training. MHC isoform composition was determined by SDS-PAGE silver staining, and mRNA levels of MHC isoforms were determined by RT-PCR. In Max group, there was an increase in MHC(2A) (49.4 to 66.7%, P < 0.01) and a decrease in MHC(2X) (33.4 to 19.5%, P < 0.01) after training, although there was no significant change in MHC(slow). In Combi group, there was also an increase in MHC(2A) (47.7 to 62.7%, P < 0.05) and a decrease in MHC(slow) (18.2 to 9.2%, P < 0.05) but no significant change in MHC(2X). An upregulation of alpha-MHC(slow) mRNA was, therefore, found in both groups as a result of training. The strength training with maximum contractions led to a shift in MHC isoform composition from 2X to 2A, whereas the combined strength training produced an MHC isoform composition shift from slow to 2A.     

Endurance training of older men: responses to submaximal exercise.

The purpose of this study was to quantify the exercise response of older subjects on a time-to-fatigue (TTF) submaximal performance test before and after a training program. Eight older men (67.4 +/- 4.8 yr) performed two maximal treadmill tests to determine maximum oxygen uptake (VO2max) and ventilation threshold (TVE) and a constant-load submaximal exercise treadmill test that required an oxygen uptake (VO2) between TVE and VO2max. The submaximal test, performed at the same absolute work rate before and after the training program, was performed to volitional fatigue to measure endurance time. The men trained under supervision at an individualized pace representing approximately 70% of VO2max (80% maximum heart rate) for 1 h, four times per week for 9 wk. Significant increases were demonstrated for VO2max (ml.kg-1.min-1; 10.6%); maximal ventilation (VE, l/min; 11.6%), and TVE (l/min; 9.8%). Weight decreased 2.1%. Performance time on the TTF test increased by 180% (7.3 +/- 3.0 to 20.4 +/- 13.5 min). The similar end points for VO2, VE, and heart rate during the TTF and maximal treadmill tests established that the TTF test was stopped because of physiological limitations. The increase in performance time among the subjects was significantly correlated with improvements in VO2max and TVE, with the submaximal work rate representing a VO2 above TVE by 88% of the difference between TVE and VO2max pretraining and 73% of this difference on posttraining values.     

Endurance training amplifies the pulsatile release of growth hormone: effects of training intensity.

The effects of intensity of run training on the pulsatile release of growth hormone (GH) were investigated in 21 eumenorrheic untrained women. The O2 consumption (VO2) at the lactate threshold (LT); fixed blood lactate concentrations (FBLC) of 2.0, 2.5, and 4.0 mM; peak VO2; maximal VO2; body composition; and pulsatile release of GH were measured. Subjects in both the at-lactate threshold (/LT, n = 9) and above-lactate threshold (greater than LT, n = 7) training groups increased VO2 at LT and FBLC of 2.0, 2.5, and 4.0 mM and VO2max after 1 yr of run training. However, the increase observed in the greater than LT group was greater than that in the /LT group (P less than 0.05). No change was observed for the control group (n = 5). No among- or within-group differences were observed for body weight, although trends for reductions in percent body fat (P less than 0.06) and fat weight (P less than 0.15) were observed in the greater than LT group, and both training groups significantly increased fat-free weight (P less than 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)     

BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures

We developed BSP‐SLIM, a new method for ligand–protein blind docking using low‐resolution protein structures. For a given sequence, protein structures are first predicted by I‐TASSER; putative ligand binding sites are transferred from holo‐template structures which are analogous to the I‐TASSER models; ligand–protein docking conformations are then constructed by shape and chemical match of ligand with the negative image of binding pockets. BSP‐SLIM was tested on 71 ligand–protein complexes from the Astex diverse set where the protein structures were predicted by I‐TASSER with an average RMSD 2.92 Å on the binding residues. Using I‐TASSER models, the median ligand RMSD of BSP‐SLIM docking is 3.99 Å which is 5.94 Å lower than that by AutoDock; the median binding‐site error by BSP‐SLIM is 1.77 Å which is 6.23 Å lower than that by AutoDock and 3.43 Å lower than that by LIGSITE^CSC. Compared to the models using crystal protein structures, the median ligand RMSD by BSP‐SLIM using I‐TASSER models increases by 0.87 Å, while that by AutoDock increases by 8.41 Å; the median binding‐site error by BSP‐SLIM increase by 0.69Å while that by AutoDock and LIGSITE^CSC increases by 7.31 Å and 1.41 Å, respectively. As case studies, BSP‐SLIM was used in virtual screening for six target proteins, which prioritized actives of 25% and 50% in the top 9.2% and 17% of the library on average, respectively. These results demonstrate the usefulness of the template‐based coarse‐grained algorithms in the low‐resolution ligand–protein docking and drug‐screening. An on‐line BSP‐SLIM server is freely available at http://zhanglab.ccmb.med.umich.edu/BSP‐SLIM . Proteins 2012. © 2011 Wiley Periodicals, Inc.     

A quantitative measure of DNA curvature enabling the comparison of predicted structures

A growing body of data indicates that the equilibrium structures of some DNA fragments are curved and that curvature is sequence-directed. We describe a quantitative measure of DNA curvature that can be used for evaluating and comparing current proposed models for the molecular basis of DNA curvature. We demonstrate that this measure, in conjunction with any given prediction model, enables both the comparison of experimental data to predictions and the scanning of nucleotide sequence databases for potential curved regions.     

Muscle activation strategies during strength training with heavy loading vs. repetitions to failure

Going to failure, or not, has probably been one of the most debated issues during the history of strength training. However, few studies have directly compared the physiological effect of failure vs. nonfailure strength training. The purpose of this study was to evaluate muscle activation strategies with electromyography (EMG) during heavy repetitions vs. repetitions to failure with lighter resistance. Fifteen healthy untrained women performed a set with heavy loading (3 repetition maximum [RM]) and a set of repetitions to failure with lower resistance (～15 RM) during lateral raise with elastic tubing. Electromyographic amplitude and median power frequency of specific shoulder and neck muscles were analyzed, and the BORG CR10 scale was used to rate perceived loading immediately after each set of exercise. During the failure set, normalized EMG was significantly lower during the first repetition and significantly higher during the latter repetitions compared with the heavy 3-RM set (p < 0.05). Normalized EMG for the examined muscles increased throughout the set to failure in a curvilinear fashion--e.g., for the trapezius from 86 to 124% maximal voluntary contraction (p < 0.001)--and reached a plateau during the final 3-5 repetitions before failure. Median power frequency for all examined muscles decreased throughout the set to failure in a linear fashion, indicating progressively increasing fatigue. In conclusion, going to complete failure during lateral raise is not necessary to recruit the entire motor unit pool in untrained women--i.e., muscle activity reached a plateau 3-5 repetitions from failure with an elastic resistance of approximately 15 RM. Furthermore, strengthening exercises performed with elastic tubing seem to be an efficient resistance exercise and a feasible and practical alternative to traditional resistance equipment.     

Similarity in adaptations to high-resistance circuit vs. traditional strength training in resistance-trained men

To compare the effects of 8 weeks of high-resistance circuit (HRC) training (3-6 sets of 6 exercises, 6 repetition maximum [RM], ～35-second interset recovery) and traditional strength (TS) training (3-6 sets of 6 exercises, 6RM, 3-minute interset recovery) on physical performance parameters and body composition, 33 healthy men were randomly assigned to HRC, TS, or a control group. Training consisted of weight lifting 3 times a week for 8 weeks. Before and after the training, 1RM strength on bench press and half squat exercises, bench press peak power output, and body composition (dual x-ray absorptiometry ) were determined. Shuttle run and 30-second Wingate tests were also completed. Upper limb (UL) and lower limb 1RM increased equally after both TS and HRC training. The UL peak power at various loads was significantly higher at posttraining for both groups (p ≤ 0.01). Shuttle-run performance was significantly better after both HRC and TS training, however peak cycling power increased only in TS training (p ≤ 0.05). Significant decreases were found in % body fat in the HRC group only; HRC and TS training both resulted in an increased lean but not bone mass. The HRC training was as effective as TS for improving weight lifting 1RM and peak power, shuttle-run performance and lean mass. Thus, HRC training promoted a similar strength-mass adaptation as traditional training while using a shorter training session duration.     

Early phase strength development: a four-week training comparison of different programs

The purpose of this study was to explore the effects of various exercise sequences in the early weeks of a strength training program. Forty-two untrained men were randomly assigned to one of 4 training regimens, which were differentiated by the order in which the exercises were performed, and trained 3 days per week for 4 weeks. Three regimens were multiple-set protocols (alternating, blocked, and semiblocked), and the fourth was a single-set protocol. The exercises were arm curls, lateral raises, and triceps extensions. Results showed that the blocked group improved significantly more on the arm curl exercise than the single-set group. No other group comparisons were significant. This finding indicates that a blocked multiple-set regimen is superior to a single-set regimen for certain upper-body exercises in the early stages of strength training.     

Specificity of training modalities on upper-body one repetition maximum performance: free weights vs. hammer strength equipment

The purpose of this study was to determine whether a relationship exists between 1-repetition maximum (1RM) performed on hammer strength (HS) machines compared to free weights (FWs) and also to develop regression equations that can accurately predict 1RM when switching from exercise modality to another. Thirty-one trained male subjects performed 1-RM lifts (1RM's) on 3 HS externally loaded machines and 3 comparable FW exercises. Subjects performed 2 1RM tests during each laboratory session, with at least 48-72 hours of recovery between each. One repetition maximum data were used to (a) determine the relationship between 1RM performed on HS vs. FW and (b) to develop regression equations that can accurately predict 1RM's when switching from 1 exercise modality to another. Statistics revealed significant differences (p < 0.05) between 1RM's performed on the HS equipment as compared to its corresponding (FW) exercise. For all exercises, 1RM's were significantly greater on the HS equipment. Regression equations were developed for all exercises, except when predicting the HS shoulder press and the HS preacher curls from their free weight counterparts, where no variables existed that could significantly predict their respective 1RM's. As 1 RMs were significantly greater when using the HS equipment compared to when using FWs, those transitioning from HS exercise to FW exercise should exercise caution.     

Ultrastructural muscle damage in young vs. older men after high-volume, heavy-resistance strength training.

This study assessed ultrastructural muscle damage in young (20-30 yr old) vs. older (65-75 yr old) men after heavy-resistance strength training (HRST). Seven young and eight older subjects completed 9 wk of unilateral leg extension HRST. Five sets of 5-20 repetitions were performed 3 days/wk with variable resistance designed to subject the muscle to near-maximal loads during every repetition. Biopsies were taken from the vastus lateralis of both legs, and muscle damage was quantified via electron microscopy. Training resulted in a 27% strength increase in both groups (P < 0.05). In biopsies before training in the trained leg and in all biopsies from untrained leg, 0-3% of muscle fibers exhibited muscle damage in both groups (P = not significant). After HRST, 7 and 6% of fibers in the trained leg exhibited damage in the young and older men, respectively (P < 0.05, no significant group differences). Myofibrillar damage was primarily focal, confined to one to two sarcomeres. Young and older men appear to exhibit similar levels of muscle damage at baseline and after chronic HRST.     

Empirical validation of SAR values predicted by FDTD modeling.

Rapid increase in the use of numerical techniques to predict current density or specific absorption rate (SAR) in sophisticated three dimensional anatomical computer models of man and animals has resulted in the need to understand how numerical solutions of the complex electrodynamics equations match with empirical measurements. This aspect is particularly important because different numerical codes and computer models are used in research settings as a guide in designing clinical devices, telecommunication systems, and safety standards. To ensure compliance with safety guidelines during equipment design, manufacturing and maintenance, realistic and accurate models could be used as a bridge between empirical data and actual exposure conditions. Before these tools are transitioned into the hands of health safety officers and system designers, their accuracy and limitations must be verified under a variety of exposure conditions using available analytical and empirical dosimetry techniques. In this paper, empirical validation of SAR values predicted by finite difference time domain (FDTD) numerical code on sphere and rat is presented. The results of this study show a good agreement between empirical and theoretical methods and, thus, offer a relatively high confidence in SAR predictions obtained from digital anatomical models based on the FDTD numerical code.     

Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures

Many proteins contain flexible structures such as loops and hinged domains. A simple root mean square deviation (RMSD) alignment of two different conformations of the same protein can be skewed by the difference between the mobile regions. To overcome this problem, we have developed a novel method to overlay two protein conformations by their atomic coordinates using a Gaussian-weighted RMSD (wRMSD) fit. The algorithm is based on the Kabsch least-squares method and determines an optimal transformation between two molecules by calculating the minimal weighted deviation between the two coordinate sets. Unlike other techniques that choose subsets of residues to overlay, all atoms are included in the wRMSD overlay. Atoms that barely move between the two conformations will have a greater weighting than those that have a large displacement. Our superposition tool has produced successful alignments when applied to proteins for which two conformations are known. The transformation calculation is heavily weighted by the coordinates of the static region of the two conformations, highlighting the range of flexibility in the overlaid structures. Lastly, we show how wRMSD fits can be used to evaluate predicted protein structures. Comparing a predicted fold to its experimentally determined target structure is another case of comparing two protein conformations of the same sequence, and the degree of alignment directly reflects the quality of the prediction.