It’s one of the most common complaints among engaged Guardians fans — why is Amed Rosario batting second? That, and when are we going to get an on-field winged G hat. Since I don’t have numbers to analyze on the latter, let’s focus on the former.

I’m of the viewpoint that Amed Rosario is a valuable player to have on any major-league roster. By two defensive metrics — ultimate zone rating and deserved runs saved — he was an above-average shortstop last year. He led the league in competitive runs to first base, displaying unrelenting hustle as a constant example to a young team. He also managed a 103 wRC+, which is a solid number for a shortstop.

Helix breakerfunction

a) CD spectroscopy This method uses the so-called circular dichroism (CD) of proteins to estimate the content of alpha helical segments in a sample. The CD effect works because proteins are chiral (they and their mirror image are different, just like our hands). Depending on the conformation of the main chain, different spectra characteristic for alpha helices or other secondary structures are observed. For more information, take a look at the Birkbeck's PPS2 course. In a similar way, infrared spectroscopy can be used to estimate alpha helical content.

Rosario walks about half of what the average No. 2 hitter does, his overall run production has been around 20% less than the average No. 2 hitter, and, perhaps most tellingly, his groundball rate has been around 10% higher than the average No. 2 hitter. It’s not that he isn’t a solid major league hitter — it’s that his skillset involving high contact, low walk-rate, and high groundball rate make him a poor choice to provide his offensive value in the top third of a lineup.

Helix breakerexamples

The Guardians are a young team and this is likely Rosario’s last year with the team. So, perhaps, it is Will Brennan, Bo Naylor, George Valera, or Brayan Rocchio who eventually shows they are fit for this role. However, the numbers make clear that transitioning Rosario to a different spot in the lineup would fit with the lineup optimization strategies we observed from other successfully hitting teams in MLB over the past two years.

With all that said, I have found myself mildly frustrated by Terry Francona’s insistence that Rosario should remain cemented into the second spot in his lineup. Rosario doesn’t walk much, he doesn’t compensate for the lack of walks with a significant amount of power, and he also has a career ground-ball rate of 50.9%. This means that over half of his baseballs put in play with one out or fewer have the potential to start a double-play if the leadoff hitter (or another batter later in the game) is on base.

However, even looking at the average production for No. 2 hitters across MLB in the same time period shows a great disparity between the league and who the Guardians are using as their two-hole hitter.

Helix breakervshelix breaker

a) While the chemical (primary) structure of proteins was known for some time, the conformation of proteins was not known until the first protein structures were solved by X-ray crystallography in 1958 (myoglobin) and in the 1960s. However, using the X-ray diffraction pattern of alpha keratin (found, for example, in horse hair) and chemical insight gained from structures of smaller molecules (e.g. the peptide plane resulting from the partial double bond character of the peptide bond, the geometry of hydrogen bonds), Pauling predicted the structure of the alpha helix correctly years earlier (paper1 and paper2 and picture.

Alphahelix breaker

The beginnings and ends of helices are called N-caps and C-caps, respectively, and they have interesting sequence and structural patterns involving main chain or side chain hydrogen bonding.

Proline is considered a helix breaker because its main chain nitrogen is not available for hydrogen bonding. Here is an example of a () at the position of a .

b) NMR chemical shifts Nuclear magnetic resonance spectroscopy measures magnetic properties of the nuclei of atoms. One of these properties, the so-called chemical shift, changes slightly depending on the chemical environment an atom is in. By measuring the chemical shift of the alpha and beta carbon in each amino acid residue, it is possible to predict the secondary structure the residue is part of.

Alpha helices are named after alpha keratin, a fibrous protein consisting of two alpha helices twisted around each other in a coiled-coil (see Coiled coil). In leucine zipper proteins (such as Gcn4), the ends of the two alpha helices bind to two opposite major grooves of DNA. The name leucine zipper comes from the regularly spaced leucine side chains from both helices that form the hydrophobic core of these structures. The structure of collagen, the most abundant human protein, is also fibrous, but it is not made up of alpha helices.

A common fold found in transmembrane proteins are alpha-helical bundles running from one side to the other side of the membrane. An alpha helix of 19 amino acids (with a length of about 30 angstroms) has the right size to cross the double-layer of a typical membrane. If the helix runs at an angle instead of perfectly perpendicular to the membrane, it has to be a bit longer. There is a write-up on opioid receptors that illustrates this fold in the Molecule of the Month series by David Goodsell (http://pdb101.rcsb.org/motm/217).

b) Determination of hand: There are several methods in X-ray crystallography where crystallographers obtain an electron density, but don't know whether it or its mirror image is correct. Historically, finding electron density that fits a helix was used to break this ambiguity. If the helix was right-handed, the electron density was used as is, but if the helix was left-handed, the mirror image was used.

Helix breakerstructure

I did not understand rumors of an extension for Rosario this spring, given that the Guardians have so many young shortstop/second-base types rising through their farm system, but I couldn’t argue with the team exploring the possibility of keeping a player who is often mentioned as a clubhouse leader in sideline reports and player interviews.

Why is proline ahelix breaker

It’s impossible for me to say how much intangible value having Rosario’s hustle in the second spot in the lineup means. It’s also impossible to say how disruptive it would be to the team chemistry to move a veteran leader to a lower spot in the lineup without a severe decline in performance. With that said, I am hopeful that Terry Francona will be mindful of the approach of good-hitting teams in baseball who are batting their best hitters second each game. Moving Andrés Giménez or Ramírez, if he is willing and comfortable, to the second spot should help reduce the number of double-plays and increase run production, overall. Additionally, even swapping Kwan and Rosario would probably be preferable to cut down on the number of potential double-plays.

These are great hitters in great lineups, so they are obviously going to look a lot better than Rosario in Cleveland lineups that finished with the 16th and 20th wRC+ in 2022 and 2021, respectively. But it shows the kind of skillset good offensive teams are using in this slot — great hitters who draw a lot of walks and put the ball in the air more often than not.

Apart from the characteristic hydrogen bonding patterns, the other identifying feature of alpha helices are the main chain torsion angles . If you plot phi against psi for each residue (so-called Ramachandran plot), you find that the phi/psi combination found in alpha helices fall into one of the three "allowed" (i.e. observed) areas for non-glycine residues. For a more detailed explanation with examples of Ramachandran plots, see Tutorial:Ramachandran Plot Inspection, Ramachandran Plot or Birkbeck's PPS95 course.

Why is glycine ahelix breaker

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On one level, I think I understand Francona’s logic. I am sure he sees Rosario as a tone-setter. Everyone who sees him hustle to first, regardless of the outcome of his at-bat, will know the same standard applies to their involvement in the game. Last season, I also believed that Francona stuck with Rosario at the spot before José Ramírez because Francona trusted that Rosario would not overthink things with the team’s best hitter behind him, as a younger player might be tempted to do. Francona is also a fan of lineup consistency and responding to established player preferences, and I’m sure both factors play a part in slotting Amed behind Steven Kwan and in front of Ramírez in 236 of the past 324 games the Guardians have played.

An is a type of secondary structure, i.e. a description of how the main chain of a protein is arranged in space. It is a repetitive regular secondary structure (just like the beta strand), i.e. all residues have similar conformation and hydrogen bonding, and it can be of arbitrary length.

I think it’s important, however, to consider how other successful teams around the league are handling the second spot in their lineups.

The first two protein structures to be determined, myoglobin and hemoglobin, consist mainly of alpha helices. Researchers were surprised to see how random the orientation of helices seemed to be. Other all alpha-helical proteins show bundles of nearly parallel (or antiparallel) helices (e.g. bacterial cytochrome c' 1e83). In structures that have beta sheets and alpha helices, one common fold is a single beta sheet that is sandwiched by layers of alpha helices on either side (for example Carboxypeptidase A). When an alpha helix runs along the surface of the protein, one side of it will show polar side chains (solvent accessible) while the other side will show non-polar side chains (part of the hydrophobic core). The alpha helix fits nicely into the major groove of DNA. Many common DNA-binding motifs, such as the helix-turn-helix (e.g. FIS protein) or the zinc finger motif (e.g. engineered zinc finger protein 2i13), feature a short alpha helix that binds to the major groove of DNA.

In an alpha helix, the main chain arranges in a with the pointing away from the helical axis. (Stereo: ) In the following, the side chains are truncated at the beta carbon (green) to allow a better view of the main chain. The alpha helix is stabilized by (shown as dashed lines) from the of one amino acid to the of a second amino acid. Because the amino acids connected by each hydrogen bond are four apart in the primary sequence, these main chain hydrogen bonds are called "n to n+4". There are . If you to a spacefilling representation, you can see how tightly packed the main chain is (no space in the middle). [The previous scenes were inspired by a beautiful set of figures in Stryer's biochemistry textbook.]

Helix breakeramino acid

Which amino acids are found in alpha helices? Some amino acids are commonly found in alpha helices and others are rare. Amino acids with a side chain whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, i.e. occur less often in alpha helices than in other secondary structure elements. Glycine, with its many possible main chain conformations, is also rarely found in helices. Knowing how likely an amino acid is to occur in an alpha helix (the so-called helix propensities), it is possible to predict where helices occur in a protein sequence.

Some amino acids are commonly found in alpha helices and others are rare. Amino acids with a side chain whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, i.e. occur less often in alpha helices than in other secondary structure elements. Glycine, with its many possible main chain conformations, is also rarely found in helices. Knowing how likely an amino acid is to occur in an alpha helix (the so-called helix propensities), it is possible to predict where helices occur in a protein sequence.

Prolines are often found near the beginning or end of an alpha helix, as in this example of (this is an ultra high resolution structure where hydrogen atoms - white - are resolved and some atoms are shown in multiple positions). At the of the helix, there is a proline that interrupts the regular pattern of n to n+4 hydrogen bonds. Instead, the helix ends with an n to n+3 hydrogen bond (one turn of a so-called 3-10 helix, see Helices in Proteins). The subsequent proline is in the center of a turn, followed by a glycine (which is part of an n to n+3 hydrogen bond also typical for turns).

c) Tracing the chain: When building a model into electron density, the first step was to place contiguous C-alpha atoms into the density (with proper spacing). To see in which direction an alpha helix goes, you look at the side chain density. If it points up, the N-terminus is on top, otherwise on the bottom. (search for Christmas tree in this course)

Another consideration, of course, is splitting up left-handed and right-handed hitters in the lineup. With Kwan cemented in the leadoff spot, it makes sense for a right-handed hitter, or switch-hitter, to be in the second spot so that a left-handed reliever does not have the platoon advantage for two lineup positions in a row late in a game.

There are multiple spectroscopic techniques that allow the detection of alpha helices in proteins without determining their three-dimensional structures