Research into synthetic antibodies offers hope for new diagnostics

January 25, 2011

Antibodies are watchdogs of human health, continuously prowling the body and registering minute changes associated with infection or disease with astonishing acuity. They also serve as biochemical memory banks, faithfully recording information about pathogens they encounter and efficiently storing this data for later use.

Stephen Albert Johnston, Neal Woodbury and their colleagues at the Biodesign Institute at ASU have been exploring mechanisms of antibody activity, particularly the ability of these sentries to bind – with high affinity and specificity – to their protein targets. A more thorough understanding of the antibody universe may lead to a new generation of rapid, low-cost diagnostic tools and speed the delivery of new vaccines and therapeutics. Download Full Image

Borrowing a script from nature, the group has been working to construct synthetic antibodies or synbodies, through a simple method developed in Johnston’s Center for Innovations in Medicine. They have also examined the broad portrait of antibody activity revealed in a sample of blood, harnessing this information for the presymptomatic diagnosis of disease. These immunosignatures, as Johnston has named them, provide a dynamic report card on human health.

In a pair of new papers, the group demonstrated a simple means of improving the binding affinity of synbodies, which are composed of 20 unit chains of amino acids, strung together in random order. They also used random peptide sequences spotted onto glass microarray slides to mine information concerning the active regions or epitopes of naturally occurring antibodies. These two projects recently appeared in the journals PloS ONE and Molecular and Cellular Proteomics, respectively.

While antibodies have been in use for biomedical research for a long time, conventional techniques for producing them have been time consuming and expensive. Normally, antibodies used for research are produced in animals, which respond to a given injected protein by producing a protein-specific antibody, which may then be extracted.

In earlier work, Johnston’s group showed that high-affinity antibody mimics can be produced synthetically by simple means. Their technique turns the traditional production approach on its head. Rather than beginning with a given protein and trying to generate a corresponding antibody, the new method involves building a synthetic antibody first, later determining the protein it effectively binds with, by screening it against a library of potential protein mates.

The first step in this process is to generate random strings of 20 amino acids. Roughly, 10,000 such random peptides are then spotted onto a glass microarray slide. The protein one is seeking an antibody to is screened against this random sequence array and peptides with high binding affinity are identified. Two such peptides can be linked together to form a synbody, whose binding affinity is the product of each separate peptide. In this way, two weakly binding peptides join forces to form a high affinity unit, useful for investigations into the proteome, the vast domain of proteins essential to virtually all biological processes.

In the PloS ONE study, lead author Matthew Greving and his collegues describe a strategy for further refinement of binding affinity in random sequence peptides. 

“The problem,” Johnston explains, is that the microarray contains about 10,000 peptides, but that is less than a quadrillionth of the possible peptides by sequence. So we’re sampling a very small part of the sequence space. ”A consequence of this is that the probability of generating a 20 amino acid sequence, that binds with optimal affinity, is pretty low."

To improve sequence affinity, a lead sequence is first selected. In the study, one such sequence was the 17 amino acid peptide TNF-1, a key regulator of immune cells. The lead sequence is then used as a template from which to generate additional peptide sequences in which a single amino acid at each subsequent position along the peptide chain is replaced with a different amino acid.

Using this method, 96 variant peptides are constructed on a microarray plate. These enhanced variants are screened against a desired protein for binding affinity and a map is produced  displaying this affinity from low to high. The most successful variants can then be assembled into a new high affinity peptide, whose binding strength is the sum of the components.

This simple, algorithmic process can rapidly optimize random sequence peptides, improving their binding affinity by 100 to 1000 times.  The method can also be used to improve the specificity of peptides, enabling the construction of binding agents able to attach to a given protein while excluding unwanted binding targets.

The MCP study asked whether a similar random peptide microarray could assist in the process of epitope mapping, in which the active binding regions of antibodies are identified. Epitope mapping is one method for determining if a given antibody is suitable for a particular application, and a faster, more cost-effective method would be of significant biomedical value.

For these experiments, antibodies of known epitope were screened against random sequence peptides on a microarray.  High affinity peptides were identified and bioinformatics techniques were used to see if the random peptides could help identify the antibody epitopes.

Two techniques were applied; one in which high affinity random sequence peptides were compared side by side with the antibody epitopes they bound with and similarities statistically analyzed. The other method searched the peptides for signature “motifs” – consisting of at least seven amino acids (or two shorter motifs in combination).  

Lead author Rebecca Halperin and colleagues were able to show that statistically useful information on epitopes could indeed be gleaned from such bioinformatic probing, bringing the prospect of high throughput, inexpensive exploration of natural antibodies a step closer.

Johnston stresses the importance of this research. “The paper asks if there are mechanisms to transfer from random sequence space to real sequence space based on antibody binding. No one has explored this as deeply as Rebecca has.”

Further refinement should allow diagnosis of the precise protein sequence causing a given illness, based purely on analysis of immune response.

Stephen Albert Johnston is the director of the Center for Innovations in Medicine at the Biodesign Institute at Arizona State University. For more info,visit:" target="_blank">

Written by Richard Harth
Biodesign Institute
Science Writer

Britt Lewis

Communications Specialist, ASU Library

Track & field opens season in New Mexico

January 25, 2011

Sun"> Devil Meet Notes (pdf)

The 2011 track & field season will get underway for Arizona State University this weekend as the Sun Devils will travel to the Convention Center in Albuquerque, N.M., to compete in the New Mexico Invitational this Friday and Saturday. The meet, being hosted by New Mexico, will be the first indoor action of the year for the Sun Devils as they work toward qualifying and competing in the NCAA Indoor Track & Field Championships, which will take place in six weeks (March 11-12) in College Station, Texas. Download Full Image

• ASU’s men enter season ranked #25, women are unranked (USTFCCCA)
• ASU will compete in New Mexico for two weeks in a row to open 2011 indoor
• Six marks carried over 2010 have ASU athletes ranked in national Top 20
• Eight Sun Devils that have earned All-America honors return this season
• Team has 13 seniors (6 women, 7 men) on the roster this season
• 27 total newcomers are on the roster this year (10 women, 17 men), including 20 true freshmen (8 women, 12 men)
• 2011 is first time since 2004 that ASU opens a season without a returning NCAA Champion on its roster (six year streak snapped)
• 19 current Sun Devils were once teammates at another school before ASU
• ASU roster features 3 nations and 19 different states
• Coach Kraft is entering his 15th year leading the program, the second-longest in program history (Baldy Castillo - 27 years)

This weekend’s meet in New Mexico will be the first of two trips this season that Arizona State will make to Albuquerque and the Convention Center. The next trip will come next weekend with the New Mexico Classic/Multis on February 4-5.

The USTFCCCA released the first of its weekly national rankings on January 6 (preseason) with the Arizona State men starting the year at No. 25 while the women are outside of the Top 25. The rankings are based purely on points earned by individual and relay athletes based upon where their season-best marks rank nationally.

Heading into the season, six marks turned in by Sun Devils last year currently have them ranked among the Top 20 in the NCAA, including two by the men and four by the women. On the men’s side, both Mason">">Mason McHenry and Jordan">">Jo... Clarke enter the indoor season ranked ninth in the 800m (1:48.04) and shot put (18.54m), respectively. For the women, Constance">"... Ezugha (6.45m) and Christabel"> Nettey (6.42m) are ranked fifth and sixth, respectively, in the long jump while Jasmine">">J... Chaney stands 16th in the 60m hurdles (8.33). The final Sun Devil in the Top 20 is Anna">">Anna Jelmini, who’s mark of 16.36m in the shot put recorded last year while competing unattached from the program while redshirting her rookie season, stands 12th overall in the nation this year.

Four men and four women on the roster in 2011 enter the season having earned All-America honors at some point in their careers, including two men (both outdoor) and two women (one indoor and one outdoor) that earned that distinction last year. In 2010, Constance">"... Ezugha (indoor long jump) and Jasmine">">J... Chaney (outdoor 400m hurdles) both earned honors for the women while the men’s team has Allante">">A... Battle (outdoor 4x400m) and Jordan">">Jo... Clarke (outdoor shot put) returning. Also returning for the men this season are a pair of 800m All-Americans in Nectaly">">... Barbosa (indoor 800m) and Mason">">Mason McHenry (outdoor 800m). On the women’s side, the Sun Devils have Cj">">Cj Navarro (outdoor discus) returning along with Dominique’ Maloy, who has collected six career honors, the most of any Sun Devil on the 2011 roster.

This week marks the start of a new season, as well as the beginning of the end for 13 seniors. The 2011 roster features six women and seven men that are seniors this year, including a pair of men that also are in their first year with the program. On the women’s side, the seniors include Jasmine">">J... Chaney, Samantha"> Henderson, Dominique’ Maloy, Cherise">">C... McNair, Brianna">">Br... Smith and Anna">">Anna Young (formerly Sperry). The men’s seniors include Nectaly">">... Barbosa, Ian">">Ian Caracciolo, Ben">">Ben Engelhardt, Casey">"... Fonnesbeck, Corey">">Corey Phallen, Michael"> Rodriguez and Zeke">">Zeke Van Patten. The two men that are in their first seasons with the program are Fonnesbeck, who graduated from Illinois last year and has one more year of eligibility as a graduate student at ASU, and Rodriguez, who spent the past three years on ASU’s club team.

Twenty-seven athletes, including 10 women and 17 men, have joined the Sun Devil program for the first time in 2011. The true freshmen include women Sarah">">Sarah Geren, Asia">">Asia Gooden, Taylor">">Ta... Hagood, Alex">">Alex Hartig, Kelsea">">K... Hawkins, Alycia">">A... Herring, Maddie">">Ma... Nossek and Shaylah">">... Simpson and men Garrett"> Baker-Slama, Jordan">">Jo... Benesh, Justin">">J... Freeman, Jared">">J... Gonzales, Ryan">">Ryan Healy, William">">Wi... Henry, Brody">">Brody Howe, Erik">">Erik Lindahl, Bryan">">Bryan McBride, Jesus">">Jesus Molina, Jesus">">Jesus Rivera and Kevin">"... Scheuerman. The non-rookie newcomers include women Eliza">">E... Gawryluk (junior) and Hailey">">Hailey Hanna (junior) and men Daniel">">D... Auberry (junior), Chris">">Chris Benard (junior), Casey">"... Fonnesbeck (graduate student), Giorgio"> Giurdanella (junior) and Michael"> Rodriguez (senior).

In 1996, Pal Arne Fagernes won the men’s javelin title at the NCAA Championships. It was not until 2004 that Arizona State had another national champion as Jacquelyn"> Johnson won the outdoor heptathlon as a true freshman. Starting in 2005, ASU had at least one returning NCAA champion on its roster for six years in a row, a streak that comes to an end this season because of graduation. The 2010 and 2009 rosters featured two returning individuals each (Ryan">">Ryan Whiting and Jason">">Jason Lewis in 2010, Whiting and Sarah">">Sarah Stevens in 2009) while the 2008 roster featured four returning champions in Johnson, Stevens, Jessica">"... Pressley and April">">A... Kubishta, all who won titles in 2007.

As the season begins, there are 19 Sun Devils on the roster that were teammates before they came to Arizona State, including transfers from two colleges and five high schools represented. Prior to their joining the Sun Devils, Eliza">">E... Gawryluk, Cameron">">C... Liston and Darius">">Darius Terry all were teammates at Northern Arizona while both Daniel">">D... Auberry and Chris">">Chris Benard join the team this season after two years together at Riverside Community College. Teammates have been reunited from five high schools as well, including four from the Valley. Freshmen Asia">">Asia Gooden and Alycia">">A... Herring are both starting their first years with ASU after running together at Ranch Verde HS in California. Locally, Desert Vista is represented by Allante">">A... Battle, Matt">">Matt Boughton, John">">John Kline, Cory">">Cory Kraft and Shaylah">">... Simpson; Sandra Day O’Connor is represented by Camille">">Ca... Olson, Lindsay">"... Prescott and Bryan">">Bryan McBride; Corona del Sol has Garrett"> Baker-Slama and Josh">">Josh Walker; and Boulder Creek alums include Roger">">Roger Dolan and Daniel">">Da... Lovell.

The Sun Devil roster in 2011 features student-athletes from 19 different states, including states as far east as New Jersey and as north as Alaska. The states represented on the roster this year include: Alaska, Arizona, California, Colorado, Idaho, Illinois, Iowa, Kansas, Minnesota, Missouri, Nevada, New Jersey, New Mexico, Ohio, Oklahoma, Texas, Washington and Wisconsin.

While there are 19 states represented, the United States is not the only nation on the roster as two women hail from outside of the U.S. Christabel"> Nettey is a hurdler and jumper that comes to Tempe by way of Surrey, British Columbia in Canada while distance runner Eliza">">E... Gawryluk is a native of Olsztyn, Poland.

Ryan">">Ryan Whiting was clearly one of the top collegiate competitors in the nation in 2010, winning NCAA titles in all three events he entered and earning a place in the Top 3 finalists of the Bowerman Award (collegiate track & field athlete of the year). The winner of the indoor shot put for the third year in a row, the outdoor shot put for the second year in a row and the discus champion, Whiting ended his career as the Track & Field News Male Athlete of the Year, USTFCCCA Co-National Field Athlete of the Year (outdoor), Pac-10 Co-Field Athlete of the Year, Pac-10 Scholar-Athlete of the Year and the prestigious Pac-10 Tom Hansen Medal of Honor recipient. Whiting, who graduated from ASU in May and is pursuing a Master’s degree at Penn State while competing professionally, closed out his days on campus as the NCAA record holder in the indoor shot put (21.73m) and second all-time in the outdoor shot put (21.97m), just three 3cm shy of the record mark on his final collegiate attempt.

The team did not score at the NCAA Indoor Championships and finished fourth at the MPSF Indoor Championships with 79.0 points scored... two true freshman qualified automatically for the NCAA Championships with both Constance">"... Ezugha and Christabel"> Nettey reaching the national meet... neither woman placed in the Top 8, but Ezugha did earn All-America honors as the eighth-highest finishing American in the event... at the MPSF Championships, the women won a trio of events to aid them in their fourth-place finish... Jasmine">">J... Chaney led the way by winning the 400m dash (53.83) before anchoring the 4x400m relay to victory in 3:38.40... Chaney was joined on the relay by Dominique’ Maloy, Keia">">Keia Pinnick and Kayla">">Kayla Sanchez... Ezugha was the other champion for ASU as she captured the long jump title with a leap of 6.45m (21-02.00), which ranks as the third-best all-time in program history... overall, 25 marks recorded on the year ranked among the Top 10 all-time in ASU history, including four in the 60m hurdles, three in the 3,000m run and two each in the long jump, pole vault, weight throw and heptathlon... in the hurdles Chaney (8.33), Christabel"> Nettey (8.46), Samantha"> Henderson (8.95) and Pinnick (8.98) recorded the fourth, fifth, eighth and ninth-best times in program history while the trio of Kari">">Kari Hardt (9:28.78), Anna">">Anna Sperry (9:28.84) and Allie">">Allie Kieffer (9:31.91) posted the sixth, seventh and eighth-best times in the 3,000m run... of the 25 Top 10 marks recorded during the indoor season, seven came from true freshman with another six coming from newcomers to the program (transfers)... academically, eight women were selected Academic All-MPSF.

The men finished seventh at the NCAA Indoor Championships with 21.0 points after placing fourth at the MPSF Indoor Championships with 75.0 points... the team’s finish at the national meet marked it’s fourth-consecutive Top 10 national finish (indoor and outdoor NCAA meets)... Ryan">">Ryan Whiting completed a three-peat in the shot put as he captured the event at the NCAA meet for the third year in a row with a winning toss of 21.52m (70-07.25) to lead the way for ASU at the meet... Jason">">Jason Lewis was once again a two-time All-American as he placed sixth in the weight throw (21.15m/69-04.75) and seventh in the shot put (18.64m/61-02.00)... Brandon">">B... Bethke was the only other individual All-American as he raced to a fourth-place finish in the 3,000m run (8:11.61)... the team of Justin">">Ju... Kremer, Ray">">Ray Miller, Donald">">D... Sanford and Joel">">Joel Phillip earned All-America honors in the 4x400m relay by finishing eighth in 3:08.51... the men won four titles at the MPSF Championships, including Lawrence">">L... Trice in the 60m dash (6.68), Sanford in the 400m dash (46.19) and Mason">">Mason McHenry, for the second year in a row, in the 800m run (1:48.89)... the 4x400m relay of Sanford, Phillip, Kremer and Allante">">A... Battle won the title in 3:07.38, the eighth-best time in school history... Whiting and Lewis both competed at the USA Indoor Championships instead of the MPSF event... Whiting took second in the shot put (21.03m/69-00.00) and earned a place on Team USA for the 2010 IAAF World Indoor Championships in Doha, Qatar, but did not compete in the international meet as it was the same weekend as the NCAA Indoor Championships... Lewis finished 10th in the shot put (17.43m/57-02.25) at the USA meet... 23 marks recorded during the season rank among the all-time Top 10 in ASU history with one being a school record... the team of Nectaly">">... Barbosa, Sanford, McHenry and Bethke combined to set the school mark in the distance medley relay as they ran 9:31.34... following the indoor season, David">">David Dumble was selected as the USTFCCCA Men’s Division National Assistant Coach of the Year after being named the West region recipient... it was his first honor on the men’s side after receiving four other awards after working with the women in 2006-08... outside of competition, Whiting and Lewis both earned NCAA Post-Graduate Scholarships to continue their educations after the outdoor season... 13 men were selected MPSF All-Academic.

In a vote of coaches around the nation, Sun Devil throws coach David">">David Dumble was selected as the 2010 USTFCCCA Men’s Division I National Assistant Coach of the Year, both indoors and outdoors. The West Region honoree both indoor and outdoor as well, Dumble has now been selected for the national honor for the fourth and fifth times, respectively, and the first on the men’s side of competition. He was honored for his efforts with the women’s throws three times previously as well.

In the classroom, numerous Sun Devils found great success, led by Ryan">">Ryan Whiting, who was named the USTFCCCA Division I Indoor & Outdoor Field Scholar of the Year. Whiting, one of 13 Sun Devils to earn national all-academic honors from the USTFCCCA, also led the way for the ASU men, who also were named the USTFCCCA Division I Outdoor Scholar Team of the Year.

In 2010, the USTFCCCA began a new award to be handed out annually to the top all-around program in the nation and naming the men’s award after former Arkansas coach, John McDonnell. Based on points earned in national team finishes at the three NCAA events (cross country, indoor track & field and outdoor track & field) with the lowest total winning, the Sun Devil men finished second overall in the inaugural awarding with 30 points while Oregon earned the trophy with 7.5 points. Arizona State, who finished ahead of Northern Arizona (42.5), Florida State (51.0) and Washington (55.0), scored finishes of 19th at the cross country meet, seventh indoors and fourth outdoors. ASU is not in the running for the 2010-11 award as the cross country team did not score as a team at the 2010 championships.

Senior Ben">">Ben Engelhardt was led the way for the Sun Devil men’s cross country team during the 2010, earning a berth into the NCAA Championships as an individual qualifier where he finished 51st overall in the national meet. An All-West Region honoree (13th place) and Second Team All-Pac-10 selection (14th place), Engelhardt was the team’s top finisher in all but one race on the season and placed in the Top 20 in five races, including 18th at the NCAA Pre-National Meet.

On the women’s side, the 2010 cross country team was led by the emergence of Lindsay">"... Prescott, who was the team’s top finisher in all six races she entered. The runner-up at the Dave Murray Invitational, Prescott earned Second Team All-Pac-10 honors after placing ninth overall at the conference meet, one of three meets in which she placed in the Top 10. She added Top 25 finishes at the NCAA Pre-National Meet (17th) and the Roy Griak Invitational (22nd).

At the end of the season, 11 different Sun Devils earned Academic All-Pac-10 honors in cross country, including four Sun Devils (three men, one woman) that were selected for first team recognition. Catherine">">... Loden, Ben">">Ben Engelhardt, Nick">">Nick Happe and Steven"> Schnieders all were selected First Team Academic All-Pac-10 while Daniel">">Da... Lovell and Doug">">Doug Smith were Second Team Academic All-Pac-10 selections. Earning honorable mention were Alyssa">">A... Allison, Kate">">Kate Lydy, Karlee">">Karlee Owens and Kauren">">Ka... Tarver for the women and Cameron">">C... Liston for the men.

Head Coach Greg">">Greg Kraft is entering his 15th year as the leader of the Sun Devil program, a tenure that has brought Arizona State back to the top of the standings in both the NCAA and Pac-10 events. Since his hiring, the program has continued to evolve into one of the more well-rounded in the nation with strength on the track and in the field as well as in cross country. Kraft and his staff have worked diligently to reach their goals of championships and success in education and that has not been more clearly seen than in the past five years as the hardware has continued to roll in. His program has annually produced some of the top individuals in the nation with 23 of the program’s 55 individual and relay national titles won since 2004 while both his teams and individual student-athletes have garnered national academic acclaim. Prior to his arrival, the program boasted one NCAA Championship (men’s outdoor track & field, 1977) and one Pac-10 Championship (men’s outdoor track & field, 1981). In the last five years, his Sun Devils have captured four national crowns (2007 women’s indoor and outdoor track & field, 2008 men’s and women’s indoor track & field) and added three Pac-10 Championships (women’s outdoor track & field, 2006-08). Kraft’s teams have finished in the Top 10 of the NCAA Track & Field Championships on 20 occasions in 14 years while the program had done so just 14 times prior to his arrival in Tempe.

As he begins his 15th year at Arizona State, Kraft’s tenure ranks as the second-longest in Sun Devil track & field history and the fourth-longest active streak among all current ASU head coaches. The only coach that has led the track & field program longer than Kraft is legendary coach Senon ‘Baldy’ Castillo, who led the way for 26 years (1954-79). Among current Sun Devil head coaches, Kraft’s 15th year ranks behind John Spini, who is in his 31st year with gymnastics; Sheila McInerney, who is in her 27th year with women’s tennis; and Randy Lein, who is in his 19th year with the men’s golf program.

The Sun Devils will send athletes to a pair of competitions next weekend, including a return visit to Albuquerque for the New Mexico Classic (Friday-Saturday) while others will travel north to Flagstaff for the NAU Team Challenge (Saturday).